From 315d7a1f19e81607368e937917414e4d59e17a0f Mon Sep 17 00:00:00 2001 From: biocompwebs Date: Tue, 31 Oct 2023 02:32:41 +0100 Subject: [PATCH] buildbot automated-update --- html/AboutMasksToolBar_8java.html | 95 - html/AboutMasksToolBar_8java_source.html | 83 - html/AddFillLabelsJDialog_8java.html | 95 - html/AddFillLabelsJDialog_8java_source.html | 127 - html/AddObjectJDialog_8java.html | 95 - html/AddObjectJDialog_8java_source.html | 105 - html/AutomaticParticle_8java.html | 95 - html/AutomaticParticle_8java_source.html | 100 - html/AutopickRunnable_8java.html | 95 - html/AutopickRunnable_8java_source.html | 119 - html/Averaging__Reducer_8java.html | 89 - html/Averaging__Reducer_8java_source.html | 84 - html/Biorad__Reader_8java.html | 89 - html/Biorad__Reader_8java_source.html | 82 - html/CTFAnalyzerImagePane_8java.html | 95 - html/CTFAnalyzerImagePane_8java_source.html | 97 - html/CTFAnalyzerJFrame_8java.html | 99 - html/CTFAnalyzerJFrame_8java_source.html | 136 - 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class  xmipp.ij.plugins.maskstoolbar.AboutMasksToolBar
 
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package  xmipp.ij.plugins.maskstoolbar
 
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1 package xmipp.ij.plugins.maskstoolbar;
2 
3 import ij.plugin.frame.PlugInFrame;
4 import javax.swing.ImageIcon;
5 import javax.swing.JLabel;
6 import javax.swing.JScrollPane;
7 import javax.swing.JTextPane;
8 
9 /*
10  * To change this template, choose Tools | Templates
11  * and open the template in the editor.
12  */
17 public class AboutMasksToolBar extends PlugInFrame {
18 
19  public AboutMasksToolBar() {
20  super("About Masks Tool Bar...");
21 
22  JLabel jlIcon = new JLabel(new ImageIcon(getClass().getResource("/resources/I2PC.png")));
23  JScrollPane jspText = new JScrollPane();
24  JTextPane jtpAbout = new JTextPane();
25 
26  jtpAbout.setContentType("text/html");
27  jtpAbout.setEditable(false);
28  jtpAbout.setText("<html>\nJuanjo Vega (<b>juanjo.vega@gmail.com</b>)<br>"
29  + "Biocomputing Unit.<br>"
30  + "National Center for Biotechnology (CNB/CSIC).<br>"
31  + "Madrid. May 2011.</html>");
32  jspText.setViewportView(jtpAbout);
33 
34  add(jlIcon, java.awt.BorderLayout.WEST);
35  add(jspText, java.awt.BorderLayout.CENTER);
36 
37  pack();
38  setLocationRelativeTo(null);
39  setResizable(false);
40  }
41 
42  @Override
43  public void run(String arg) {
44  setVisible(true);
45  }
46 }
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class  xmipp.viewer.windows.AddFillLabelsJDialog
 
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package  xmipp.viewer.windows
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import java.awt.Component;
29 import java.awt.Dimension;
30 import java.awt.GridBagConstraints;
31 import java.awt.GridBagLayout;
32 import java.awt.Insets;
33 import java.awt.event.ActionEvent;
34 import java.util.ArrayList;
35 import java.util.Enumeration;
36 import java.util.Hashtable;
37 import java.util.List;
38 
39 import javax.swing.BorderFactory;
40 import javax.swing.JComboBox;
41 import javax.swing.JLabel;
42 import javax.swing.JPanel;
43 import javax.swing.JTextField;
44 
45 import xmipp.jni.MDLabel;
46 import xmipp.jni.MetaData;
47 import xmipp.utils.XmippDialog;
48 import xmipp.utils.XmippWindowUtil;
49 import xmipp.viewer.models.ColumnInfo;
50 import xmipp.viewer.models.MetadataGalleryTableModel;
51 
52 
53 public class AddFillLabelsJDialog extends XmippDialog {
54  private static final long serialVersionUID = 1L;
55  protected MetadataGalleryTableModel gallery;
56 
57  protected boolean fillMode = false;
58  protected GridBagConstraints gbc = new GridBagConstraints();
59  protected int label;
60  protected List<ColumnInfo> labels = null;
61  protected Hashtable<String, JLabel> dictLabels = new Hashtable<String, JLabel>();
62  protected Hashtable<String, JTextField> dictTexts = new Hashtable<String, JTextField>();
63  protected Hashtable<String, JPanel> dictPanels = new Hashtable<String, JPanel>();
64  protected JPanel mainPanel;
65  protected JComboBox jcbLabel, jcbFillMode;
66 
71  public AddFillLabelsJDialog(GalleryJFrame parent,
72  List<ColumnInfo> labels) {
73  super(parent, "Add new label", true);
74  this.gallery = (MetadataGalleryTableModel) parent.gallery;
75  this.labels = labels;
76  initComponents();
77  }// constructor AddFillLabelsJDialog
78 
80  public AddFillLabelsJDialog(GalleryJFrame parent, int label) {
81  super(parent, "Fill label values", true);
82  this.label = label;
83  initComponents();
84  }// constructor AddFillLabelsJDialog
85 
87  public boolean isFillMode() {
88  return this.labels == null;
89  }
90 
95  protected void addPair(JPanel panel, String text, int row, Component c) {
96  JLabel label = new JLabel(text);
97  dictLabels.put(text, label);
98  gbc.anchor = GridBagConstraints.EAST;
99  panel.add(label, XmippWindowUtil.getConstraints(gbc, 0, row));
100  if (c == null) {
101  c = new JTextField(10);
102  dictTexts.put(text, (JTextField) c);
103  }
104  gbc.anchor = GridBagConstraints.WEST;
105  panel.add(c, XmippWindowUtil.getConstraints(gbc, 1, row));
106  }
107 
109  private JComboBox createLabelsCombo() {
110  jcbLabel = new JComboBox();
111  boolean found = false;
112  for (int label = MDLabel.MDL_OBJID + 1; label < MDLabel.MDL_LAST_LABEL; ++label) {
113  found = false;
114  for (ColumnInfo ci : this.labels)
115  if (ci.label == label) {
116  found = true;
117  break;
118  }
119  if (!found) {
120  String name = MetaData.getLabelName(label);
121  if (!name.startsWith("emx_"))
122  jcbLabel.addItem(name);
123  }
124  }
125  jcbLabel.addActionListener(this);
126  return jcbLabel;
127  }
128 
130  private JPanel addPairsPanel(String option, int panelRow, String... values) {
131  JPanel panel = new JPanel(new GridBagLayout());
132  int row = 0;
133  for (String value : values) {
134  addPair(panel, value, row++, null);
135  }
136  mainPanel.add(panel,
137  XmippWindowUtil.getConstraints(gbc, 0, panelRow, 2));
138  dictPanels.put(option, panel);
139  panel.setBorder(BorderFactory.createTitledBorder("Params"));
140  panel.setVisible(false);
141  return panel;
142  }
143 
144  @Override
145  protected void createContent(JPanel panel) {
146  setResizable(false);
147  mainPanel = new JPanel(new GridBagLayout());
148  gbc.insets = new Insets(5, 5, 0, 0);
149 
150  Component c = null;
151  if (isFillMode()) {
152  JTextField jtext = new JTextField(MetaData.getLabelName(label));
153  jtext.setEditable(false);
154  c = jtext;
155  setPreferredSize(new Dimension(250, 200));
156  } else {
157  c = createLabelsCombo();
158  setPreferredSize(new Dimension(350, 200));
159  }
160  addPair(mainPanel, "Label", 0, c);
161  String[] opts = { MetaData.FILL_CONSTANT, MetaData.FILL_LINEAR, MetaData.FILL_RAND_UNIFORM,
162  MetaData.FILL_RAND_GAUSSIAN };
163  jcbFillMode = new JComboBox(opts);
164  jcbFillMode.addActionListener(this);
165  addPair(mainPanel, "Fill mode", 1, jcbFillMode);
166  addPairsPanel(opts[0], 2, "value").setVisible(true);
167  addPairsPanel(opts[1], 3, "start", "step");
168  addPairsPanel(opts[2], 4, "min", "max");
169  addPairsPanel(opts[3], 5, "mean", "std");
170 
171  panel.add(mainPanel);
172 
173  }// function initComponents
174 
176  public String getFillMode() {
177  return (String) jcbFillMode.getSelectedItem();
178  }
179 
181  public int getLabel() {
182  if (isFillMode())
183  return label;
184  else {
185  try {
186  return MetaData.str2Label((String) jcbLabel.getSelectedItem());
187  } catch (Exception e) {
188  showException(e);
189  }
190  return MDLabel.MDL_UNDEFINED;
191  }
192  }
193 
194  public String getValue(String key) {
195  JTextField jtf = dictTexts.get(key);
196  return jtf.getText();
197  }
198 
199  public String[] getValues(){
200  String[] values = null;
201  String mode = getFillMode();
202  if (mode.equalsIgnoreCase(MetaData.FILL_CONSTANT))
203  values = new String[] { getValue("value") };
204  else if (mode.equalsIgnoreCase(MetaData.FILL_LINEAR))
205  values = new String[] { getValue("start"), getValue("step") };
206  else if (mode.equalsIgnoreCase(MetaData.FILL_RAND_UNIFORM))
207  values = new String[] { getValue("min"), getValue("max") };
208  else if (mode.equalsIgnoreCase(MetaData.FILL_RAND_GAUSSIAN))
209  values = new String[] { getValue("mean"), getValue("std") };
210 
211  return values;
212  }
213 
214  @Override
215  public void handleActionPerformed(ActionEvent evt) {
216  JComboBox jcb = (JComboBox) evt.getSource();
217  if (jcb == jcbFillMode) {
218  String fillMode = getFillMode();
219  for (Enumeration<String> keys = dictPanels.keys(); keys
220  .hasMoreElements();) {
221  String keyMode = keys.nextElement();
222  dictPanels.get(keyMode).setVisible(fillMode.equals(keyMode));
223  }
224  }
225  }// function actionPerformed
226 
228 // @Override
229 // public void handleOk() {
230 // try {
231 // gallery.fillLabel(getLabel(), getFillMode(), dictTexts.get("value").getText());
232 // } catch (Exception e) {
233 // XmippDialog.showException(parent, e);
234 // }
235 // }
236 
237 }// class AddFillLabelsJDialog
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Definition: XmippDialog.java:217
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AddFillLabelsJDialog(GalleryJFrame parent, List< ColumnInfo > labels)
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AddFillLabelsJDialog(GalleryJFrame parent, int label)
Definition: AddFillLabelsJDialog.java:80
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Definition: MetaData.java:53
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import java.awt.Dimension;
29 import java.awt.GridBagConstraints;
30 import java.awt.GridBagLayout;
31 
32 import javax.swing.JList;
33 import javax.swing.JPanel;
34 import javax.swing.JScrollPane;
35 import javax.swing.JTable;
36 import javax.swing.ListSelectionModel;
37 import javax.swing.LookAndFeel;
38 
39 import xmipp.jni.MetaData;
40 import xmipp.utils.XmippDialog;
41 import xmipp.utils.XmippWindowUtil;
42 import xmipp.viewer.RowHeaderRenderer;
43 import xmipp.viewer.models.GalleryRowHeaderModel;
44 import xmipp.viewer.models.ImageGalleryTableModel;
45 import xmipp.viewer.models.MetadataRowTableModel;
46 
47 public class AddObjectJDialog extends XmippDialog {
48  private static final long serialVersionUID = 1L;
49  private JTable table;
50  private MetadataRowTableModel model;
51  // This will be used for check for results from the dialog
52  public MetaData md;
53  GridBagConstraints gbc = new GridBagConstraints();
54  ImageGalleryTableModel gallery;
55 
56  public AddObjectJDialog(GalleryJFrame parent) {
57  super(parent, "Classes", true);
58  this.gallery = parent.gallery;
59  this.md = gallery.data.getMetaDataRow();
60  initComponents();
61  }// constructor AddObjectJDialog
62 
63  @Override
64  protected void createContent(JPanel panel) {
65  setResizable(false);
66  panel.setLayout(new GridBagLayout());
67  gbc.anchor = GridBagConstraints.EAST;
68 
69  JPanel groupstbpn = new JPanel();
70  JScrollPane sp = new JScrollPane();
71  //groupstbpn.setBorder(BorderFactory.createTitledBorder("Classes"));
72  groupstbpn.add(sp);
73  sp.setOpaque(true);
74  try {
75  model = new MetadataRowTableModel((GalleryJFrame)parent, md);
76  JList rowHeader = new JList();
77  rowHeader.setModel(new GalleryRowHeaderModel(model.data));
78  LookAndFeel.installColorsAndFont(rowHeader, "TableHeader.background",
79  "TableHeader.foreground", "TableHeader.font");
80  rowHeader.setCellRenderer(new RowHeaderRenderer());
81 
82  sp.setRowHeaderView(rowHeader);
83  table = new JTable(model);
84  model.setupTable(table);
85  table.setPreferredScrollableViewportSize(new Dimension(350, 200));
86  sp.setViewportView(table);
87  int h = model.getCellSize().height;
88  rowHeader.setFixedCellHeight(h);
89  table.setRowHeight(h);
90  } catch (Exception e) {
91  // TODO Auto-generated catch block
92  e.printStackTrace();
93  }
94  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
95 
96  // listen to selection changes (only one row selected)
97  table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
98  }// function initComponents
99 
100 }// class AddObjectJDialog
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class  xmipp.viewer.particlepicker.training.model.AutomaticParticle
 
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package  xmipp.viewer.particlepicker.training.model
 
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 import xmipp.utils.XmippMessage;
4 import xmipp.viewer.particlepicker.ParticlePicker;
5 
6 public class AutomaticParticle extends ManualParticle {
7 
8  private boolean deleted;
9 
10  public AutomaticParticle(int x, int y, ParticlePicker picker, SupervisedPickerMicrograph micrograph, double cost, boolean deleted) {
11  super(x, y, picker, micrograph, cost);
12  if(cost> 1)
13  throw new IllegalArgumentException(XmippMessage.getNoSuchFieldValueMsg("cost", cost));
14  this.deleted = deleted;
15  }
16 
17  public void setDeleted(boolean deleted)
18  {
19  this.deleted = deleted;
20  }
21 
22  public boolean isDeleted()
23  {
24  return deleted;
25  }
26  public boolean isUnavailable()
27  {
28  return deleted || ! aboveThreshold();
29  }
30  public boolean aboveThreshold()
31  {
32  return getCost() >= ((SupervisedPickerMicrograph)micrograph).getThreshold();
33  }
34 
35 
36 
37 
38 
39 }
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xmipp.viewer.particlepicker.training.model.AutomaticParticle.AutomaticParticle
AutomaticParticle(int x, int y, ParticlePicker picker, SupervisedPickerMicrograph micrograph, double cost, boolean deleted)
Definition: AutomaticParticle.java:10
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static String getNoSuchFieldValueMsg(String field, Object value)
Definition: XmippMessage.java:52
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double getCost()
Definition: Particle.java:42
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.viewer.particlepicker.training;
8 
9 import xmipp.jni.Classifier;
10 import xmipp.jni.Particle;
11 import xmipp.jni.PickingClassifier;
12 import xmipp.utils.XmippWindowUtil;
13 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame;
14 import xmipp.viewer.particlepicker.training.model.GenericClassifier;
15 import xmipp.viewer.particlepicker.training.model.MicrographState;
16 import xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker;
17 import xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph;
18 
19 import javax.swing.*;
20 
25 public class AutopickRunnable implements Runnable
26  {
27 
28  private SupervisedPickerJFrame frame;
29  private Particle[] autopickRows;
30  private SupervisedPickerMicrograph micrograph;
31  private final SupervisedParticlePicker picker;
32  private final Classifier classifier;
33 
34  public AutopickRunnable(SupervisedPickerJFrame frame, SupervisedPickerMicrograph micrograph)
35  {
36  this.frame = frame;
37  this.micrograph = micrograph;
38  this.picker = frame.getParticlePicker();
39  this.classifier = picker.getClassifier();
40  }
41 
42  public void run()
43  {
44 
45  micrograph.getAutomaticParticles().clear();
46  boolean isGeneric = !(classifier instanceof PickingClassifier);
47 
48  if (!isGeneric)
49  {
50  micrograph.setState(MicrographState.Supervised);
51  micrograph.setAutopickpercent(picker.getAutopickpercent());
52  autopickRows = ((PickingClassifier)classifier).autopick(micrograph.getFile(), micrograph.getAutopickpercent());
53  picker.loadParticles(micrograph, autopickRows);
54  picker.saveData(micrograph);
55  }
56  else
57  {
58  GenericClassifier gc = (GenericClassifier) classifier;
59  gc.autopick(micrograph);
60  // Despite we run autopick in one micrographs, there are cases
61  // in which the command will pick all of them and we want
62  // to load the particles from all
63  if (gc.doPickAll()) {
64  for (SupervisedPickerMicrograph mic : picker.getMicrographs())
65  picker.loadMicrographData(mic);
66  }
67  else
68  picker.loadMicrographData(micrograph);
69  }
70 
71  final boolean updateAllMicrographs = isGeneric && ((GenericClassifier) classifier).doPickAll();
72  // Runs inside of the Swing UI thread
73  SwingUtilities.invokeLater(new Runnable() {
74  public void run() {
75  frame.setChanged(false);
76 
77  // Select the worse particle as active
78  frame.getCanvas().refreshActive(null);
79 
80  frame.getCanvas().repaint();
81  frame.getCanvas().setEnabled(true);
82  XmippWindowUtil.releaseGUI(frame.getRootPane());
83  frame.updateMicrographsModel(updateAllMicrographs);
84  }
85  });
86  }
87 
88  }
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AutopickRunnable(SupervisedPickerJFrame frame, SupervisedPickerMicrograph micrograph)
Definition: AutopickRunnable.java:34
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void loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
Definition: SupervisedParticlePicker.java:1102
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static void releaseGUI(JRootPane panel)
Definition: XmippWindowUtil.java:242
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xmipp.viewer.particlepicker.training.model.GenericClassifier.autopick
void autopick(SupervisedPickerMicrograph micrograph)
Definition: GenericClassifier.java:86
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abstract void refreshActive(PickerParticle p)
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1 import ij.*;
2 import ij.process.*;
3 import ij.measure.Calibration;
4 import ij.gui.*;
5 import java.awt.*;
6 import ij.plugin.*;
7 
8 public class Averaging_Reducer implements PlugIn {
9  static int xshrink=2, yshrink=2;
10  double product;
11  int[] pixel = new int[3];
12  int[] sum = new int[3];
13  int samples;
14 
15  public void run(String arg) {
16  ImagePlus imp = IJ.getImage();
17  if (showDialog()) {
18  ImagePlus imp2 = shrink(imp);
19  imp2.show();
20  imp2.setSlice(imp2.getStackSize()/2);
21  imp2.getProcessor().resetMinAndMax();
22  }
23  }
24 
25  public ImagePlus shrink(ImagePlus imp) {
26  ImageStack stack1 = imp.getStack();
27  ImageStack stack2 = new ImageStack(imp.getWidth()/xshrink,imp.getHeight()/yshrink);
28  int n = stack1.getSize();
29  for (int i=1; i<=n; i++) {
30  IJ.showStatus(i+"/"+n);
31  IJ.showProgress(i, n);
32  ImageProcessor ip2 = shrink(stack1.getProcessor(i));
33  stack2.addSlice(null, ip2);
34  }
35  ImagePlus imp2 = new ImagePlus("Reduced "+imp.getShortTitle(), stack2);
36  imp2.setCalibration(imp.getCalibration());
37  Calibration cal2 = imp2.getCalibration();
38  if (cal2.scaled()) {
39  cal2.pixelWidth *= xshrink;
40  cal2.pixelHeight *= yshrink;
41  }
42  return imp2;
43  }
44 
45  public ImageProcessor shrink(ImageProcessor ip) {
46  if (ip instanceof FloatProcessor)
47  return shrinkFloat(ip);
48  samples = ip instanceof ColorProcessor?3:1;
49  int w = ip.getWidth()/xshrink;
50  int h = ip.getHeight()/yshrink;
51  ImageProcessor ip2 = ip.createProcessor(w, h);
52  for (int y=0; y<h; y++)
53  for (int x=0; x<w; x++)
54  ip2.putPixel(x, y, getAverage(ip, x, y));
55  return ip2;
56  }
57 
58  int[] getAverage(ImageProcessor ip, int x, int y) {
59  for (int i=0; i<samples; i++)
60  sum[i] = 0;
61  for (int y2=0; y2<yshrink; y2++) {
62  for (int x2=0; x2<xshrink; x2++) {
63  pixel = ip.getPixel(x*xshrink+x2, y*yshrink+y2, pixel);
64  for (int i=0; i<samples; i++)
65  sum[i] += pixel[i];
66  }
67  }
68  for (int i=0; i<samples; i++)
69  sum[i] = (int)(sum[i]/product+0.5);
70  return sum;
71  }
72 
73  boolean showDialog() {
74  GenericDialog gd = new GenericDialog("Image Shrink");
75  gd.addNumericField("X Shrink Factor:", xshrink, 0);
76  gd.addNumericField("Y Shrink Factor:", yshrink, 0);
77  gd.showDialog();
78  if (gd.wasCanceled())
79  return false;
80  xshrink = (int) gd.getNextNumber();
81  yshrink = (int) gd.getNextNumber();
82  product = xshrink*yshrink;
83  return true;
84  }
85 
86  ImageProcessor shrinkFloat(ImageProcessor ip) {
87  int w = ip.getWidth()/xshrink;
88  int h = ip.getHeight()/yshrink;
89  ImageProcessor ip2 = ip.createProcessor(w, h);
90  for (int y=0; y<h; y++)
91  for (int x=0; x<w; x++)
92  ip2.putPixelValue(x, y, getFloatAverage(ip, x, y));
93  return ip2;
94  }
95 
96  float getFloatAverage(ImageProcessor ip, int x, int y) {
97  double sum = 0.0;
98  for (int y2=0; y2<yshrink; y2++)
99  for (int x2=0; x2<xshrink; x2++)
100  sum += ip.getPixelValue(x*xshrink+x2, y*yshrink+y2);
101  return (float)(sum/product);
102  }
103 
104 }
Averaging_Reducer.shrink
ImageProcessor shrink(ImageProcessor ip)
Definition: Averaging_Reducer.java:45
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Averaging_Reducer.shrink
ImagePlus shrink(ImagePlus imp)
Definition: Averaging_Reducer.java:25
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Averaging_Reducer.run
void run(String arg)
Definition: Averaging_Reducer.java:15
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Averaging_Reducer
Definition: Averaging_Reducer.java:8
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1 import ij.*;
2 import ij.io.*;
3 import ij.util.Tools;
4 import ij.plugin.*;
5 import java.io.*;
6 import java.util.zip.GZIPInputStream;
7 
8 import ij.measure.*;
9 import java.awt.image.*;
10 
22 public class Biorad_Reader extends ImagePlus implements PlugIn {
23 
24  private final int NOTE_SIZE = 96;
25  private BufferedInputStream f;
26  private String directory;
27  private String fileName;
28  private String notes = "";
29  private int lutOffset = -1;
30 
31  public void run(String arg) {
32  OpenDialog od = new OpenDialog("Open Biorad...", arg);
33  directory = od.getDirectory();
34  fileName = od.getFileName();
35  if (fileName==null)
36  return;
37  IJ.showStatus("Opening: " + directory + fileName);
38  FileInfo fi = null;
39  try {fi = getHeaderInfo();}
40  catch (Exception e) {
41  IJ.showStatus("");
42  IJ.showMessage("BioradReader", ""+e);
43  return;
44  }
45  if (fi!=null) {
46 
47  if(fileName.toLowerCase().endsWith(".gz") && IJ.getVersion().compareTo("1.38s")<0) {
48  IJ.error("ImageJ 1.38s or later required to open gzipped Biorad PIC files");
49  return;
50  }
51 
52  FileOpener fo = new FileOpener(fi);
53  ImagePlus imp = fo.open(false);
54  if(IJ.debugMode)IJ.log("imp="+imp);
55  if (imp==null)
56  return;
57 
58  setStack(fileName, imp.getStack());
59  setFileInfo(fi);
60  if(IJ.debugMode) IJ.log("FileInfo="+fi);
61  try {
62  int pixelLength=1;
63  switch (fi.fileType) { // ghj 4/3/06
64  case FileInfo.GRAY8: pixelLength=1; break;
65  case FileInfo.GRAY16_UNSIGNED:pixelLength=2; break;
66  }
67  Calibration BioRadCal = getBioRadCalibration(fi.width, fi.height, fi.nImages, pixelLength); // ghj 4/3/0
68  setCalibration(BioRadCal);
69  } catch (Exception e) {
70  IJ.showStatus("");
71  String msg = e.getMessage();
72  if (e==null) msg = ""+e;
73  if (msg.indexOf("EOF")==-1)
74  IJ.showMessage("BioradReader", msg);
75  return;
76  }
77 
78  boolean hasLut = false;
79 
80  if (lutOffset!=-1) {
81  try {hasLut = getLut(fi);}
82  catch (Exception e) {
83  IJ.showStatus("");
84  IJ.showMessage("BioradReader",
85  "Can't read LUT from file because "+e);
86  hasLut = false;
87  }
88  }
89 
90  if (hasLut) {
91  ColorModel cm =
92  new IndexColorModel(8, 256, fi.reds, fi.greens, fi.blues);
93  getProcessor().setColorModel(cm);
94  getStack().setColorModel(cm);
95  }
96 
97  if (!notes.equals(""))
98  setProperty("Info", notes);
99  if(IJ.debugMode)IJ.log("arg=|"+arg+"|");
100  if (arg.equals("")) show();
101  }
102  if(IJ.debugMode)IJ.log("done");
103  }
104 
105  int getByte() throws IOException {
106  int b = f.read();
107  if (b ==-1) throw new IOException("unexpected EOF");
108  return b;
109  }
110 
111  int getShort() throws IOException {
112  int b0 = getByte();
113  int b1 = getByte();
114  return ((b1 << 8) + b0);
115  }
116 
117  int getInt() throws IOException {
118  int b0 = getShort();
119  int b1 = getShort();
120  return ((b1<<16) + b0);
121  }
122 
123  void openFile() throws IOException {
124  // Note that this has been changed to cope with gzipped files
125  if (fileName.toLowerCase().endsWith(".pic.gz") ) {
126  // gzipped pic file
127  f = new BufferedInputStream(new GZIPInputStream(new FileInputStream(directory+fileName)));
128  } else {
129  // regular PIC file
130  f = new BufferedInputStream(new FileInputStream(directory+fileName));
131  }
132  }
133 
134  FileInfo getHeaderInfo() throws IOException {
135  openFile();
136  int width = getShort(); // 0-1
137  int height = getShort(); // 2-3
138  int nImages = getShort(); // 4-5
139  f.skip(8);
140  int byte_format = getShort(); //14-15
141  f.skip(38);
142  int magicNumber = getShort(); // 54-55
143  f.close();
144 
145  // A Biorad .PIC file should have 12345 in bytes 54-55
146  String notBioradPicFile =
147  "This does not seem to be a Biorad Pic File";
148  if (magicNumber!=12345)
149  throw new IOException(notBioradPicFile);
150 
151  FileInfo fi = new FileInfo();
152  fi.fileFormat = FileInfo.RAW;
153  fi.fileName = fileName;
154  fi.directory = directory;
155  fi.width = width;
156  fi.height = height;
157  fi.nImages = nImages;
158  fi.offset = 76;
159 
160  switch (byte_format) {
161  case 1:
162  fi.fileType = FileInfo.GRAY8;
163  break;
164  case 0:
165  fi.fileType = FileInfo.GRAY16_UNSIGNED;
166  fi.intelByteOrder = true; // ghj 4/3/06
167  break;
168  }
169  if(IJ.debugMode)IJ.log("fileType ("+FileInfo.GRAY8+","+FileInfo.GRAY16_UNSIGNED+")="+fi.fileType);
170  return fi;
171  }
172 
175  Calibration getBioRadCalibration(int width, int height, int nImages,int pixelLength) // ghj 4/3/06
176  throws IOException {
177  Calibration BioRadCal = new Calibration();
178  int NoteFlag, NoteType, Offset;
179  String NoteContent = new String();
180  byte[] TempByte = new byte[80];
181  byte[] RawNote = new byte[80];
182  double ScaleX, ScaleY;
183  double ScaleZ=0, framesPerSecond = 0, frameInterval = 0;
184  boolean xyt = false;
185 
186  Offset = 76 + height * width * nImages*pixelLength; // ghj 4/3/06
187  openFile();
188  f.skip(Offset);
189  if(IJ.debugMode)IJ.log("getBioRadCalibration");
194  do {
195  f.skip(2);
196  NoteFlag = getInt(); // 2-5
197  f.skip(4);
198  NoteType = getShort(); // 10-11
199  f.skip(4);
200 
201  // store bytes 16-95 in a byte array
202  f.read(RawNote);
203 
204  // replace illegal characters with 32
205  byte ch;
206  for (int i=0; i<80; i++) {
207  ch = RawNote[i];
208  TempByte[i] = (ch>=32 && ch<=126)?ch:32;
209  }
210  String Note = new String(TempByte);
211  notes += Note + "\n";
212  // save note for Image/Show Info command
213 
216  if (NoteType!=1) {
217  NoteContent = getField(Note,1);
221  if (NoteContent.indexOf("AXIS_2") >= 0 ) {
222  //IJ.showMessage(Note);
223  //IJ.showMessage(getField(Note, 4));
224  ScaleX = s2d(getField(Note, 4));
225  BioRadCal.pixelWidth = ScaleX;
226  // fifth field contains units (mostly microns)
227  BioRadCal.setUnit(getField(Note, 5));
228  } else if ( NoteContent.indexOf("AXIS_3") >= 0 ) {
229  // contains Y-axis calibration
230  //IJ.showMessage(Note);
231  //IJ.showMessage(getField(Note, 4));
232  ScaleY = s2d( getField(Note, 4));
233  BioRadCal.pixelHeight = ScaleY;
234  BioRadCal.setUnit(getField(Note, 5));
235  } else if ( NoteContent.indexOf("AXIS_4") >= 0 ) {
236  // contains Z-axis calibration
237  //IJ.showMessage(Note);
238  //IJ.showMessage(getField(Note, 4));
239  ScaleZ = s2d( getField(Note, 4));
240  BioRadCal.pixelDepth = ScaleZ;
241  if (getField(Note,5).indexOf("Seconds")>=0) {
242  xyt = true;
243  }
249  } else if ( NoteContent.indexOf("INFO_FRAME_RATE")>=0 ) {
250  // Contains frame rate
251  //IJ.showMessage(Note);
252  //IJ.showMessage(getField(Note, 3));
253  framesPerSecond = s2d(getField(Note,3));
254  frameInterval = 1/framesPerSecond;
255  BioRadCal.frameInterval = frameInterval;
256  }
257  }
258  if(IJ.debugMode)IJ.log("Offset ="+Offset );
259  Offset += NOTE_SIZE; // Jump to next note
260  // stop if this was the last note
261  } while ( NoteFlag != 0 & f.available()>=NOTE_SIZE);
262  if(IJ.debugMode)IJ.log("lut?");
266  lutOffset = Offset;
267  if (xyt) {
273  BioRadCal.pixelDepth = frameInterval;
274  }
275  f.close();
276  if(IJ.debugMode)IJ.log("BioRadCal"+BioRadCal);
277  return BioRadCal; // return the filled biorad calibration
278  }
279 
283  boolean getLut(FileInfo fi) throws IOException {
284 
285  openFile();
286  f.skip(lutOffset);
287 
288  fi.reds = new byte[256];
289  fi.greens = new byte[256];
290  fi.blues = new byte[256];
291 
292  boolean hasLut = false;
293 
294  if (f.available()>=768) {
295  hasLut = true;
296  f.read(fi.reds);
297  f.read(fi.greens);
298  f.read(fi.blues);
299  }
300 
301  f.close();
302 
303  return hasLut;
304  }
305 
306  /* Extracts a certain field from a string. A space is considered
307  as the field delimiter. */
308  String getField(String str, int fieldIndex) {
309  char delimiter = ' ';
310  int startIndex=0, endIndex;
311  for (int i=1; i<fieldIndex; i++)
312  startIndex = str.indexOf(delimiter, startIndex+1);
313  endIndex = str.indexOf(delimiter, startIndex+1);
314  if (startIndex>=0 && endIndex>=0)
315  return str.substring(startIndex, endIndex);
316  else
317  return "";
318  }
319 
323  double s2d(String s) {
324  return Tools.parseDouble(s);
325  }
326 }
327 
328 /*
329  Bio-Rad(TM) .PIC Image File Information
330  (taken from: "Introductory Edited Version 1.0", issue 1/12/93.)
331  (Location of Image Calibration Parameters in Comos 6.03 and MPL .PIC files)
332 
333  The general structure of Bio-Rad .PIC files is as follows:
334 
335  HEADER (76 bytes)
336  Image data (#1)
337  .
338  .
339  Image data (#npic)
340  NOTE (#1)
341  . ; NOTES are optional.
342  .
343  NOTE (#notes)
344  RGB LUT (color Look Up Table)
345 
346 
347  Header Information:
348 
349  The header of Bio-Rad .PIC files is fixed in size, and is 76 bytes.
350 
351  ------------------------------------------------------------------------------
352  'C' Definition byte size Information
353  (bytes)
354  ------------------------------------------------------------------------------
355  int nx, ny; 0 2*2 image width and height in pixels
356  int npic; 4 2 number of images in file
357  int ramp1_min, ramp1_max; 6 2*2 LUT1 ramp min. and max.
358  NOTE *notes; 10 4 no notes=0; has notes=non zero
359  BOOL byte_format; 14 2 bytes=TRUE(1); words=FALSE(0)
360  int n; 16 2 image number within file
361  char name[32]; 18 32 file name
362  int merged; 50 2 merged format
363  unsigned color1; 52 2 LUT1 color status
364  unsigned file_id; 54 2 valid .PIC file=12345
365  int ramp2_min, ramp2_max; 56 2*2 LUT2 ramp min. and max.
366  unsigned color2; 60 2 LUT2 color status
367  BOOL edited; 62 2 image has been edited=TRUE(1)
368  int _lens; 64 2 Integer part of lens magnification
369  float mag_factor; 66 4 4 byte real mag. factor (old ver.)
370  unsigned dummy[3]; 70 6 NOT USED (old ver.=real lens mag.)
371  ------------------------------------------------------------------------------
372 
373  Additional information about the HEADER structure:
374 
375  Bytes Description Details
376  ------------------------------------------------------------------------------
377  0-9 nx, ny, npic, ramp1_min, ramp1_max; (all are 2-byte integers)
378 
379  10-13 notes NOTES are present in the file, otherwise there are
380  none. NOTES follow immediately after image data at
381  the end of the file. Each note os 96 bytes long.
382 
383  14-15 byte_format Read as a 2 byte integer. If this is set to 1, then
384  each pixel is 8-bits; otherwise pixels are 16-bits.
385 
386  16-17 n Only used in COMOS/SOM when the file is loaded into
387  memory.
388 
389  18-49 name The name of the file (without path); zero terminated.
390 
391  50-51 merged see Note 1.
392 
393  52-53 colour1
394 
395  54-55 file_id Read as a 2 byte integer. Aways set to 12345.
396  Just a check that the file is in Bio-Rad .PIC format.
397 
398  56-59 ramp2_min/max Read as 2 byte integers.
399 
400  60-61 color2 Read as a 2 byte integer.
401 
402  62-63 edited Not used in disk files.
403 
404  64-65 int_lens Read as a 2 byte integer.
405  Integer part of the objective lens used.
406 
407  66-69 mag_factor Read as a 4-byte real.
408 
409  mag. factor=(float)(dispbox.dy*2)/(float)(512.0*scandata.ly)
410 
411  where: dispbox.dy = the width of the image.
412  scandata.ly = the width of the scan region.
413 
414  the pixel size in microns can be calculated as follows:
415 
416  pixel size = scale_factor/lens/mag_factor
417 
418  where: lens = the objective lens used as a floating pt. number
419  scale_factor = the scaling number setup for the system
420  on which the image was collected.
421 
422  70-75 dummy[3] Last 6 bytes not used in current version of disk file
423  format. (older versions stored a 4 byte real lens mag
424  here.)
425  ------------------------------------------------------------------------------
426 
427  Note 1 : Values stored in bytes 50-51 :
428 
429  0 : Merge off
430  1 : 4-bit merge
431  2 : Alternate 8-bit merge
432  3 : Alternate columns merge
433  4 : Alternate rows merge
434  5 : Maximum pixel intensity merge
435  6 : 256 colour optimised merge with RGB LUT saved at the end
436  of each merge.
437  7 : As 6 except that RGB LUT saved after all the notes.
438 
439 
440  Information about NOTE structure and the RGB LUT are not included in this
441  file. Please see the Bio-Rad manual for more information.
442 
443 
444  ==============================================================================
445 
446  Info added by Geert Meesen from MRC-600 and MRC-1024 Manuals.
447 
448  -------------------------------------------------------------
449 
450  Note Structure :
451 
452  Bytes Description Details
453  ------------------------------------------------------------------------------
454  0-1 Display level of this note
455 
456  2-5 =0 if this is the last note, else there is another note (32 bit integer)
457 
458  10-11 Note type := 1 for live collection note,
459  := 2 for note including file name,
460  := 3 if note for multiplier file,
461  := 4, 5, etc.,; additional descriptive notes
462 
463  16-95 Text of note (80 bytes)
464 
465 
466  =============================================================================
467 
468  Info added by Geert Meesen from personal experiments.
469 
470  ------------------------------------------------------------
471 
472  - Until now I only have experience with 8-bit images from the MRC-1024 confocal microscope.
473  The newer microscopes (Radiance 2000, for example) are capable of generating 16 bit images,
474  I think. I have access to such a microscope and will try to find out later. For now it
475  should be possible to look at the byte-word flag in the header.
476 
477  - I have experience with two types of images :
478  --- One slice in the Z-direction, 3 channels of recording. This type is stored as a three-slice image
479  with the 3 channels in consecutive layers. (Single-Slice)
480  --- Different Z slices with only one channel. (Z-stack)
481 
482  - The header should contain some info about the pixel-size, but until now I was not really
483  able to interpret this info. It's easier to extract the info from the notes at the end.
484  You can find 3 notes saying something like (from AUPCE.NOT, a Z-stack file)
485 
486  AXIS_2 001 0.000000e+00 2.999667e-01 microns
487  AXIS_3 001 0.000000e+00 2.999667e-01 microns
488  AXIS_4 001 0.000000e+00 1.000000e+00 microns
489  AXIS_9 011 0.000000e+00 1.000000e+00 RGB channel
490 
491  These lines give the pixelsize for the X (axis_2), Y (axis_3) and Z (axis_4) axis in the units mentioned. I don't
492  know if this unit is always 'microns'.
493 
494  For a Single-Slice images you get ( from AB003A.NOT, a Single-Slice image) :
495 
496  AXIS_2 001 0.000000e+00 1.799800e+00 microns
497  AXIS_3 001 0.000000e+00 1.799800e+00 microns
498  AXIS_4 011 0.000000e+00 1.000000e+00 RGB channel
499 
500  It seems that AXIS_4 is used for indicating an RGB channel image.
501 */
Biorad_Reader
Definition: Biorad_Reader.java:22
-
Biorad_Reader.run
void run(String arg)
Definition: Biorad_Reader.java:31
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package  xmipp.viewer.ctf
 
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1 package xmipp.viewer.ctf;
2 
3 import ij.ImagePlus;
4 
5 import java.awt.Color;
6 import java.awt.Dimension;
7 import java.awt.Graphics;
8 import java.awt.event.MouseEvent;
9 import java.awt.event.MouseListener;
10 import java.awt.event.MouseMotionListener;
11 import java.awt.event.MouseWheelEvent;
12 import java.awt.event.MouseWheelListener;
13 
14 import javax.swing.JPanel;
15 
16 public class CTFAnalyzerImagePane extends JPanel implements MouseListener, MouseWheelListener, MouseMotionListener
17 {
18 
19  private int x0;
20  private int y0;
21  private int x1;
22  private int y1;
23  private double profileangle;
24  private ImagePlus imp;
25  private int radius;
26  private CTFAnalyzerJFrame frame;
27 
28 
29  public CTFAnalyzerImagePane(ImagePlus imp, CTFAnalyzerJFrame frame)
30  {
31  this.imp = imp;
32  this.frame = frame;
33  setPreferredSize(new Dimension(imp.getWidth(), imp.getHeight()));
34 
35  radius = imp.getWidth() / 2;
36  x0 = radius;
37  y0 = radius;
38  profileangle = 0;
39  x1 = x0 + (int) (radius * Math.cos(profileangle));
40  y1 = y0 + (int) (radius * Math.sin(profileangle));
41  setToolTipText("Use mouse to move profile");
42  addMouseListener(this);
43  addMouseWheelListener(this);
44  addMouseMotionListener(this);
45  }
46 
47 
48  public double getProfileangle()
49  {
50  return profileangle;
51  }
52 
53 
54  public int getX0()
55  {
56  return x0;
57  }
58 
59 
60  public int getY0()
61  {
62  return y0;
63  }
64 
65 
66  public int getX1()
67  {
68  return x1;
69  }
70 
71 
72  public int getY1()
73  {
74  return y1;
75  }
76 
77 
78  public void paintComponent(Graphics g)
79  {
80  super.paintComponent(g);
81 
82  g.drawImage(imp.getImage(), 0, 0, this);
83  g.setColor(Color.green);
84  g.drawLine(x0, y0, x1, y1);
85 
86  }
87 
88  private void updateProfile(MouseEvent e)
89  {
90  int y = radius - e.getY();
91  int x = e.getX() - radius;
92  double angle = -Math.atan2(y, x);
93  updateProfile(angle);
94  }
95 
96  private void updateProfile(double angle)
97  {
98  profileangle = angle;
99  x1 = x0 + (int) (radius * Math.cos(profileangle));
100  y1 = y0 + (int) (radius * Math.sin(profileangle));
101  repaint();
102  frame.fillGraphics();
103  }
104 
105 
106  @Override
107  public void mouseWheelMoved(MouseWheelEvent e)
108  {
109  int rotation = e.getWheelRotation();//1 or -1
110  updateProfile(profileangle + rotation * Math.toRadians(5));
111 
112  }
113 
114 
115  @Override
116  public void mouseClicked(MouseEvent e)
117  {
118  updateProfile(e);
119 
120  }
121 
122 
123 
124 
125  @Override
126  public void mouseEntered(MouseEvent arg0)
127  {
128  // TODO Auto-generated method stub
129 
130  }
131 
132 
133  @Override
134  public void mouseExited(MouseEvent arg0)
135  {
136  // TODO Auto-generated method stub
137 
138  }
139 
140 
141  @Override
142  public void mousePressed(MouseEvent arg0)
143  {
144  // TODO Auto-generated method stub
145 
146  }
147 
148 
149  @Override
150  public void mouseReleased(MouseEvent e)
151  {
152  updateProfile(e);
153 
154  }
155 
156 
157  @Override
158  public void mouseDragged(MouseEvent e)
159  {
160  updateProfile(e);
161 
162  }
163 
164 
165  @Override
166  public void mouseMoved(MouseEvent arg0)
167  {
168  // TODO Auto-generated method stub
169 
170  }
171 
172 }
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xmipp.viewer.ctf.CTFAnalyzerImagePane.CTFAnalyzerImagePane
CTFAnalyzerImagePane(ImagePlus imp, CTFAnalyzerJFrame frame)
Definition: CTFAnalyzerImagePane.java:29
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1 package xmipp.viewer.ctf;
2 
3 import ij.ImagePlus;
4 import ij.gui.Line;
5 import ij.gui.ProfilePlot;
6 import java.awt.BasicStroke;
7 import java.awt.Color;
8 import java.awt.GridBagConstraints;
9 import java.awt.GridBagLayout;
10 import java.awt.Insets;
11 import java.awt.event.ActionEvent;
12 import java.awt.event.ActionListener;
13 import java.io.BufferedWriter;
14 import java.io.File;
15 import java.io.FileWriter;
16 import java.util.Arrays;
17 import java.util.List;
18 import javax.swing.BorderFactory;
19 import javax.swing.ButtonGroup;
20 import javax.swing.JButton;
21 import javax.swing.JCheckBox;
22 import javax.swing.JFrame;
23 import javax.swing.JPanel;
24 import javax.swing.JRadioButton;
25 import javax.swing.JTabbedPane;
26 import org.jfree.chart.ChartFactory;
27 import org.jfree.chart.ChartPanel;
28 import org.jfree.chart.ChartUtilities;
29 import org.jfree.chart.JFreeChart;
30 import org.jfree.chart.plot.PlotOrientation;
31 import org.jfree.chart.plot.XYPlot;
32 import org.jfree.chart.renderer.xy.XYItemRenderer;
33 import org.jfree.data.xy.XYSeries;
34 import org.jfree.data.xy.XYSeriesCollection;
35 import xmipp.jni.ImageGeneric;
36 import xmipp.jni.CTFDescription;
37 import xmipp.jni.MDLabel;
38 import xmipp.jni.MetaData;
39 import xmipp.utils.XmippDialog;
40 import xmipp.utils.XmippFileChooser;
41 import xmipp.utils.XmippLabel;
42 import xmipp.utils.XmippWindowUtil;
43 import xmipp.ij.commons.XmippImageConverter;
44 
45 
46 
47 public class CTFAnalyzerJFrame extends JFrame implements ActionListener
48 {
49 
50  private ImagePlus imp;
51  private JPanel graphicpn;
52  private JPanel imagepn;
53  private CTFDescription ctfmodel;
54  private int samples;
55  private double[] xvalues;
56  private XYSeriesCollection collection;
57  private ChartPanel radialchartpn;
58  private JPanel actionspn;
59  private JRadioButton ctfrb;
60  private JRadioButton psdrb;
61  private GridBagConstraints constraints;
62  private JCheckBox theorethicalpsdchb;
63  private JCheckBox envelopepsdchb;
64  private JCheckBox noisechb;
65  private CTFAnalyzerImagePane imageprofilepn;
66  private JTabbedPane tabspn;
67  private String psdfile;
68  private ChartPanel avgchartpn;
69  double[] ctf_avgplot, theorethicalpsd_avgplot, envelope_avgplot, bgnoise_avgplot, psdprofile_avgplot, difference_avgplot;
70  double[] ctfplot, theorethicalpsdplot, envelopeplot, bgnoiseplot, psdprofileplot, difference;
71  private JButton exportbt;
72  private JButton exportavgbt;
73  private XmippFileChooser fc;
74  private JCheckBox differencechb;
75  private final static BasicStroke plotsStroke = new BasicStroke(1.5f);
76  private final static Color COLOR_PROFILE = Color.BLACK;
77  private final static Color COLOR_BACKGROUND_NOISE = Color.RED;
78  private final static Color COLOR_ENVELOPE = Color.GREEN;
79  private final static Color COLOR_PSD = Color.BLUE;
80  private final static Color COLOR_CTF = Color.MAGENTA;
81  private final static Color COLOR_DIFFERENCE = Color.orange;
82  private ImagePlus profileimp;
83 
84 
85 
86  public CTFAnalyzerJFrame(String psdEnhancedFile, String ctffile, String psdfile)
87  {
88  try
89  {
90  this.imp = this.getThumbnail(psdEnhancedFile);
91  this.psdfile = psdfile;
92  this.profileimp = this.getThumbnail(psdfile);
93  ctfmodel = new CTFDescription(ctffile);
94  double samplingRate = getSamplingRate(ctffile);
95  samples = this.imp.getWidth() / 2;
96  xvalues = getXValues(samples, samplingRate);
97  initComponents();
98  } catch (Exception e) {
99  e.printStackTrace();
100  }
101  }
102 
103  public CTFAnalyzerJFrame(String psdEnhancedFile, CTFDescription ctfdescription, String psdfile, double samplingRate)
104  {
105  try
106  {
107  this.imp = this.getThumbnail(psdEnhancedFile);
108  this.psdfile = psdfile;
109  this.profileimp = this.getThumbnail(psdfile);
110  ctfmodel = ctfdescription;
111  samples = this.imp.getWidth() / 2;
112  xvalues = getXValues(samples, samplingRate);
113  initComponents();
114  } catch (Exception e) {
115  e.printStackTrace();
116  }
117  }
118 
119  /* Load the image with a size of 256 pixels. */
120  private ImagePlus getThumbnail(String imagefile)
121  {
122  ImagePlus imp = null;
123  try
124  {
125  ImageGeneric img = new ImageGeneric(imagefile);
126  img.read(256, 256, ImageGeneric.FIRST_IMAGE);
127  imp = XmippImageConverter.readToImagePlus(img);
128  // Free the C-image memory
129  img.destroy();
130  } catch (Exception e) {
131  e.printStackTrace();
132  }
133  return imp;
134  }
135 
136  private void initComponents()
137  {
138  setTitle("CTF Analyzer");
139  fc = new XmippFileChooser();
140 
141  constraints = new GridBagConstraints();
142  constraints.insets = new Insets(0, 5, 0, 5);
143  constraints.anchor = GridBagConstraints.NORTHWEST;
144  // constraints.fill = GridBagConstraints.HORIZONTAL;
145  setLayout(new GridBagLayout());
146  JPanel contentpn = new JPanel(new GridBagLayout());
147  contentpn.setBorder(BorderFactory.createEtchedBorder());
148  add(contentpn, XmippWindowUtil.getConstraints(constraints, 0, 0));
149  imagepn = new JPanel(new GridBagLayout());
150  imagepn.setBorder(BorderFactory.createTitledBorder("PSD Image"));
151  imageprofilepn = new CTFAnalyzerImagePane(imp, this);
152  imagepn.add(imageprofilepn, XmippWindowUtil.getConstraints(constraints, 0, 0));
153  contentpn.add(imagepn, XmippWindowUtil.getConstraints(constraints, 0, 0, 1));
154 
155  initGraphicPanes();
156  contentpn.add(actionspn, XmippWindowUtil.getConstraints(constraints, 0, 1, 1, 1));
157  contentpn.add(graphicpn, XmippWindowUtil.getConstraints(constraints, 1, 0, 1, 3));
158 
159  JPanel actionspn = new JPanel();
160  exportbt = XmippWindowUtil.getTextButton("Export Graphics", this);
161  actionspn.add(exportbt, XmippWindowUtil.getConstraints(constraints, 0, 1));
162 // exportavgbt = XmippWindowUtil.getTextButton("Export Average Graphics", this);
163 // actionspn.add(exportavgbt, XmippWindowUtil.getConstraints(constraints, 1, 1));
164  add(actionspn, XmippWindowUtil.getConstraints(constraints, 0, 1));
165  enableDisplay();
166  pack();
167  setVisible(true);
168  }
169 
170  private void initGraphicPanes()
171  {
172  actionspn = new JPanel(new GridBagLayout());
173  actionspn.setBorder(BorderFactory.createTitledBorder("Display"));
174  ctfrb = new JRadioButton(getCTFLabel());
175  ctfrb.addActionListener(new FillGraphicsActionListener());
176  ctfrb.addActionListener(new EnableDisplayActionListener());
177 
178  psdrb = new JRadioButton(getPSDProfileLabel());
179  psdrb.addActionListener(new FillGraphicsActionListener());
180  psdrb.addActionListener(new EnableDisplayActionListener());
181  ButtonGroup drawbg = new ButtonGroup();
182  drawbg.add(ctfrb);
183  drawbg.add(psdrb);
184  ctfrb.setSelected(true);
185  actionspn.add(ctfrb, XmippWindowUtil.getConstraints(constraints, 0, 0));
186  actionspn.add(psdrb, XmippWindowUtil.getConstraints(constraints, 0, 1));
187 
188  constraints.insets = new Insets(0, 20, 0, 5);
189  theorethicalpsdchb = new JCheckBox(getTheorethicalPSDLabel());
190  theorethicalpsdchb.addActionListener(new FillGraphicsActionListener());
191  envelopepsdchb = new JCheckBox(getEnvelopeLabel());
192  envelopepsdchb.addActionListener(new FillGraphicsActionListener());
193  noisechb = new JCheckBox(getBGNoiseLabel());
194  noisechb.addActionListener(new FillGraphicsActionListener());
195  differencechb = new JCheckBox(getDifferenceLabel());
196  differencechb.addActionListener(new FillGraphicsActionListener());
197 
198  actionspn.add(theorethicalpsdchb, XmippWindowUtil.getConstraints(constraints, 0, 2));
199  actionspn.add(envelopepsdchb, XmippWindowUtil.getConstraints(constraints, 0, 3));
200  actionspn.add(noisechb, XmippWindowUtil.getConstraints(constraints, 0, 4));
201  actionspn.add(differencechb, XmippWindowUtil.getConstraints(constraints, 0, 5));
202 
203  graphicpn = new JPanel();
204  tabspn = new JTabbedPane();
205  JPanel tab1pn = new JPanel();
206  JPanel tab2pn = new JPanel();
207  tabspn.addTab("Radial Profile", tab1pn);
208  tabspn.addTab("Radial Average", tab2pn);
209  graphicpn.add(tabspn);
210  JFreeChart chart = ChartFactory
211  .createXYLineChart("", XmippLabel.LABEL_SAMPLING, showCTF() ? getCTFLabel() : getPSDProfileLabel(), collection, PlotOrientation.VERTICAL, true, true, false);
212 
213  radialchartpn = createChartPanel(chart);
214  JFreeChart avgchart = ChartFactory
215  .createXYLineChart("", XmippLabel.LABEL_SAMPLING, showCTF() ? getCTFLabel() : getPSDProfileLabel(), collection, PlotOrientation.VERTICAL, true, true, false);
216 
217  avgchartpn = createChartPanel(avgchart);
218  fillGraphics();
219  tab1pn.add(radialchartpn);
220  tab2pn.add(avgchartpn);
221  }
222 
223 
224 
225  private static ChartPanel createChartPanel(JFreeChart chart)
226  {
227  XYPlot plot = (XYPlot) chart.getPlot();
228  plot.setDomainPannable(true);
229  plot.setRangePannable(true);
230 
231  List<Integer> list = Arrays.asList(new Integer[] { new Integer(0), new Integer(1) });
232  plot.mapDatasetToDomainAxes(0, list);
233  plot.mapDatasetToRangeAxes(0, list);
234 
235  ChartUtilities.applyCurrentTheme(chart);
236 
237  return new ChartPanel(chart);
238  }
239 
240  public boolean isRadialProfile()
241  {
242  return tabspn.getSelectedIndex() == 0;
243  }
244 
245  void fillGraphics()
246  {
247  fillRadialGraphics();
248  fillAvgGraphics();
249  }
250 
251  private void fillAvgGraphics()
252  {
253  if (psdprofile_avgplot == null)// avg data does not change, calculated
254  // only once
255  {
256  int x0 = imageprofilepn.getX0();
257  int y0 = imageprofilepn.getY0();
258  // // Get profile.
259  Line line;
260  double[] avgprofileplot = new double[samples];
261  double angle;
262  int x1, y1;
263 
264  for (int i = 0; i < 360; i++)
265  {
266  angle = Math.toRadians(-i);
267 
268  // Make line roi.
269  x1 = x0 + (int) (samples * Math.cos(angle));
270  y1 = y0 + (int) (samples * Math.sin(angle));
271 
272  line = new Line(x0, y0, x1, y1);
273  imp.setRoi(line);
274  profileimp.setRoi(line);
275  // Get profile.
276  ProfilePlot profilePlot = new ProfilePlot(profileimp);
277  psdprofile_avgplot = profilePlot.getProfile();
278 
279  // Total summatory.
280  sum(avgprofileplot, psdprofile_avgplot);
281  }
282 
283  // Get profile average.
284  for (int i = 0; i < avgprofileplot.length; i++)
285  avgprofileplot[i] /= 360;
286  psdprofile_avgplot = avgprofileplot;
287 
288  // Get rest of profiles average.
289  ctfmodel.CTFAverageProfiles(samples);
290 
291  bgnoise_avgplot = ctfmodel.avgprofiles[CTFDescription.BACKGROUND_NOISE];
292  envelope_avgplot = ctfmodel.avgprofiles[CTFDescription.ENVELOPE];
293  theorethicalpsd_avgplot = ctfmodel.avgprofiles[CTFDescription.PSD];
294  ctf_avgplot = ctfmodel.avgprofiles[CTFDescription.CTF];
295  difference_avgplot = new double[bgnoiseplot.length];
296  double a, b;
297  for (int i = 0; i < xvalues.length; i++)
298  {
299  a = psdprofile_avgplot[i];//Math.pow(10, psdprofileplot[i] * 0.1);
300  b = bgnoise_avgplot[i]; //Math.pow(10, bgnoiseplot[i] * 0.1);
301  difference_avgplot[i] = a - b;//Math.log10(a - b);
302  //difference_avgplot[i] = Math.log10(Math.pow(10, psdprofile_avgplot[i] * 0.1) - Math.pow(10, bgnoise_avgplot[i] * 0.1));
303  }
304  }
305  XYPlot plot = getAvgPlot();
306  XYSeriesCollection collection = getXYSeriesCollection(plot, psdprofile_avgplot, ctf_avgplot, theorethicalpsd_avgplot, envelope_avgplot, bgnoise_avgplot, difference_avgplot);
307  plot.setDataset(0, collection);
308  plot.getRangeAxis().setLabel(showCTF() ? getCTFLabel() : getPSDProfileLabel());
309  }
310 
311  private XYPlot getAvgPlot(){
312  return ((XYPlot) avgchartpn.getChart().getPlot());
313  }
314 
315  private XYPlot getRadialPlot(){
316  return ((XYPlot) radialchartpn.getChart().getPlot());
317  }
318 
319  private void fillRadialGraphics()
320  {
321  int x0 = imageprofilepn.getX0();
322  int y0 = imageprofilepn.getY0();
323  // // Get profile.
324  Line line;
325 
326  line = new Line(x0, y0, imageprofilepn.getX1(), imageprofilepn.getY1());
327  imp.setRoi(line);
328  profileimp.setRoi(line);
329  psdprofileplot = new ProfilePlot(profileimp).getProfile();
330 
331 
332  ctfmodel.CTFProfile(imageprofilepn.getProfileangle(), samples);
333  bgnoiseplot = ctfmodel.profiles[CTFDescription.BACKGROUND_NOISE];
334  envelopeplot = ctfmodel.profiles[CTFDescription.ENVELOPE];
335  theorethicalpsdplot = ctfmodel.profiles[CTFDescription.PSD];
336  ctfplot = ctfmodel.profiles[CTFDescription.CTF];
337  difference = new double[bgnoiseplot.length];
338  double a, b;
339  for (int i = 0; i < xvalues.length; i++)
340  {
341  a = psdprofileplot[i];//Math.pow(10, psdprofileplot[i] * 0.1);
342  b = bgnoiseplot[i]; //Math.pow(10, bgnoiseplot[i] * 0.1);
343  difference[i] = a - b;//Math.log10(a - b);
344  }
345 
346  XYPlot plot = ((XYPlot) radialchartpn.getChart().getPlot());
347 
348  XYSeriesCollection collection = getXYSeriesCollection(plot, psdprofileplot, ctfplot, theorethicalpsdplot, envelopeplot, bgnoiseplot, difference);
349 
350  plot.setDataset(0, collection);
351  plot.getRangeAxis().setLabel(showCTF() ? getCTFLabel(): getPSDProfileLabel());
352  }
353 
354  private static void sum(double a[], double b[])
355  {
356  for (int i = 0; i < a.length; i++)
357  {
358  a[i] += b[i];
359  }
360  }
361 
362  private XYSeriesCollection getXYSeriesCollection(XYPlot plot, double[] psdprofileplot, double[] ctfplot, double[] theorethicalpsdplot, double[] envelopeplot,
363  double[] bgnoiseplot, double[] differenceplot)
364  {
365  double max = -Double.MAX_VALUE;
366  double min = Double.MAX_VALUE;
367  collection = new XYSeriesCollection();
368  serie_index = 0;
369 
370  if (showCTF())
371  addSeries(plot, XmippLabel.CB_PLOT_CTF, COLOR_CTF, ctfplot, 1, -1);
372  else if (showPSD())
373  {
374 
375 
377  for (int i = 5; i < xvalues.length; i++)
378  {
379  max = Math.max(max, psdprofileplot[i]);
380  min = Math.min(min, psdprofileplot[i]);
381  }
382  max += Math.abs(max) * 0.1;
383  min -= Math.abs(min) * 0.1;
385  addSeries(plot, getPSDProfileLabel(), COLOR_PROFILE, psdprofileplot, max, min);
386 
387  if (showBGNoise())
388  {
389  addSeries(plot, getBGNoiseLabel(), COLOR_BACKGROUND_NOISE, bgnoiseplot, max, min);
390 
391  }
392  if(showDifference())
393  {
394 
395  addSeries(plot, getDifferenceLabel(), COLOR_DIFFERENCE, differenceplot, max, min);
396  }
397  if (showEnvelope())
398  addSeries(plot, getEnvelopeLabel(), COLOR_ENVELOPE, envelopeplot, max, min);
399 
400  if (showTheorethicalPSD())
401  addSeries(plot, getTheorethicalPSDLabel(), COLOR_PSD, theorethicalpsdplot, max, min);
402  }
403  return collection;
404 
405  }
406 
407 
408  private void addSeries(XYPlot plot, String name, Color c, double[] yvalues, double max, double min){
409 
410  collection.addSeries(createSeries(name, xvalues, yvalues, max, min));
411  customizeSerie(plot, c);
412  }
413 
414  private int serie_index;
415  private void customizeSerie(XYPlot plot, Color c){
416  XYItemRenderer renderer = plot.getRenderer();
417  renderer.setSeriesPaint(serie_index, c);
418  plot.getRenderer().setSeriesStroke(serie_index, plotsStroke);
419  ++serie_index;
420  }
421 
422  private static XYSeries createSeries(String name, double[] xs, double[] values, double max, double min)
423  {
424  XYSeries series = new XYSeries(name);
425  for (int i = 0; i < xs.length; i++)
426  {
427  if (values[i] > min && values[i] < max)
428  series.add(xs[i], values[i]);
429  }
430  return series;
431  }
432 
433 
434  private void customizeSeriesRenderes(XYPlot plot, boolean show_bgnoise, boolean show_envelope,
435  boolean show_psd, boolean show_ctf) {
436  serie_index = 0;
437 
438  if (show_ctf) {
439  customizeSerie(plot, COLOR_CTF);
440  } else {
441  // 0: Profile.
442  customizeSerie(plot, COLOR_PROFILE);
443 
444  // 1: BGNoise.
445  if (show_bgnoise) {
446  customizeSerie(plot, COLOR_BACKGROUND_NOISE);
447  customizeSerie(plot, COLOR_DIFFERENCE);
448  }
449 
450  // 2: BGNoise.
451  if (show_envelope)
452  customizeSerie(plot, COLOR_ENVELOPE);
453 
454  // 3: PSD.
455  if (show_psd)
456  customizeSerie(plot, COLOR_PSD);
457  }
458  }
459 
460  private boolean showPSD()
461  {
462  return psdrb.isSelected();
463  }
464 
465  private boolean showTheorethicalPSD()
466  {
467  return theorethicalpsdchb.isSelected();
468  }
469 
470  private boolean showEnvelope()
471  {
472  return envelopepsdchb.isSelected();
473  }
474 
475  private boolean showBGNoise()
476  {
477  return noisechb.isSelected();
478  }
479 
480  private boolean showCTF()
481  {
482  return ctfrb.isSelected();
483  }
484 
485  private boolean showDifference()
486  {
487  return differencechb.isSelected();
488  }
489 
490  private static double[] getXValues(int length, double Tm)
491  {
492  double values[] = new double[length];
493  double factor = 1 / (length * 2 * Tm);
494 
495  for (int i = 0; i < length; i++)
496  {
497  values[i] = (double) i * factor;
498  }
499 
500  return values;
501  }
502 
503  private double getSamplingRate(String CTFFilename)
504  {
505  double samplingRate = 1.0;
506  double downsampling = 1.0;
507 
508  try
509  {
510  MetaData md = new MetaData(CTFFilename);
511  samplingRate = md.getValueDouble(MDLabel.MDL_CTF_SAMPLING_RATE, md.firstObject());
512  if (md.containsLabel(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED))
513  downsampling = md.getValueDouble(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED, md.firstObject());
514  md.destroy();
515  }
516  catch (Exception ex)
517  {
518  ex.printStackTrace();
519  }
520  //System.out.printf("sampling rate: %f downsampling:%f\n", samplingRate, downsampling);
521  return samplingRate * downsampling;
522  }
523 
524  class FillGraphicsActionListener implements ActionListener
525  {
526 
527  @Override
528  public void actionPerformed(ActionEvent e)
529  {
530  fillGraphics();
531  envelopepsdchb.setEnabled(psdrb.isSelected());
532  }
533 
534  }
535 
536  class EnableDisplayActionListener implements ActionListener
537  {
538 
539  @Override
540  public void actionPerformed(ActionEvent e)
541  {
542  enableDisplay();
543  }
544 
545  }
546 
547  private void enableDisplay()
548  {
549  theorethicalpsdchb.setEnabled(showPSD());
550  envelopepsdchb.setEnabled(showPSD());
551  noisechb.setEnabled(showPSD());
552  differencechb.setEnabled(showPSD());
553 
554  }
555 
556  @Override
557  public void actionPerformed(ActionEvent e)
558  {
559  int result = fc.showSaveDialog(this);
560  boolean export = result == XmippFileChooser.APPROVE_OPTION;
561  if (export)
562  {
563  File file = fc.getSelectedFile();
564  if (file != null)
565  {
566 
567  boolean saved = export(file.getAbsolutePath());
568  if (saved)
569  XmippDialog.showInfo(this, "File saved successfully.");
570  }
571  }
572 
573  }
574 
575  private boolean export(String path) {
576 
577 
578  try {
579  FileWriter fstream = new FileWriter(path);
580  BufferedWriter out = new BufferedWriter(fstream);
581 
582  String hformat = "%40s%36s AVG";
583  String vformat = "%40.4f%40.4f";
584  // Header.
585  out.write(String.format("%40s", "X"));
586  if(showCTF())
587  out.write(String.format(hformat, getCTFLabel(), getCTFLabel()));
588  if(showPSD())
589  out.write(String.format(hformat, getPSDProfileLabel(), getPSDProfileLabel()));
590  if(showTheorethicalPSD())
591  out.write(String.format(hformat, getTheorethicalPSDLabel(), getTheorethicalPSDLabel()));
592  if(showEnvelope())
593  out.write(String.format(hformat, getEnvelopeLabel(), getEnvelopeLabel()));
594  if(showBGNoise())
595  out.write(String.format(hformat, getBGNoiseLabel(), getBGNoiseLabel()));
596  if(showDifference())
597  out.write(String.format(hformat, getDifferenceLabel(), getDifferenceLabel()));
598  out.newLine();
599 
600  for (int i = 0; i < ctfplot.length; i++) {
601  out.write(String.format("%40.4f", xvalues[i]));
602  if(showCTF())
603  out.write(String.format(vformat, ctfplot[i], ctf_avgplot[i]));
604  if(showPSD())
605  out.write(String.format(vformat, psdprofileplot[i], psdprofile_avgplot[i]));
606  if(showTheorethicalPSD())
607  out.write(String.format(vformat, theorethicalpsdplot[i], theorethicalpsd_avgplot[i]));
608  if(showEnvelope())
609  out.write(String.format(vformat, envelopeplot[i], envelope_avgplot[i]));
610  if(showBGNoise())
611  out.write(String.format(vformat, bgnoiseplot[i], bgnoise_avgplot[i]));
612  if(showDifference())
613  out.write(String.format(vformat, difference[i], difference_avgplot[i]));
614 
615  out.newLine();
616  }
617 
618 
619  out.close();
620 
621  return true;
622  } catch (Exception ex) {
623  ex.printStackTrace();
624  XmippDialog.showError(this, ex.getMessage());
625  }
626 
627  return false;
628  }
629 
630  public String getDifferenceLabel()
631  {
632  return String.format("%s - %s", XmippLabel.LABEL_PSD, XmippLabel.CB_PLOT_BGNOISE);
633  }
634 
635  private String getTheorethicalPSDLabel()
636  {
637  // TODO Auto-generated method stub
638  return String.format("Log(%s)", "Theoretical " + XmippLabel.LABEL_PSD);
639  }
640 
641  public String getPSDProfileLabel()
642  {
643  return XmippLabel.LABEL_PSD;
644  }
645 
646  public String getEnvelopeLabel()
647  {
648  return XmippLabel.CB_PLOT_ENVELOPE;
649  }
650 
651  public String getCTFLabel()
652  {
653  return XmippLabel.LABEL_CTF;
654  }
655 
656 
657  public String getBGNoiseLabel()
658  {
659  return XmippLabel.CB_PLOT_BGNOISE;
660  }
661 
662 
663 }
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xmipp.viewer.ctf.CTFAnalyzerJFrame.CTFAnalyzerJFrame
CTFAnalyzerJFrame(String psdEnhancedFile, CTFDescription ctfdescription, String psdfile, double samplingRate)
Definition: CTFAnalyzerJFrame.java:103
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xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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static final String CB_PLOT_ENVELOPE
Definition: XmippLabel.java:63
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xmipp.utils.XmippLabel.LABEL_SAMPLING
static final String LABEL_SAMPLING
Definition: XmippLabel.java:220
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xmipp.utils.XmippLabel.CB_PLOT_CTF
static final String CB_PLOT_CTF
Definition: XmippLabel.java:65
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xmipp.jni.CTFDescription.BACKGROUND_NOISE
static final int BACKGROUND_NOISE
Definition: CTFDescription.java:5
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xmipp.jni.MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED
static final int MDL_CTF_DOWNSAMPLE_PERFORMED
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Definition: MDLabel.java:155
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boolean showInfo(String message)
Definition: XmippDialog.java:199
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Definition: ImageGeneric.java:126
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xmipp.jni.CTFDescription.ENVELOPE
static final int ENVELOPE
Definition: CTFDescription.java:6
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native long firstObject()
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xmipp.utils.XmippLabel.LABEL_CTF
static final String LABEL_CTF
Definition: XmippLabel.java:218
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xmipp.utils.XmippLabel.CB_PLOT_BGNOISE
static final String CB_PLOT_BGNOISE
Definition: XmippLabel.java:62
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static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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void CTFAverageProfiles(int samples)
Definition: CTFDescription.java:56
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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xmipp.jni.MDLabel.MDL_CTF_SAMPLING_RATE
static final int MDL_CTF_SAMPLING_RATE
< Name for another CTF model (std::string)
Definition: MDLabel.java:82
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xmipp.viewer.ctf.CTFAnalyzerJFrame.CTFAnalyzerJFrame
CTFAnalyzerJFrame(String psdEnhancedFile, String ctffile, String psdfile)
Definition: CTFAnalyzerJFrame.java:86
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Definition: XmippLabel.java:219
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CTFCanvas.java
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1 package xmipp.viewer.ctf;
2 
3 import ij.ImagePlus;
4 import ij.gui.ImageCanvas;
5 import ij.gui.ImageWindow;
6 
7 import java.awt.Color;
8 import java.awt.Graphics;
9 import java.awt.Rectangle;
10 import java.awt.event.MouseEvent;
11 import java.awt.event.MouseListener;
12 import java.awt.event.MouseMotionListener;
13 
14 import xmipp.utils.DEBUG;
15 
16 @SuppressWarnings("serial")
17 public class CTFCanvas extends ImageCanvas {
18 
19  private CTFRecalculateImageWindow master;
20  private int width;
21 
22  public CTFCanvas(ImagePlus imp) {
23  super(imp);
24  }
25 
26  public void setMaster(CTFRecalculateImageWindow master){
27  this.master = master;
28  ImagePlus imp = master.getImagePlus();
29  width = imp.getWidth();
30  }
31 
32  public void paint(Graphics g)
33  {
34  super.paint(g);
35  g.setColor(Color.blue);
36  paintFreqCircle(g, master.getLowFreq());
37  paintFreqCircle(g, master.getHighFreq());
38  }
39 
40  public void paintFreqCircle(Graphics g, double freq){
41  double size = width * magnification;
42  int outer = (int)(size * freq * 2);
43  int offset = (int)(size - outer) / 2;
44  g.drawOval(offset, offset, outer, outer);
45  }
46 
47 }
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xmipp.viewer.ctf.CTFCanvas.paint
void paint(Graphics g)
Definition: CTFCanvas.java:32
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void setMaster(CTFRecalculateImageWindow master)
Definition: CTFCanvas.java:26
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CTFCanvas(ImagePlus imp)
Definition: CTFCanvas.java:22
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void paintFreqCircle(Graphics g, double freq)
Definition: CTFCanvas.java:40
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1 package xmipp.jni;
2 
3 public class CTFDescription {
4 
5  public static final int BACKGROUND_NOISE = 0;
6  public static final int ENVELOPE = 1;
7  public static final int PSD = 2;
8  public static final int CTF = 3;
9  public double[][] profiles, avgprofiles;
10  public double FMAX; // Calculated when a file is loaded.
11  public double downsampling;
12  // pointer to Image class in C++ space. Needed by native library.
13  long peer;
14 
15  // Initialize library.
16  static {
17  System.loadLibrary("XmippJNI");
18  //storeIds();
19  }
20 
21  // Catching some ids
22  //private static native void storeIds();
23 
24  // Functions to create objects: Internally calls to "Produce_side_info()"
25  protected native void create();
26 
27  // Destructor.
28  protected synchronized native void destroy();
29 
30  // Reading.
31  public native void read_(String filename) throws Exception;
32 
33  public void read(String filename) throws Exception {
34  read_(filename);
35  MetaData md = new MetaData(filename);
36  if (md.containsLabel(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED))
37  downsampling = md.getValueDouble(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED, md.firstObject());
38  else
39  downsampling = 1.0;
40  md.destroy();
41 
42  FMAX = getFMAX()/downsampling;
43  }
44 
45  // Data.
46  private native double getFMAX();
47 
48  private native double[][] CTFProfile(double angle, double FMAX, int samples);
49 
50  public void CTFProfile(double angle, int samples) {
51  profiles = CTFProfile(angle, FMAX, samples);
52  }
53 
54  private native double[][] CTFAverageProfile(double FMAX, int samples);
55 
56  public void CTFAverageProfiles(int samples) {
57  avgprofiles = CTFAverageProfile(FMAX, samples);
58  }
59 
60  //non-native functions
61  //constructor
62  public CTFDescription() {
63  create();
64  }
65 
66  public CTFDescription(String filename) throws Exception {
67  this();
68  read(filename);
69  }
70 
71  // Should be called by GarbageCollector before destroying
72  @Override
73  protected void finalize() throws Throwable {
74  super.finalize();
75  destroy();
76  }
77 }
xmipp.jni.MetaData.containsLabel
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Definition: CTFDescription.java:66
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static final int BACKGROUND_NOISE
Definition: CTFDescription.java:5
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static final int MDL_CTF_DOWNSAMPLE_PERFORMED
< Iceness of the micrograph
Definition: MDLabel.java:155
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xmipp.jni.CTFDescription.CTFProfile
void CTFProfile(double angle, int samples)
Definition: CTFDescription.java:50
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Definition: CTFDescription.java:6
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void CTFAverageProfiles(int samples)
Definition: CTFDescription.java:56
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1 package xmipp.viewer.windows;
2 
3 //import ij.IJ;
4 import ij.ImagePlus;
5 //import ij.gui.ImageCanvas;
6 //import ij.gui.ImageWindow;
7 import ij.gui.Line;
8 import ij.gui.ProfilePlot;
9 
10 import java.awt.BasicStroke;
11 import java.awt.BorderLayout;
12 import java.awt.Color;
13 import java.awt.GridBagConstraints;
14 import java.awt.GridBagLayout;
15 import java.awt.Insets;
16 import java.awt.Point;
17 //import java.awt.Scrollbar;
18 import java.awt.event.ActionEvent;
19 import java.awt.event.ActionListener;
20 import java.awt.event.ItemEvent;
21 import java.awt.event.ItemListener;
22 import java.awt.event.MouseWheelEvent;
23 import java.awt.event.MouseWheelListener;
24 import java.io.BufferedWriter;
25 import java.io.File;
26 import java.io.FileWriter;
27 import java.util.Arrays;
28 import java.util.List;
29 
30 import javax.swing.ButtonGroup;
31 import javax.swing.JButton;
32 import javax.swing.JCheckBox;
33 import xmipp.utils.XmippFileChooser;
34 
35 import javax.swing.JFrame;
36 import javax.swing.JPanel;
37 import javax.swing.JRadioButton;
38 import javax.swing.JScrollBar;
39 import javax.swing.JTabbedPane;
40 import javax.swing.UIManager;
41 
42 import org.jfree.chart.ChartFactory;
43 import org.jfree.chart.ChartPanel;
44 import org.jfree.chart.ChartUtilities;
45 import org.jfree.chart.JFreeChart;
46 import org.jfree.chart.plot.PlotOrientation;
47 import org.jfree.chart.plot.XYPlot;
48 import org.jfree.chart.renderer.xy.XYItemRenderer;
49 import org.jfree.data.xy.XYDataset;
50 import org.jfree.data.xy.XYSeries;
51 import org.jfree.data.xy.XYSeriesCollection;
52 
53 import xmipp.ij.commons.XmippUtil;
54 import xmipp.ij.commons.XmippImageConverter;
55 import xmipp.jni.CTFDescription;
56 import xmipp.jni.ImageGeneric;
57 import xmipp.jni.MDLabel;
58 import xmipp.jni.MetaData;
59 import xmipp.utils.DEBUG;
60 import xmipp.utils.XmippDialog;
61 import xmipp.utils.XmippLabel;
62 import xmipp.utils.XmippWindowUtil;
63 
64 /*
65  * To change this template, choose Tools | Templates
66  * and open the template in the editor.
67  */
72 @SuppressWarnings("serial")
73 public class CTFProfileWindow extends JFrame implements ItemListener, ActionListener {
74 
75  private final static BasicStroke plotsStroke = new BasicStroke(2.0f);
76  private final static int MAX_VALUE = 360;
77  private final static Color COLOR_PROFILE = Color.BLACK;
78  private final static Color COLOR_BACKGROUND_NOISE = Color.RED;
79  private final static Color COLOR_ENVELOPE = Color.GREEN;
80  private final static Color COLOR_PSD = Color.BLUE;
81  private final static Color COLOR_CTF = Color.MAGENTA;
82  private final static Color COLOR_DIFFERENCE = Color.orange;
83  private final static Color COLOR_DISABLED = UIManager.getColor("ComboBox.disabledForeground");
84  private ImagePlus psdimage;
85  private JScrollBar scrollbar;
86  private CTFDescription ctfmodel;
87  private Point centerDisplay, centerPSD;
88  private int displayLength, samples;
89  private double angle;
90  private JCheckBox cbBgNoise, cbEnvelope, cbPSDTheo;
91  private JRadioButton rbPSD, rbCTF;
92  private JPanel panelPlot, panelPlotAVG;
93  private XYSeriesCollection datasetProfile, datasetAVG;
94  private ChartPanel chartPanelProfile, chartPanelAVG;
95  private XmippFileChooser fc = new XmippFileChooser();
96  private JButton bExportProfile, bExportAVG;
97  private double xValues[];
98  private double Tm;
99  private JButton iconbt;
100 
101  public CTFProfileWindow(ImagePlus imp, String CTFFilename, String PSDFilename) {
102 
103  try {
104  //ImageCanvas imc = imp.getCanvas();
105  //imc.setEnabled(false); // Clicks won't remove selection ;)
106 
107  Tm = getSamplingRate(CTFFilename);
108  System.out.println("Tm="+Tm);
109 
110  ctfmodel = new CTFDescription(CTFFilename);
111  ImageGeneric image = new ImageGeneric(PSDFilename);
112  image.setUseLogarithm(false);
113 
114  psdimage = XmippImageConverter.readToImagePlus(image);
115  psdimage.setTitle(PSDFilename);
116 
117  removeAll();
118  GridBagConstraints gc = new GridBagConstraints();
119  setLayout(new GridBagLayout());
120 
121  scrollbar = new JScrollBar(JScrollBar.HORIZONTAL);
122  scrollbar.setMaximum(MAX_VALUE + scrollbar.getVisibleAmount());
123  scrollbar.addAdjustmentListener(new java.awt.event.AdjustmentListener() {
124 
125  public void adjustmentValueChanged(java.awt.event.AdjustmentEvent evt) {
126  updatePlots();
127  }
128  });
129 
130  iconbt = new JButton(XmippUtil.getImageIcon(imp.getImage(), 300, 300));
131  iconbt.setToolTipText("Load CTF Profile");
132  iconbt.setBorderPainted(false);
133  iconbt.setContentAreaFilled(false);
134  iconbt.setFocusPainted(false);
135  iconbt.setOpaque(false);
136 
137  JPanel panelImage = new JPanel(new BorderLayout());
138  panelImage.add(iconbt, BorderLayout.CENTER);
139  panelImage.add(scrollbar, BorderLayout.SOUTH);
140  addMouseWheelListener(new MouseWheelListener() {
141 
142  public void mouseWheelMoved(MouseWheelEvent e) {
143  int MAXSCROLL = scrollbar.getMaximum() - scrollbar.getVisibleAmount();
144 
145  int newValue = (scrollbar.getValue() + e.getUnitsToScroll())
146  % MAXSCROLL;
147 
148  if (newValue < 0) {
149  newValue = newValue + MAXSCROLL;
150  }
151 
152  scrollbar.setValue(newValue);
153  updatePlots();
154  }
155  });
156 
157  JTabbedPane jtpPlots = new JTabbedPane();
158  panelPlot = new JPanel();
159  panelPlotAVG = new JPanel();
160 
161  jtpPlots.add(XmippLabel.LABEL_TAB_PROFILE, panelPlot);
162  jtpPlots.add(XmippLabel.LABEL_TAB_RADIAL_AVERAGE, panelPlotAVG);
163 
164  JPanel pCenter = new JPanel(new BorderLayout());
165  pCenter.add(jtpPlots);
166 
167  // Check boxes for plots
168  rbCTF = new JRadioButton(XmippLabel.CB_PLOT_CTF, true);
169  rbPSD = new JRadioButton(XmippLabel.CB_PLOT_PSD, false);
170  ButtonGroup bg = new ButtonGroup();
171  bg.add(rbCTF);
172  bg.add(rbPSD);
173  cbPSDTheo = new JCheckBox("PSD (Theoretical)", true);
174  cbBgNoise = new JCheckBox(XmippLabel.CB_PLOT_BGNOISE, false);
175  cbEnvelope = new JCheckBox(XmippLabel.CB_PLOT_ENVELOPE, false);
176 
177  cbPSDTheo.addItemListener(this);
178  cbBgNoise.addItemListener(this);
179  cbEnvelope.addItemListener(this);
180  rbPSD.addItemListener(this);
181  rbCTF.addItemListener(this);
182 
183  bExportProfile = XmippWindowUtil.getTextButton(XmippLabel.BUTTON_EXPORT_PROFILE, this);
184  bExportAVG = XmippWindowUtil.getTextButton(XmippLabel.BUTTON_EXPORT_RADIAL_AVERAGE, this);
185 
186  JPanel panelCBoxes = new JPanel(new GridBagLayout());
187  gc.anchor = GridBagConstraints.WEST;
188  panelCBoxes.add(rbCTF, XmippWindowUtil.getConstraints(gc, 0, 0));
189  panelCBoxes.add(rbPSD, XmippWindowUtil.getConstraints(gc, 1, 0));
190  panelCBoxes.add(cbPSDTheo, XmippWindowUtil.getConstraints(gc, 1, 1));
191  panelCBoxes.add(cbBgNoise, XmippWindowUtil.getConstraints(gc, 1, 2));
192  gc.insets = new Insets(0, 0, 10, 10);
193  panelCBoxes.add(cbEnvelope, XmippWindowUtil.getConstraints(gc, 1, 3));
194  gc.weightx = 1.0;
195  panelCBoxes.add(bExportProfile, XmippWindowUtil.getConstraints(gc, 0, 4, 2));
196  panelCBoxes.add(bExportAVG, XmippWindowUtil.getConstraints(gc, 0, 5, 2));
197  // Adds panels.
198  add(panelImage, XmippWindowUtil.getConstraints(gc, 0, 0));
199  add(pCenter, XmippWindowUtil.getConstraints(gc, 1, 0, 2, 2));
200  gc.anchor = GridBagConstraints.EAST;
201  add(panelCBoxes,XmippWindowUtil.getConstraints(gc, 0, 1));
202 // // Store initial values.
203  centerDisplay = new Point(imp.getWidth() / 2, imp.getHeight() / 2);
204  centerPSD = new Point(psdimage.getWidth() / 2, psdimage.getHeight() / 2);
205 
206  displayLength = (int) (imp.getWidth() / 2);
207  samples = (int) (psdimage.getWidth() / 2);
208 
209  xValues = getXValues(samples, Tm);
210 
211  setCBEnableStatus();
212  updatePlots();
213 // updateRadialAverage();
214 
215  // Trick: setting no resizable allows to pack properly.
216  setResizable(false);
217  pack();
218  //setResizable(true);
219  } catch (Exception e) {
220  e.printStackTrace();
221  }
222  }
223 
224  /*
225  * When checkbox changes, plots will be redisplayed, but data is the same,
226  * so there is no need to recalculate anything.
227  */
228  public void itemStateChanged(ItemEvent ie) {
229  if (ie.getSource() == rbCTF) {
230  setCBEnableStatus();
231  }
232 
233  // Restores general view.
234  chartPanelProfile.restoreAutoBounds();
235  chartPanelAVG.restoreAutoBounds();
236 
237  updatePlots();
238  updateRadialAverage();
239  }
240 
241  public void actionPerformed(ActionEvent ae) {
242  if (fc.showSaveDialog(this) == XmippFileChooser.APPROVE_OPTION) {
243  File file = fc.getSelectedFile();
244  if (file != null) {
245  JFreeChart chart = null;
246  if (ae.getSource() == bExportProfile) {
247  chart = chartPanelProfile.getChart();
248  } else if (ae.getSource() == bExportAVG) {
249  chart = chartPanelAVG.getChart();
250  }
251 
252  if (export(file.getAbsolutePath(), chart)) {
253  XmippDialog.showInfo(this, "File saved successfully.");
254  }
255  }
256  }
257  }
258 
259  private void setCBEnableStatus() {
260  boolean showPSD = !rbCTF.isSelected();
261  cbPSDTheo.setEnabled(showPSD);
262  cbBgNoise.setEnabled(showPSD);
263  cbEnvelope.setEnabled(showPSD);
264  }
265 
266  private boolean showBGNoise() {
267  return cbBgNoise.isEnabled() && cbBgNoise.isSelected();
268  }
269 
270  private boolean showEnvelope() {
271  return cbEnvelope.isEnabled() && cbEnvelope.isSelected();
272  }
273 
274  private boolean showPSD() {
275  return rbPSD.isSelected() && cbPSDTheo.isSelected();
276  }
277 
278  private boolean showCTF() {
279  return rbCTF.isSelected();
280  }
281 
282  private void updatePlots() {
283  calculatePlots();
284 
285  boolean show_ctf = showCTF();
286 
287  if (chartPanelProfile != null) {
288  XYPlot plot = ((XYPlot) chartPanelProfile.getChart().getPlot());
289  plot.setDataset(0, datasetProfile);
290  plot.getRangeAxis().setLabel(show_ctf ? XmippLabel.LABEL_CTF : XmippLabel.LABEL_PSD);
291  } else {
292  JFreeChart chart = ChartFactory.createXYLineChart(
293  "", XmippLabel.LABEL_SAMPLING,
294  show_ctf ? XmippLabel.LABEL_CTF : XmippLabel.LABEL_PSD,
295  datasetProfile,
296  PlotOrientation.VERTICAL,
297  true, true, false);
298 
299  chartPanelProfile = createChartPanel(chart);
300  panelPlot.add(chartPanelProfile);
301  }
302 
303  customizeSeriesRenderes((XYPlot) chartPanelProfile.getChart().getPlot(),
304  showBGNoise(), showEnvelope(), showPSD(), show_ctf);
305  }
306 
307  private void updateRadialAverage() {
308  calculateRadialAverageProfile();
309 
310  boolean show_ctf = showCTF();
311 
312  if (chartPanelAVG != null) {
313  XYPlot plot = ((XYPlot) chartPanelAVG.getChart().getPlot());
314  plot.setDataset(0, datasetAVG);
315  plot.getRangeAxis().setLabel(show_ctf ? XmippLabel.LABEL_CTF : XmippLabel.LABEL_PSD);
316  } else {
317  JFreeChart chart = ChartFactory.createXYLineChart(
318  "",
319  XmippLabel.LABEL_SAMPLING,
320  show_ctf ? XmippLabel.LABEL_CTF : XmippLabel.LABEL_PSD,
321  datasetAVG, PlotOrientation.VERTICAL,
322  true, true, false);
323 
324  chartPanelAVG = createChartPanel(chart);
325  panelPlotAVG.add(chartPanelAVG);
326  }
327 
328  customizeSeriesRenderes((XYPlot) chartPanelAVG.getChart().getPlot(),
329  showBGNoise(), showEnvelope(), showPSD(), show_ctf);
330  }
331 
332  private static ChartPanel createChartPanel(JFreeChart chart) {
333  XYPlot plot = (XYPlot) chart.getPlot();
334  plot.setDomainPannable(true);
335  plot.setRangePannable(true);
336 
337  List<Integer> list = Arrays.asList(new Integer[]{
338  new Integer(0), new Integer(1)
339  });
340  plot.mapDatasetToDomainAxes(0, list);
341  plot.mapDatasetToRangeAxes(0, list);
342  ChartUtilities.applyCurrentTheme(chart);
343 
344  return new ChartPanel(chart);
345  }
346 
347 
348  private int serie_index;
349 
350  private void customizeSerie(XYPlot plot, Color c){
351  XYItemRenderer renderer = plot.getRenderer();
352  renderer.setSeriesPaint(serie_index, c);
353  plot.getRenderer().setSeriesStroke(serie_index, plotsStroke);
354  ++serie_index;
355  }
356 
357  private void customizeSeriesRenderes(XYPlot plot, boolean show_bgnoise, boolean show_envelope,
358  boolean show_psd, boolean show_ctf) {
359 
360 
361  serie_index = 0;
362 
363  if (show_ctf) {
364  customizeSerie(plot, COLOR_CTF);
365  } else {
366  // 0: Profile.
367  customizeSerie(plot, COLOR_PROFILE);
368 
369  // 1: BGNoise.
370  if (show_bgnoise) {
371  customizeSerie(plot, COLOR_BACKGROUND_NOISE);
372  customizeSerie(plot, COLOR_DIFFERENCE);
373  }
374 
375  // 2: BGNoise.
376  if (show_envelope)
377  customizeSerie(plot, COLOR_ENVELOPE);
378 
379  // 3: PSD.
380  if (show_psd)
381  customizeSerie(plot, COLOR_PSD);
382  }
383  }
384 
385  private static XYSeriesCollection createSeriesCollection(double[] xs,
386  double profile[], double bgNoise[], double envelope[], double psd[],
387  double ctf[], boolean show_bgnoise, boolean show_envelope,
388  boolean show_psd, boolean show_ctf) {
389 
390  double max = Double.MAX_VALUE;
391  double min = -1;
392  XYSeriesCollection collection = new XYSeriesCollection();
393 
394  if (show_ctf) {
395  collection.addSeries(createSeries(XmippLabel.CB_PLOT_CTF, xs, ctf, max, min));
396  } else {
397  collection.addSeries(createSeries(XmippLabel.CB_PLOT_PROFILE, xs, profile, max, min));
398 
399  //min = max;
400  max = -max;
401  for (int i = 0; i < xs.length; i++){
402  max = Math.max(max, profile[i]);
403  //min = Math.min(min, profile[i]);
404  }
405  max += Math.abs(max) * 0.1;
406  //min -= Math.abs(min) * 0.1;
407 
408  if (show_bgnoise) {
409  collection.addSeries(createSeries(XmippLabel.CB_PLOT_BGNOISE, xs, bgNoise, max, min));
410  double[] difference = new double[bgNoise.length];
411  for (int i = 0; i < xs.length; i++)
412  difference[i] = profile[i] - bgNoise[i];
413  collection.addSeries(createSeries(XmippLabel.CB_PLOT_DIFFERENCE, xs, difference, max, min));
414  }
415  if (show_envelope) {
416  collection.addSeries(createSeries(XmippLabel.CB_PLOT_ENVELOPE, xs, envelope, max, min));
417  }
418  if (show_psd) {
419  collection.addSeries(createSeries(XmippLabel.CB_PLOT_PSD, xs, psd, max, min));
420  }
421  }
422 
423  return collection;
424  }
425 
426  private static XYSeries createSeries(String name, double[] xs, double[] values, double max, double min) {
427  XYSeries series = new XYSeries(name);
428  for (int i = 0; i < xs.length; i++) {
429  if (values[i] > min && values[i] < max)
430  series.add(xs[i], values[i]);
431  }
432 
433  return series;
434  }
435 
436  private double getSamplingRate(String CTFFilename) {
437  double samplingRate = 1.0;
438  double downsampling = 1.0;
439 
440  try {
441  MetaData md = new MetaData(CTFFilename);
442  samplingRate = md.getValueDouble(MDLabel.MDL_CTF_SAMPLING_RATE, md.firstObject());
443  if (md.containsLabel(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED))
444  downsampling = md.getValueDouble(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED, md.firstObject());
445  md.destroy();
446  } catch (Exception ex) {
447  ex.printStackTrace();
448  }
449 
450  return samplingRate * downsampling;
451  }
452 
453  private void calculatePlots() {
454  double value = scrollbar.getValue();
455  angle = Math.toRadians(-value);
456 
457  // Makes line roi...
458  int xDisplay = centerDisplay.x + (int) (displayLength * Math.cos(angle));
459  int yDisplay = centerDisplay.y + (int) (displayLength * Math.sin(angle));
460 
461  int xPSD = centerPSD.x + (int) (samples * Math.cos(angle));
462  int yPSD = centerPSD.y + (int) (samples * Math.sin(angle));
463 
464  // Over display...
465  //IJ.selectWindow();
466  //IJ.makeLine(centerDisplay.x, centerDisplay.y, xDisplay, yDisplay);
467 
468  // ...and internal PSD.
469  Line line = new Line(centerPSD.x, centerPSD.y, xPSD, yPSD);
470  psdimage.setRoi(line);
471 
472 // // Get profile.
473  ProfilePlot profilePlot = new ProfilePlot(psdimage);
474  double[] plotProfile = profilePlot.getProfile();
475 
476  ctfmodel.CTFProfile(angle, samples);
477 
478  double[] plotBgNoise = ctfmodel.profiles[CTFDescription.BACKGROUND_NOISE];
479  double[] plotEnvelope = ctfmodel.profiles[CTFDescription.ENVELOPE];
480  double[] plotPSD = ctfmodel.profiles[CTFDescription.PSD];
481  double[] plotCTF = ctfmodel.profiles[CTFDescription.CTF];
482 
483  datasetProfile = createSeriesCollection(
484  xValues, plotProfile, plotBgNoise, plotEnvelope, plotPSD, plotCTF,
485  showBGNoise(), showEnvelope(), showPSD(), showCTF());
486  }
487 
488  private void calculateRadialAverageProfile() {
489  double[] plotAVGprofile = new double[samples];
490 
491  for (int i = 0; i < MAX_VALUE; i++) {
492  double current_angle = Math.toRadians(-i);
493 
494  // Make line roi.
495  int xPSD = centerPSD.x + (int) (samples * Math.cos(current_angle));
496  int yPSD = centerPSD.y + (int) (samples * Math.sin(current_angle));
497 
498 // Line line = new Line(centerPSD.x, centerPSD.y, xPSD, yPSD);
499 // psdimage.setRoi(line);
500 
501  // Get profile.
502  ProfilePlot profilePlot = new ProfilePlot(psdimage);
503  double profile[] = profilePlot.getProfile();
504 
505  // Total summatory.
506  sum(plotAVGprofile, profile);
507  }
508 
509  // Get profile average.
510  div(plotAVGprofile, MAX_VALUE);
511 
512  // Get rest of profiles average.
513  ctfmodel.CTFAverageProfiles(samples);
514 
515  double[] plotAVGbgnoise = ctfmodel.avgprofiles[CTFDescription.BACKGROUND_NOISE];
516  double[] plotAVGenvelope = ctfmodel.avgprofiles[CTFDescription.ENVELOPE];
517  double[] plotAVGpsd = ctfmodel.avgprofiles[CTFDescription.PSD];
518  double[] plotAVGctf = ctfmodel.avgprofiles[CTFDescription.CTF];
519 
520  datasetAVG = createSeriesCollection(
521  xValues, plotAVGprofile, plotAVGbgnoise, plotAVGenvelope, plotAVGpsd, plotAVGctf,
522  showBGNoise(), showEnvelope(), showPSD(), showCTF());
523  }
524 
525  private boolean export(String path, JFreeChart chart) {
526  XYPlot plot = (XYPlot) chart.getPlot();
527  XYDataset dataset = plot.getDataset();
528  int series = dataset.getSeriesCount();
529  int items = dataset.getItemCount(0);
530 
531  try {
532  FileWriter fstream = new FileWriter(path);
533  BufferedWriter out = new BufferedWriter(fstream);
534 
535  // Header.
536  out.write("X\t");
537  for (int i = 0; i < series; i++) {
538  out.write(dataset.getSeriesKey(i) + "\t");
539  //System.out.print(dataset.getSeriesKey(i) + "\t");
540  }
541  out.newLine();
542 
543  for (int item = 0; item < items; item++) {
544  out.write(dataset.getXValue(0, item) + "\t");
545  for (int serie = 0; serie < series; serie++) {
546  out.write(dataset.getYValue(serie, item) + "\t");
547  }
548  out.newLine();
549  }
550  out.close();
551 
552  return true;
553  } catch (Exception ex) {
554  //ex.printStackTrace();
555  XmippDialog.showError(this, ex.getMessage());
556  }
557 
558  return false;
559  }
560 
561  private static double[] getXValues(int length, double Tm) {
562  double values[] = new double[length];
563  double factor = 1 / (length * 2 * Tm);
564 
565  for (int i = 0; i < length; i++) {
566  values[i] = (double) i * factor;
567  }
568 
569  return values;
570  }
571 
572  private static void sum(double a[], double b[]) {
573  for (int i = 0; i < a.length; i++) {
574  a[i] += b[i];
575  }
576  }
577 
578  private static void div(double array[], double value) {
579  for (int i = 0; i < array.length; i++) {
580  array[i] /= value;
581  }
582  }
583 }
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xmipp.jni.MetaData.containsLabel
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static final String CB_PLOT_ENVELOPE
Definition: XmippLabel.java:63
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xmipp.ij.commons.XmippUtil.getImageIcon
static Icon getImageIcon(Image imp, int width, int height)
Definition: XmippUtil.java:70
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static final String LABEL_TAB_RADIAL_AVERAGE
Definition: XmippLabel.java:227
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Definition: XmippLabel.java:220
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CTFProfileWindow(ImagePlus imp, String CTFFilename, String PSDFilename)
Definition: CTFProfileWindow.java:101
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static final String CB_PLOT_CTF
Definition: XmippLabel.java:65
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static final String CB_PLOT_DIFFERENCE
Definition: XmippLabel.java:66
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static final String CB_PLOT_PSD
Definition: XmippLabel.java:64
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synchronized native void destroy()
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static final String LABEL_TAB_PROFILE
Definition: XmippLabel.java:226
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static final String BUTTON_EXPORT_RADIAL_AVERAGE
Definition: XmippLabel.java:60
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static final int BACKGROUND_NOISE
Definition: CTFDescription.java:5
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xmipp.jni.MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED
static final int MDL_CTF_DOWNSAMPLE_PERFORMED
< Iceness of the micrograph
Definition: MDLabel.java:155
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boolean showInfo(String message)
Definition: XmippDialog.java:199
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static final int ENVELOPE
Definition: CTFDescription.java:6
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static final String LABEL_CTF
Definition: XmippLabel.java:218
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static final String CB_PLOT_BGNOISE
Definition: XmippLabel.java:62
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xmipp.utils.XmippWindowUtil.getTextButton
static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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void CTFAverageProfiles(int samples)
Definition: CTFDescription.java:56
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Definition: XmippDialog.java:211
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static final String BUTTON_EXPORT_PROFILE
Definition: XmippLabel.java:59
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static final String CB_PLOT_PROFILE
Definition: XmippLabel.java:61
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void setUseLogarithm(boolean useLogarithm)
Definition: ImageGeneric.java:118
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Definition: XmippImageConverter.java:82
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native double getValueDouble(int label, long objId)
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Definition: XmippWindowUtil.java:105
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static final int MDL_CTF_SAMPLING_RATE
< Name for another CTF model (std::string)
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.viewer.ctf;
6 
7 import ij.IJ;
8 import ij.ImagePlus;
9 import ij.gui.ImageLayout;
10 import ij.gui.ImageWindow;
11 import ij.gui.Roi;
12 import ij.process.EllipseFitter;
13 import ij.process.ImageStatistics;
14 import java.awt.BorderLayout;
15 import java.awt.Component;
16 import java.awt.GridBagConstraints;
17 import java.awt.GridBagLayout;
18 import java.awt.Insets;
19 import java.awt.Panel;
20 import java.awt.Rectangle;
21 import java.awt.event.ActionEvent;
22 import java.awt.event.ActionListener;
23 import java.awt.event.MouseEvent;
24 import java.awt.event.MouseListener;
25 import java.awt.event.WindowAdapter;
26 import java.awt.event.WindowEvent;
27 import javax.swing.JButton;
28 import javax.swing.JLabel;
29 import javax.swing.JPanel;
30 import javax.swing.JSpinner;
31 import javax.swing.SpinnerNumberModel;
32 import static javax.swing.WindowConstants.DO_NOTHING_ON_CLOSE;
33 import javax.swing.event.ChangeEvent;
34 import javax.swing.event.ChangeListener;
35 import xmipp.ij.commons.XmippApplication;
36 import xmipp.jni.EllipseCTF;
37 import xmipp.utils.XmippDialog;
38 import xmipp.utils.XmippWindowUtil;
39 import xmipp.viewer.models.GalleryData;
40 import xmipp.viewer.windows.GalleryJFrame;
41 
46 public class CTFRecalculateImageWindow extends ImageWindow implements ActionListener, ChangeListener{
47 
48  private JButton recalculatebt, cancelbt;
49  protected EllipseFitter ellipseFitter = new EllipseFitter();
50  private EllipseCTF ellipseCTF;
51  private String PSDFilename, sortFn;
52  private int row;
53  private JSpinner spinnerLowFreq;
54  private JSpinner spinnerHighFreq;
55  private CTFCanvas canvas;
56  private GalleryData data;
57  protected TasksEngine tasksEngine;
58  private final boolean[] selection;
59 
60  public CTFRecalculateImageWindow(GalleryData data, boolean[] selection, ImagePlus imp, String psd, EllipseCTF ellipsectf,
61  TasksEngine tasksEngine, int row, String sortFn) {
62  super(imp, new CTFCanvas(imp));
63  XmippApplication.addInstance(true);
64  this.selection = selection;
65  this.data = data;
66  this.PSDFilename = psd;
67  this.sortFn = sortFn;
68  this.row = row;
69  this.tasksEngine = tasksEngine;
70  ellipseCTF = ellipsectf;
71 
72  recalculatebt = XmippWindowUtil.getTextButton("Ok", this);
73  recalculatebt.setEnabled(false);
74  cancelbt = XmippWindowUtil.getTextButton("Cancel", new ActionListener() {
75 
76  @Override
77  public void actionPerformed(ActionEvent ae) {
78  exit();
79  }
80  });
81 
82  canvas = (CTFCanvas)imp.getCanvas();
83  canvas.addMouseListener(new MouseListener() {
84 
85  public void mouseClicked(MouseEvent e) {
86  }
87 
88  public void mousePressed(MouseEvent e) {
89  }
90 
91  public void mouseReleased(MouseEvent e) {
92  // If there is no ellipse ROI, button is disabled.
93  recalculatebt.setEnabled(fitEllipse());
94  }
95 
96  public void mouseEntered(MouseEvent e) {
97  }
98 
99  public void mouseExited(MouseEvent e) {
100  }
101  });
102 
103  canvas.setMaster(this);
104 
105 
106  Panel previousContent = new Panel();
107  previousContent.setLayout(new ImageLayout(ic));
108 
109  Component components[] = getComponents();
110  for (int i = 0; i < components.length; i++) {
111  previousContent.add(components[i]);
112  }
113 
114  removeAll();
115  setLayout(new BorderLayout());
116 
117  add(previousContent, BorderLayout.CENTER);
118 
119  Panel panel = new Panel(new GridBagLayout());
120  GridBagConstraints gbc = new GridBagConstraints();
121  gbc.insets = new Insets(5, 5, 5, 5);
122 
123 
124  panel.add(new JLabel("Draw an ellipse to fit the first zero"),XmippWindowUtil.getConstraints(gbc, 0, 0, 4));
125 
126  panel.add(new JLabel("Low freq"), XmippWindowUtil.getConstraints(gbc, 0, 1));
127  spinnerLowFreq = new JSpinner(new SpinnerNumberModel(0.05, 0.0, 0.5, 0.01));
128  panel.add(spinnerLowFreq, XmippWindowUtil.getConstraints(gbc, 1, 1));
129  panel.add(new JLabel("High freq"), XmippWindowUtil.getConstraints(gbc, 2, 1));
130  spinnerLowFreq.addChangeListener(this);
131 
132  spinnerHighFreq = new JSpinner(new SpinnerNumberModel(0.5, 0.0, 0.5, 0.01));
133  panel.add(spinnerHighFreq, XmippWindowUtil.getConstraints(gbc, 3, 1));
134  JPanel actionspn = new JPanel();
135  actionspn.add(cancelbt);
136  actionspn.add(recalculatebt);
137  panel.add(actionspn, XmippWindowUtil.getConstraints(gbc, 1, 2, 3, 1, GridBagConstraints.HORIZONTAL));
138  spinnerHighFreq.addChangeListener(this);
139 
140  add(panel, BorderLayout.SOUTH);
141 
142  setMaximumSize(getPreferredSize());
143 
144  pack();
145  imp.updateImage();
146  IJ.setTool("ellipse");
147  }
148 
149  public double getLowFreq(){
150  return ((Double)spinnerLowFreq.getValue()).doubleValue();
151  }
152 
153  public double getHighFreq(){
154  return ((Double)spinnerHighFreq.getValue()).doubleValue();
155  }
156 
157  public boolean fitEllipse() {
158  boolean fitted = false;
159  Roi roi = imp.getRoi();
160 
161  if (roi != null && roi.isArea()) {
162  IJ.run(imp, "Fit Ellipse", "");
163  ImageStatistics is = imp.getStatistics();
164 
165  ellipseFitter = new EllipseFitter();
166  ellipseFitter.fit(imp.getProcessor(), is);
167 
168  // Centers ellipse in image.
169  roi = imp.getRoi();
170  if (roi != null) {
171  Rectangle r = roi.getBounds();
172 
173  double xCenter = r.x + r.width / 2;
174  double yCenter = r.y + r.height / 2;
175 
176  double dx = imp.getWidth() / 2 - xCenter;
177  double dy = imp.getHeight() / 2 - yCenter;
178 
179  roi.setLocation((int) (r.x + dx), (int) (r.y + dy));
180  imp.draw();
181 
182  // Store values for later use.
183  fitted = true;
184  ellipseCTF.calculateDefocus(ellipseFitter.minor / 2, ellipseFitter.major / 2);
185  IJ.showStatus(String.format("Defocus(U,V)=%f,%f Angstroms", ellipseCTF.getDefocusU(),ellipseCTF.getDefocusV()));
186  }
187  }
188 
189  return fitted;
190  }
191 
192  private void recalculateCTF() {
193  if(getLowFreq() == 0)
194  {
195  XmippDialog.showError(null, "Low freq must be above zero");
196  return;
197  }
198  ellipseCTF.calculateDefocus(ellipseFitter.minor / 2, ellipseFitter.major / 2);
199  ellipseCTF.setFreqRange(getLowFreq(), getHighFreq());
200  ellipseCTF.setEllipseFitter(ellipseFitter);
201  // Add "estimate..." to tasks.
202  data.recalculateCTF(row, selection, ellipseCTF, sortFn);
203  exit();
204  }
205 
206  @Override
207  public void actionPerformed(ActionEvent e) {
208  recalculateCTF();
209  }
210 
211  @Override
212  public void stateChanged(ChangeEvent arg0) {
213  getImagePlus().updateAndRepaintWindow();
214  }
215 
216 
217  public void exit()
218  {
219  setVisible(false);
220  dispose();
221  XmippApplication.removeInstance(true);
222  }
223 
224  @Override
225  public void windowClosing(WindowEvent e)
226  {
227 
228  super.windowClosing(e);
229  XmippApplication.removeInstance(true);
230  }
231 
232 }
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void setMaster(CTFRecalculateImageWindow master)
Definition: CTFCanvas.java:26
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xmipp.viewer.models.GalleryData.recalculateCTF
void recalculateCTF(int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)
Definition: GalleryData.java:1728
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xmipp.jni.EllipseCTF.calculateDefocus
void calculateDefocus(double minor, double major)
Definition: EllipseCTF.java:90
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void setFreqRange(double lowFreq, double highFreq)
Definition: EllipseCTF.java:72
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void setEllipseFitter(EllipseFitter ellipseFitter)
Definition: EllipseCTF.java:27
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static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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xmipp.viewer.ctf.CTFRecalculateImageWindow.CTFRecalculateImageWindow
CTFRecalculateImageWindow(GalleryData data, boolean[] selection, ImagePlus imp, String psd, EllipseCTF ellipsectf, TasksEngine tasksEngine, int row, String sortFn)
Definition: CTFRecalculateImageWindow.java:60
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boolean showError(String message)
Definition: XmippDialog.java:211
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static void removeInstance(boolean isijwindow)
Definition: XmippApplication.java:28
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static void addInstance(boolean isijwindow)
Definition: XmippApplication.java:18
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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1 
2 /*
3  * To change this template, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 package xmipp.utils;
7 
8 import java.util.ArrayList;
9 import java.util.Iterator;
10 import java.util.LinkedHashMap;
11 import java.util.Map;
12 
17 public class Cache<K, T> extends LinkedHashMap<K, T> {
18 
19  public final static int MEMORY_SIZE = 134217728;// 128 MB = 128 * 1024 * 1024 Bytes.
20  public final static int MAXPXSIZE = 4; // 4 Bytes => 4 * 8 = 32 bits as maximum pixel size.
21  private int limit; // Max number of elements in cache.
22 
23  public Cache() {
24  this(100);
25  }
26 
27  public Cache(int limit) {
28  super(limit + 1);
29 
30  this.limit = limit;
31  }
32 
33  public static int getLimit(int thumb_width, int thumb_height)
34  {
35  int imageSize = thumb_height * thumb_width * Cache.MAXPXSIZE;
36  int elements = imageSize > 0 ? Cache.MEMORY_SIZE / imageSize : 1;
37  if(elements > 512)//Too many elements cause memory issues
38  elements = 512;
39  return elements;
40  }
41 
42  @SuppressWarnings("element-type-mismatch")
43  public void resize(int limit) {
44  // If new limit is lower than previous, remaining items are removed.
45  DEBUG.printMessage(" *** Cache: resizing to: [" + limit + "] elements");
46  //DEBUG.printMessage(" *** this.limit: [" + this.limit + "] / limit: [" + limit + "]");
47 
48  if (this.limit > limit && limit < size()) {
49  Iterator iter = keySet().iterator();
50  int items2remove = size() - limit;
51  ArrayList toRemove = new ArrayList(items2remove);
52 
53  // To avoid synchronizing problems, store items in a temporary array...
54  while (items2remove-- > 0) {
55  toRemove.add(iter.next());
56  }
57 
58  // ...and remove them later.
59  for (Object o : toRemove) {
60  remove(o);
61  }
62  }
63 
64  this.limit = limit;
65  }
66 
67  @Override
68  public T get(Object key) {
69  T object = super.get((K) key);
70 
71  if (object != null) { // Object has been referenced, so place it at higher position.
72  remove((K) key);
73  put((K) key, (T) object);
74  }
75 
76  return object;
77  }
78 
80  @Override
81  protected boolean removeEldestEntry(Map.Entry eldest) {
82  return size() > limit;
83  }
84 }
xmipp.utils.Cache.MAXPXSIZE
static final int MAXPXSIZE
Definition: Cache.java:20
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xmipp.utils.Cache.Cache
Cache(int limit)
Definition: Cache.java:27
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xmipp.utils.Cache.MEMORY_SIZE
static final int MEMORY_SIZE
Definition: Cache.java:19
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xmipp.utils.Cache.getLimit
static int getLimit(int thumb_width, int thumb_height)
Definition: Cache.java:33
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xmipp.utils.Cache.removeEldestEntry
boolean removeEldestEntry(Map.Entry eldest)
Definition: Cache.java:81
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xmipp.utils.Cache.resize
void resize(int limit)
Definition: Cache.java:43
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xmipp.utils.DEBUG.printMessage
static void printMessage(String message)
Definition: DEBUG.java:18
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class  xmipp.jni.CastWriteMode
 
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package  xmipp.jni
 
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1 package xmipp.jni;
2 
3 public class CastWriteMode {
4  public static final int CW_CAST = 0; //Only cast the data type ///
5  public static final int CW_CONVERT = 1; //Convert the data from one type to another ///
6  public static final int CW_ADJUST = 2; //Adjust the histogram to fill the gray level range ///
7  public static final int CW_LAST_LABEL = 3; // **** NOTE ****: Do keep this label always at the end ///
8 }
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xmipp.jni.CastWriteMode.CW_LAST_LABEL
static final int CW_LAST_LABEL
Definition: CastWriteMode.java:7
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xmipp.jni.CastWriteMode.CW_CONVERT
static final int CW_CONVERT
Definition: CastWriteMode.java:5
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xmipp.jni.CastWriteMode.CW_ADJUST
static final int CW_ADJUST
Definition: CastWriteMode.java:6
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xmipp.jni.CastWriteMode.CW_CAST
static final int CW_CAST
Definition: CastWriteMode.java:4
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class  xmipp.viewer.particlepicker.training.model.CenterParticleTask
 
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package  xmipp.viewer.particlepicker.training.model
 
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 import javax.swing.SwingWorker;
4 
5 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas;
6 
7 public class CenterParticleTask extends SwingWorker<String, Object>
8 {
9 
10  private static SupervisedPickerCanvas canvas;
11  private ManualParticle particle;
12  private SupervisedParticlePicker ppicker;
13 
14 
15  public CenterParticleTask(SupervisedPickerCanvas canvas, SupervisedParticlePicker ppicker, ManualParticle particle)
16  {
17  this.canvas = canvas;
18  this.ppicker = ppicker;
19  this.particle = particle;
20  }
21 
22 
23 
24  @Override
25  protected String doInBackground() throws Exception
26  {
27  try
28  {
29 
30  ppicker.centerParticle(particle);
31 
32  }
33  catch (Exception e)
34  {
35  throw new IllegalArgumentException(e);
36  }
37 
38  return "";
39  }
40 
41  @Override
42  protected void done() {
43  canvas.repaint();
44  }
45 
46 }
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xmipp.viewer.particlepicker.training.model.CenterParticleTask.CenterParticleTask
CenterParticleTask(SupervisedPickerCanvas canvas, SupervisedParticlePicker ppicker, ManualParticle particle)
Definition: CenterParticleTask.java:15
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class  xmipp.viewer.models.ClassInfo
 
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package  xmipp.viewer.models
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.models;
27 
28 import java.awt.Color;
29 import javax.swing.Icon;
30 import xmipp.utils.ColorIcon;
31 
33 public class ClassInfo {
34  public String comment;
35  public ColorIcon icon;
36  public int index; // index of the class
37  public int numberOfClasses; // Classes assigned to superclass
38  public long numberOfImages; // total images assigned to superclass
39 
41  public ClassInfo(String name, Color c) {
42  comment = name;
43  icon = new ColorIcon(c, 16, 16, 3, true, true);
44  }
45 
47  public ClassInfo(String name, Color c, int numberOfImages) {
48  comment = name;
49  icon = new ColorIcon(c, 16, 16, 3, true, true);
50  this.numberOfImages = numberOfImages;
51  }
52 
53  public String getComment() {
54  return comment;
55  }
56 
57  public void setComment(String value) {
58  comment = value;
59  }
60 
61  public Color getColor() {
62  return icon.getColor();
63  }
64 
65  public void setColor(Color value) {
66  icon.setColor(value);
67  }
68 
69  public Icon getIcon() {
70  return icon;
71  }
72 }// class ClassInfo
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xmipp.viewer.models.ClassInfo.setComment
void setComment(String value)
Definition: ClassInfo.java:57
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xmipp.viewer.models.ClassInfo.ClassInfo
ClassInfo(String name, Color c)
Definition: ClassInfo.java:41
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xmipp.viewer.models.ClassInfo.ClassInfo
ClassInfo(String name, Color c, int numberOfImages)
Definition: ClassInfo.java:47
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xmipp.utils.ColorIcon.setColor
void setColor(Color value)
Definition: ColorIcon.java:72
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xmipp.viewer.models.ClassInfo.setColor
void setColor(Color value)
Definition: ClassInfo.java:65
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-Classes

class  xmipp.viewer.windows.ClassesJDialog
 
class  xmipp.viewer.windows.ClassesJDialog.ClassesTableModel
 
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-Packages

package  xmipp.viewer.windows
 
-
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/ClassesJDialog_8java_source.html b/html/ClassesJDialog_8java_source.html deleted file mode 100644 index 9d9074fe..00000000 --- a/html/ClassesJDialog_8java_source.html +++ /dev/null @@ -1,136 +0,0 @@ - - - - - - - -Xmipp: xmippViz/java/src/xmipp/viewer/windows/ClassesJDialog.java Source File - - - - - - - - - -
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ClassesJDialog.java
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import java.awt.Color;
29 import java.awt.Dimension;
30 import java.awt.GridBagConstraints;
31 import java.awt.GridBagLayout;
32 import java.awt.event.ActionEvent;
33 import java.util.ArrayList;
34 
35 import javax.swing.BorderFactory;
36 import javax.swing.JButton;
37 import javax.swing.JFileChooser;
38 import javax.swing.JPanel;
39 import javax.swing.JScrollPane;
40 import javax.swing.JTable;
41 import javax.swing.ListSelectionModel;
42 import javax.swing.event.ListSelectionEvent;
43 import javax.swing.event.ListSelectionListener;
44 import javax.swing.table.AbstractTableModel;
45 
46 import xmipp.jni.Filename;
47 import xmipp.jni.MDLabel;
48 import xmipp.jni.MetaData;
49 import xmipp.utils.ColorEditor;
50 import xmipp.utils.ColorRenderer;
51 import xmipp.utils.DEBUG;
52 import xmipp.utils.XmippDialog;
53 import xmipp.utils.XmippFileChooser;
54 import xmipp.utils.XmippWindowUtil;
55 import xmipp.viewer.models.ClassInfo;
56 import xmipp.viewer.models.ImageGalleryTableModel;
57 
58 public class ClassesJDialog extends XmippDialog {
59  private static final long serialVersionUID = 1L;
60  private JTable tableClasses;
61  private JButton btnAdd, btnDelete, btnSave, btnOpen;
62  private ClassesTableModel model;
63  // This will be used for check for results from the dialog
64  private ArrayList<ClassInfo> classes;
65  GridBagConstraints gbc = new GridBagConstraints();
66  ImageGalleryTableModel gallery;
67  JPanel panelButtons;
68 
69  public ClassesJDialog(GalleryJFrame parent) {
70  super(parent, "Classes", true);
71  // this.classes = classes;
72  this.gallery = parent.gallery;
73  this.classes = gallery.data.getClasses();
74  this.btnOkText = "Select";
75  // disposeOnClose = false;
76  initComponents();
77  enableDelete(false);
78  }// constructor ColumnsJDialog
79 
80  private JButton createButton(String icon) {
81  JButton btn = XmippWindowUtil.getIconButton(icon, this);
82  btn.setFocusable(false);
83  panelButtons.add(btn);
84  return btn;
85  }
86 
87  protected void createToolbarButtons() {
88  panelButtons = new JPanel();
89  btnAdd = createButton("add.gif");
90  btnDelete = createButton("delete.gif");
91  btnSave = createButton("save.gif");
92  }
93 
94  @Override
95  protected void createContent(JPanel panel) {
96  setResizable(false);
97  panel.setLayout(new GridBagLayout());
98  gbc.anchor = GridBagConstraints.EAST;
99 
100  JPanel groupstbpn = new JPanel();
101  JScrollPane sp = new JScrollPane();
102  groupstbpn.setBorder(BorderFactory.createTitledBorder("Classes"));
103  groupstbpn.add(sp);
104  sp.setOpaque(true);
105  model = new ClassesTableModel();
106  tableClasses = new JTable(model);
107  tableClasses
108  .setPreferredScrollableViewportSize(new Dimension(350, 200));
109  sp.setViewportView(tableClasses);
110  tableClasses.setDefaultRenderer(Color.class, new ColorRenderer());
111  tableClasses.setDefaultEditor(Color.class, new ColorEditor());
112  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
113  createToolbarButtons();
114  panel.add(panelButtons, XmippWindowUtil.getConstraints(gbc, 1, 0));
115 
116  // listen to selection changes (only one row selected)
117  tableClasses.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
118  tableClasses.getSelectionModel().addListSelectionListener(
119  new ListSelectionListener() {
120  @Override
121  public void valueChanged(ListSelectionEvent e) {
122  enableDelete(getSelectedClass() >= 0);
123  }
124  });
125  }// function initComponents
126 
128  @Override
129  public boolean showDialog() {
130  gallery.data.updateClassesInfo();
131  this.classes = gallery.data.getClasses();
132  return super.showDialog();
133  }
134 
135  public void resetClasses() {
136  this.classes = null;
137  }
138 
139  private void enableDelete(boolean value) {
140  // btnAdd.setEnabled(value);
141  btnDelete.setEnabled(value);
142  btnOk.setEnabled(value);
143  }// function enableUpDown
144 
145  @Override
146  public void handleActionPerformed(ActionEvent evt) {
147  JButton btn = (JButton) evt.getSource();
148  if (btn == btnAdd) {
149  model.addNewRow();
150  int row = model.getRowCount() - 1;
151  tableClasses.editCellAt(row, 0);
152  tableClasses.setRowSelectionInterval(row, row);
153  } else if (btn == btnDelete) {
154  int row = getSelectedClass();
155  gallery.removeClass(row);
156  model.fireTableRowsDeleted(row, row);
157  } else if (btn == btnSave) {
158  try {
159  //Read an array of metadatas containing the super-classes selection
160  // the first element will contain the metadata with the 'classes' block
161  // and then one 'images' block for each class
162  MetaData[] mds = gallery.data.getClassesMd();
163  XmippFileChooser fc = new XmippFileChooser();
164  if (fc.showSaveDialog(parent) == JFileChooser.APPROVE_OPTION) {
165  String filename = fc.getSelectedPath();
166  MetaData md = mds[0];
167  md.write("classes" + Filename.SEPARATOR + filename);
168  long[] ids = md.findObjects();
169  // DEBUG.printFormat("mds: %s, ids:%s", mds.length,
170  // ids.length);
171  int i = 1;
172  for (long id : ids) {
173  int ref = md.getValueInt(MDLabel.MDL_REF, id);
174  mds[i].writeBlock(Filename.getClassBlockName(ref)
175  + Filename.SEPARATOR + filename);
176  ++i;
177  }
178  }
179  } catch (Exception e) {
180  showException(e);
181  }
182  }
183  }// function actionPerformed
184 
185  public int getSelectedClass() {
186  return tableClasses.getSelectedRow();
187  }
188 
189  public ClassInfo getClassInfo(int index) {
190  return classes.get(index);
191  }
192 
194  class ClassesTableModel extends AbstractTableModel {
195  private static final long serialVersionUID = 1L;
196 
197  private String[] columns = { "Comment", "# Classes", "# Images",
198  "Color" };
199 
200  public ClassesTableModel() {
201  }
202 
203  @Override
204  public Class getColumnClass(int column) {
205  return getValueAt(0, column).getClass();
206  }
207 
208  @Override
209  public String getColumnName(int columnIndex) {
210  return columns[columnIndex];
211  }
212 
213  @Override
214  public int getColumnCount() {
215  if (classes == null)
216  return 0;
217  return columns.length;
218  }
219 
220  @Override
221  public int getRowCount() {
222  if (classes == null)
223  return 0;
224  return classes.size();
225  }
226 
227  @Override
228  public boolean isCellEditable(int row, int column) {
229  return (column == 0 || column == 3);
230  }
231 
232  @Override
233  public void setValueAt(Object value, int row, int column) {
234  ClassInfo cli = classes.get(row);
235  switch (column) {
236  case 0:
237  cli.setComment((String) value);
238  break;
239  case 3:
240  cli.setColor((Color) value);
241  gallery.fireTableDataChanged();
242  break;
243  default:
244  showError(String.format("Column %d is not editable", column));
245  }
246 
247  }
248 
249  @Override
250  public Object getValueAt(int row, int column) {
251  ClassInfo cli = classes.get(row);
252  switch (column) {
253  case 0:
254  return cli.getComment();
255  case 1:
256  return cli.numberOfClasses;
257  case 2:
258  return cli.numberOfImages;
259  case 3:
260  return cli.getColor();
261  default:
262  return null;
263  }
264  }
265 
266  public void addNewRow() {
267  int newPos = classes.size();
268  gallery.data.addClass(new ClassInfo("NewClass", getNextColor()));
269  fireTableRowsInserted(newPos, newPos);
270  }
271 
272  final int amount = 100;
273  final int lowerLimit = 0x101010;
274  final int upperLimit = 0xE0E0D0;
275  final int colorStep = (upperLimit - lowerLimit) / amount;
276  int colorCounter = 0;
277 
278  Color getNextColor() {
279  DEBUG.printFormat("getNextColor, counter:%d\n", colorCounter);
280  return new Color(upperLimit - colorStep * colorCounter++);
281  }
282 
283  }// class ColumnsTableModel
284 
285 }// class ColumnsJDialog
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native void write(String filename)
- - - - - - -
xmipp.jni.MetaData.writeBlock
native void writeBlock(String filename)
-
xmipp.viewer.windows.ClassesJDialog.ClassesJDialog
ClassesJDialog(GalleryJFrame parent)
Definition: ClassesJDialog.java:69
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boolean showException(Exception e)
Definition: XmippDialog.java:217
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void setComment(String value)
Definition: ClassInfo.java:57
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static void printFormat(String format, Object...objects)
Definition: DEBUG.java:24
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native int getValueInt(int label, long objId)
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static String getClassBlockName(int ref)
Definition: Filename.java:385
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ArrayList< ClassInfo > getClasses()
Definition: GalleryData.java:1491
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xmipp.viewer.windows.ClassesJDialog.handleActionPerformed
void handleActionPerformed(ActionEvent evt)
Definition: ClassesJDialog.java:146
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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static final int MDL_REF
< 3D Class to which the image belongs (int)
Definition: MDLabel.java:312
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static JButton getIconButton(String icon, ActionListener listener)
Definition: XmippWindowUtil.java:124
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xmipp.viewer.models.ClassInfo.setColor
void setColor(Color value)
Definition: ClassInfo.java:65
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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xmipp.jni.Filename.SEPARATOR
static final String SEPARATOR
Definition: Filename.java:8
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class  xmipp.jni.Classifier
 
class  xmipp.jni.Classifier.Parameter
 
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1 package xmipp.jni;
2 
3 import java.util.List;
4 
5 public abstract class Classifier
6 {
7  protected List<Classifier.Parameter> params;
8 
9  public abstract int getTrainingParticlesMinimum();
10 
11  public abstract void setSize(int psize);
12  protected boolean applyChanges;
13 
14  public boolean isApplyChanges() {
15  return applyChanges;
16  }
17 
18 
19  public void setApplyChanges(boolean applyChanges) {
20  this.applyChanges = applyChanges;
21  }
22 
23 
24 
25  public class Parameter
26  {
27  public String name;
28  public String label;
29  public String help;
30  public String value;
31 
32  public Parameter(String name, String label, String help, String value)
33  {
34  this.name = name;
35  this.label = label;
36  this.help = help;
37  this.value = value;
38  }
39 
40  }
41 
42  public List<Classifier.Parameter> getParams()
43  {
44  return params;
45  }
46 
47  public abstract boolean needsTraining();
48 
49 
50 
51 
52 }
xmipp.jni.Classifier.setSize
abstract void setSize(int psize)
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xmipp.jni.Classifier.getParams
List< Classifier.Parameter > getParams()
Definition: Classifier.java:42
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xmipp.jni.Classifier.isApplyChanges
boolean isApplyChanges()
Definition: Classifier.java:14
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xmipp.jni.Classifier.setApplyChanges
void setApplyChanges(boolean applyChanges)
Definition: Classifier.java:19
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abstract boolean needsTraining()
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xmipp.jni.Classifier.getTrainingParticlesMinimum
abstract int getTrainingParticlesMinimum()
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xmipp.jni.Classifier.params
List< Classifier.Parameter > params
Definition: Classifier.java:7
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xmipp.jni.Classifier.Parameter.Parameter
Parameter(String name, String label, String help, String value)
Definition: Classifier.java:32
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1 /*
2  * Copyright (c) 1995, 2008, Oracle and/or its affiliates. All rights reserved.
3  *
4  * Redistribution and use in source and binary forms, with or without
5  * modification, are permitted provided that the following conditions
6  * are met:
7  *
8  * - Redistributions of source code must retain the above copyright
9  * notice, this list of conditions and the following disclaimer.
10  *
11  * - Redistributions in binary form must reproduce the above copyright
12  * notice, this list of conditions and the following disclaimer in the
13  * documentation and/or other materials provided with the distribution.
14  *
15  * - Neither the name of Oracle or the names of its
16  * contributors may be used to endorse or promote products derived
17  * from this software without specific prior written permission.
18  *
19  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
20  * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
21  * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
22  * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
23  * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
24  * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
25  * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
26  * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
27  * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
28  * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
29  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
30  */
31 
32 package xmipp.utils;
33 
34 /*
35  * ColorEditor.java (compiles with releases 1.3 and 1.4) is used by
36  * TableDialogEditDemo.java.
37  */
38 
39 import java.awt.Color;
40 import java.awt.Component;
41 import java.awt.event.ActionEvent;
42 import java.awt.event.ActionListener;
43 import java.util.regex.Matcher;
44 import java.util.regex.Pattern;
45 
46 import javax.swing.AbstractCellEditor;
47 import javax.swing.JButton;
48 import javax.swing.JColorChooser;
49 import javax.swing.JTable;
50 import javax.swing.table.TableCellEditor;
51 
52 public class ColorEditor extends AbstractCellEditor implements TableCellEditor,
53  ActionListener {
54  Color currentColor;
55  JButton button;
56  protected static final String EDIT = "edit";
57  private float position;
58 
59  public ColorEditor() {
60  this(0.0f);
61  }
62 
63  public ColorEditor(float position) {
64  this.position = position;
65 
66  // Set up the editor (from the table's point of view),
67  // which is a button.
68  // This button brings up the color chooser dialog,
69  // which is the editor from the user's point of view.
70  button = new JButton();
71  button.addActionListener(this);
72  button.setBorderPainted(false);
73  }
74 
78  public void actionPerformed(ActionEvent e) {
79  button.setBackground(currentColor);
80  Color c = JColorChooser
81  .showDialog(button, "Pick a Color", currentColor);
82  if (c != null)
83  currentColor = c;
84  fireEditingStopped();
85  }
86 
87  // Implement the one CellEditor method that AbstractCellEditor doesn't.
88  public Object getCellEditorValue() {
89  return currentColor;
90  }
91 
92  // Implement the one method defined by TableCellEditor.
93  public Component getTableCellEditorComponent(JTable table, Object value,
94  boolean isSelected, int row, int column) {
95  currentColor = (Color) value;
96  return button;
97  }
98 
99  public static Color stringToColor(String input) {
100  try {
101  return Color.decode("0x" + input);
102  }
103  catch (Exception ex){
104  ex.printStackTrace();
105  return null;
106  }
107  }
108 
109  public static String colorToString(Color c) {
110  if (c == null)
111  return null;
112  String rgb = Integer.toHexString(c.getRGB());
113  return rgb.substring(2, rgb.length());
114  }
115 }
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xmipp.utils.ColorEditor.stringToColor
static Color stringToColor(String input)
Definition: ColorEditor.java:99
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xmipp.utils.ColorEditor.getTableCellEditorComponent
Component getTableCellEditorComponent(JTable table, Object value, boolean isSelected, int row, int column)
Definition: ColorEditor.java:93
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xmipp.utils.ColorEditor.ColorEditor
ColorEditor(float position)
Definition: ColorEditor.java:63
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xmipp.utils.ColorEditor.colorToString
static String colorToString(Color c)
Definition: ColorEditor.java:109
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xmipp.utils.ColorEditor.EDIT
static final String EDIT
Definition: ColorEditor.java:56
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xmipp.utils.ColorEditor.actionPerformed
void actionPerformed(ActionEvent e)
Definition: ColorEditor.java:78
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1 package xmipp.viewer.particlepicker;
2 
3 import java.awt.Color;
4 import java.awt.FlowLayout;
5 import java.awt.GridBagConstraints;
6 import java.awt.GridBagLayout;
7 import java.awt.Insets;
8 import java.util.ArrayList;
9 import java.util.Collections;
10 import java.util.HashMap;
11 import java.util.List;
12 import java.util.Map;
13 
14 import javax.swing.JLabel;
15 import javax.swing.JPanel;
16 
17 
18 import xmipp.jni.MetaData;
19 import xmipp.utils.ColorIcon;
20 import xmipp.utils.XmippWindowUtil;
21 
22 public class ColorHelper
23 {
24  int id;
25  String name;
26  private double max;
27  private double min;
28  private double range;
29 
30  private final static int LOW = 0;
31  private final static int HIGH = 255;
32  private final static int HALF = (HIGH + 1) / 2;
33 
34  private final static Map<Integer, Color> map = initNumberToColorMap();
35  private static int factor;
36 
37 
38 
39  public ColorHelper(int id, String name, Color color, MetaData md)
40  {
41  this.id = id;
42  this.name = name;
43  max = Math.rint(md.getColumnMax(id) * 100)/100;
44  min = Math.rint(md.getColumnMin(id) * 100)/100;
45  range = max - min;
46  }
47 
48  public ColorHelper(int id, String name, MetaData md)
49  {
50  this(id, name, getNextColor(), md);
51  }
52 
53 
54  private static Color[] colors = new Color[] { Color.BLUE, Color.CYAN, Color.GREEN, Color.MAGENTA, Color.ORANGE, Color.PINK, Color.YELLOW };
55  private static int nextcolor;
56 
57  public static Color getNextColor()
58  {
59  Color next = colors[nextcolor];
60  nextcolor++;
61  if (nextcolor == colors.length)
62  nextcolor = 0;
63  return next;
64  }
65 
66  public static Color[] getSampleColors() {
67  return colors;
68  }
69 
70  public String toString()
71  {
72  return name;
73  }
74 
75 
76 
77  public String getName()
78  {
79  return name;
80  }
81 
82  public int getId()
83  {
84  return id;
85  }
86 
87  public Color getColor(double score)
88  {
89 
90  double percent = 1;
91  if(range > 0)
92  percent = (score - min)/range;
93  Color scorecolor = numberToColorPercentage(percent);
94  return scorecolor;
95  }
96 
97 
98 
104  public static Color numberToColor(final double value) {
105  if (value < 0 || value > 100) {
106  return null;
107  }
108  return numberToColorPercentage(value / 100);
109  }
110 
116  public static Color numberToColorPercentage(final double value) {
117  if (value < 0 || value > 1) {
118  return null;
119  }
120  Double d = value * factor;
121  int index = d.intValue();
122  if (index == factor) {
123  index--;
124  }
125  return map.get(index);
126  }
127 
128  public static JPanel getColorMap()
129  {
130  JPanel mappn = new JPanel(new FlowLayout(FlowLayout.LEFT, 0, 0));
131  for(int i = 0; i < map.size(); i += 10)
132  mappn.add(new JLabel(new ColorIcon(map.get(i), 1, 20, 0, false, false)));
133  return mappn;
134  }
135 
136 
140  private static Map<Integer, Color> initNumberToColorMap() {
141  HashMap<Integer, Color> localMap = new HashMap<Integer, Color>();
142  int r = LOW;
143  int g = LOW;
144  int b = HALF;
145 
146  // factor (increment or decrement)
147  int rF = 0;
148  int gF = 0;
149  int bF = 1;
150 
151  int count = 0;
152  // 1276 steps
153  while (true) {
154  localMap.put(count++, new Color(r, g, b));
155  if (b == HIGH) {
156  gF = 1; // increment green
157  }
158  if (g == HIGH) {
159  bF = -1; // decrement blue
160  // rF = +1; // increment red
161  }
162  if (b == LOW) {
163  rF = +1; // increment red
164  }
165  if (r == HIGH) {
166  gF = -1; // decrement green
167  }
168  if (g == LOW && b == LOW) {
169  rF = -1; // decrement red
170  }
171  if (r < HALF && g == LOW && b == LOW) {
172  break; // finish
173  }
174  r += rF;
175  g += gF;
176  b += bF;
177  r = rangeCheck(r);
178  g = rangeCheck(g);
179  b = rangeCheck(b);
180  }
181  initList(localMap);
182  return localMap;
183  }
184 
188  private static void initList(final HashMap<Integer, Color> localMap) {
189  List<Integer> list = new ArrayList<Integer>(localMap.keySet());
190  Collections.sort(list);
191  Integer min = list.get(0);
192  Integer max = list.get(list.size() - 1);
193  factor = max + 1;
194  }
195 
200  private static int rangeCheck(final int value) {
201  if (value > HIGH) {
202  return HIGH;
203  } else if (value < LOW) {
204  return LOW;
205  }
206  return value;
207  }
208 
209  public double getMin()
210  {
211  return min;
212  }
213 
214  public double getMax()
215  {
216  return max;
217  }
218 
219 
220 
221 }
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xmipp.viewer.particlepicker.ColorHelper.ColorHelper
ColorHelper(int id, String name, Color color, MetaData md)
Definition: ColorHelper.java:39
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native double getColumnMin(int column)
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xmipp.viewer.particlepicker.ColorHelper.numberToColor
static Color numberToColor(final double value)
Definition: ColorHelper.java:104
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ColorHelper(int id, String name, MetaData md)
Definition: ColorHelper.java:48
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native double getColumnMax(int column)
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static Color numberToColorPercentage(final double value)
Definition: ColorHelper.java:116
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1 package xmipp.utils;
2 
3 import java.awt.Color;
4 import java.awt.Component;
5 import java.awt.Graphics;
6 
7 import javax.swing.Icon;
8 
14 public class ColorIcon implements Icon
15 {
16  private Color color;
17  private int width, height;
18  private int gap;
19  private boolean rounded;
20  private boolean withborder;
21  private static final int ROUND_WIDTH = 3;
22 
23  public ColorIcon(Color c)
24  {
25  this(c, 16, 16);
26  }
27 
28  public ColorIcon(Color c, int w, int h)
29  {
30  this(c, w, h, 0, true, true);
31  }
32 
33  public ColorIcon(Color c, int w, int h, int g, boolean isRounded, boolean withborder)
34  {
35  color = c;
36  width = w;
37  height = h;
38  gap = g;
39  rounded = isRounded;
40  this.withborder = withborder;
41 
42  }// Constructor
43 
44  // Implement the Icon Interface
50  @Override
51  public int getIconWidth()
52  {
53  return width;
54  }
55 
61  @Override
62  public int getIconHeight()
63  {
64  return height;
65  }
66 
67  public Color getColor()
68  {
69  return color;
70  }
71 
72  public void setColor(Color value)
73  {
74  color = value;
75  }
76 
77  public int getGap()
78  {
79  return gap;
80  }
81 
82  public void setGap(int g)
83  {
84  gap = g;
85  }
86 
99  @Override
100  public void paintIcon(Component c, Graphics g, int x, int y)
101  {
102  x += gap;
103  y += gap;
104  int w = width - 2 * gap;
105  int h = height - 2 * gap;
106  g.setColor(color);
107  if (rounded)
108  g.fillRoundRect(x, y, w, h, ROUND_WIDTH, ROUND_WIDTH);
109  else
110  g.fillRect(x, y, w, h);
111  if (withborder)
112  {
113  g.setColor(Color.black);
114  if (rounded)
115  g.drawRoundRect(x, y, w, h, ROUND_WIDTH, ROUND_WIDTH);
116  else
117  g.drawRect(x, y, w, h);
118  }
119  }
120 
121 }// class ColoredRectangleIcon
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void setGap(int g)
Definition: ColorIcon.java:82
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ColorIcon(Color c, int w, int h)
Definition: ColorIcon.java:28
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ColorIcon(Color c, int w, int h, int g, boolean isRounded, boolean withborder)
Definition: ColorIcon.java:33
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void setColor(Color value)
Definition: ColorIcon.java:72
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void paintIcon(Component c, Graphics g, int x, int y)
Definition: ColorIcon.java:100
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1 /***************************************************************************
2  * Authors: Airen Zaldivar Peraza (azaldivar@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 
27 package xmipp.utils;
28 
29 import java.awt.Color;
30 import java.awt.Component;
31 
32 import javax.swing.JLabel;
33 import javax.swing.JTable;
34 import javax.swing.table.TableCellRenderer;
35 
42 public class ColorRenderer extends JLabel implements TableCellRenderer
43 {
44  private Color color;
45 
46  public ColorRenderer() {
47  setOpaque(true); //MUST do this for background to show up.
48  setHorizontalAlignment(JLabel.CENTER);
49  }
50 
51  @Override
52  public Component getTableCellRendererComponent(JTable table,
53  Object value, boolean isSelected, boolean hasFocus, int row,
54  int column) {
55  color = (Color)value;
56  setIcon(new ColorIcon(color));
57  return this;
58  }
59 
60 }
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xmipp.utils.ColorRenderer.getTableCellRendererComponent
Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)
Definition: ColorRenderer.java:52
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Color_Transformer.java File Reference
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class  Color_Transformer
 
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Color_Transformer.java
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1 import ij.*;
2 import ij.plugin.filter.PlugInFilter;
3 import ij.process.*;
4 import ij.gui.*;
5 import java.awt.*;
6 
32 public class Color_Transformer implements PlugInFilter{
33  private ImagePlus imp; // Original image
34  private ImageStack sstack; // Stack result
35  private int width; // Width of the original image
36  private int height; // Height of the original image
37  private int size; // Total number of pixels
38  private float[] c1, c2, c3; // Colour space values
39  private float[] rf, gf, bf; // r, g, b values
40  private String colourspace; // Colour space chosen
41  private String title; // Name of the original image
42  private String n1, n2, n3; // Names for every layer on the stack
43 
44 
45  public int setup(String arg, ImagePlus imp){
46  this.imp = imp;
47  if (arg.equals("about"))
48  {showAbout(); return DONE;}
49  return DOES_ALL;
50  }
51 
52  public boolean showDialog(){
53  String[] colourspaces = {"XYZ",
54  "Yxy",
55  "YUV",
56  "YIQ",
57  "Luv",
58  "Lab",
59  "AC1C2",
60  "I1I2I3",
61  "Yuv",
62  "YQ1Q2",
63  "HSI",
64  "HSV",
65  "HSL",
66  "LCHLuv",
67  "LSHLuv",
68  "LSHLab"};
69  GenericDialog gd = new GenericDialog("Colour Transform");
70  gd.addChoice("Colour space:", colourspaces, colourspaces[0]);
71  gd.showDialog();
72  if (gd.wasCanceled())
73  return false;
74  colourspace = colourspaces[gd.getNextChoiceIndex()];
75  return true;
76  }
77 
78  public void run(ImageProcessor ip) {
79  if (!showDialog())
80  return;
81  int offset, i;
82  width = ip.getWidth();
83  height = ip.getHeight();
84  size = width*height;
85  c1 = new float[size];
86  c2 = new float[size];
87  c3 = new float[size];
88  rf = new float[size];
89  gf = new float[size];
90  bf = new float[size];
91  for (int row = 0; row < height; row++){
92  offset = row*width;
93  for (int col = 0; col < width; col++) {
94  i = offset + col;
95  int c = ip.getPixel(col, row);
96  rf[i] = ((c&0xff0000)>>16)/255f; //R 0..1
97  gf[i] = ((c&0x00ff00)>>8)/255f; //G 0..1
98  bf[i] = (c&0x0000ff)/255f; //B 0..1
99  }
100  }
101 
102  if(colourspace.equals("XYZ")){
103  n1 = "X";
104  n2 = "Y";
105  n3 = "Z";
106  getXYZ();
107  }
108  if(colourspace.equals("Yxy")){
109  n1 = "Y";
110  n2 = "x";
111  n3 = "y";
112  getYxy();
113  }
114  if(colourspace.equals("YUV")){
115  n1 = "Y";
116  n2 = "U";
117  n3 = "V";
118  getYUV();
119  }
120  if(colourspace.equals("YIQ")){
121  n1 = "Y";
122  n2 = "I";
123  n3 = "Q";
124  getYIQ();
125  }
126  if(colourspace.equals("AC1C2")){
127  n1 = "A";
128  n2 = "C1";
129  n3 = "C2";
130  getAC1C2();
131  }
132  if(colourspace.equals("Luv")){
133  n1 = "L";
134  n2 = "u";
135  n3 = "v";
136  getLuv();
137  }
138  if(colourspace.equals("Lab")){
139  n1 = "L";
140  n2 = "a";
141  n3 = "b";
142  getLab();
143  }
144  if(colourspace.equals("I1I2I3")){
145  n1 = "I1";
146  n2 = "I2";
147  n3 = "I3";
148  getI1I2I3();
149  }
150  if(colourspace.equals("Yuv")){
151  n1 = "Y";
152  n2 = "u";
153  n3 = "v";
154  getYuv();
155  }
156  if(colourspace.equals("YQ1Q2")){
157  n1 = "Y";
158  n2 = "Q1";
159  n3 = "Q2";
160  getYQ1Q2();
161  }
162  if(colourspace.equals("HSI")){
163  n1 = "I";
164  n2 = "H";
165  n3 = "S";
166  getHSI();
167  }
168  if(colourspace.equals("HSV")){
169  n1 = "V";
170  n2 = "H";
171  n3 = "S";
172  getHSV();
173  }
174  if(colourspace.equals("HSL")){
175  n1 = "L";
176  n2 = "H";
177  n3 = "S";
178  getHSL();
179  }
180  if(colourspace.equals("LCHLuv")){
181  n1 = "L";
182  n2 = "H";
183  n3 = "C";
184  getLCHLuv();
185  }
186  if(colourspace.equals("LSHLuv")){
187  n1 = "L";
188  n2 = "H";
189  n3 = "S";
190  getLSHLuv();
191  }
192  if(colourspace.equals("LSHLab")){
193  n1 = "L";
194  n2 = "H";
195  n3 = "S";
196  getLCHLab();
197  }
198 
199  title = imp.getTitle();
200  sstack=new ImageStack(width,height); // Create new float stack for output
201 
202  ImagePlus imc1=NewImage.createFloatImage(n1,width,height,1,NewImage.FILL_BLACK);
203  ImageProcessor ipc1=imc1.getProcessor();
204  ipc1.setPixels(c1);
205  sstack.addSlice(n1,ipc1);
206 
207  ImagePlus imc2=NewImage.createFloatImage(n2,width,height,1,NewImage.FILL_BLACK);
208  ImageProcessor ipc2=imc2.getProcessor();
209  ipc2.setPixels(c2);
210  sstack.addSlice(n2,ipc2);
211 
212  ImagePlus imc3=NewImage.createFloatImage(n3,width,height,1,NewImage.FILL_BLACK);
213  ImageProcessor ipc3=imc3.getProcessor();
214  ipc3.setPixels(c3);
215  sstack.addSlice(n3,ipc3);
216 
217  ImagePlus imluv=new ImagePlus(colourspace,sstack);
218  imluv.show();
219  IJ.resetMinAndMax();
220 
221  }
222 
223 
224  public void getXYZ(){
225  // http://www.easyrgb.com/math.html
226  for(int q=0; q<size; q++){
227  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
228  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
229  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
230 
231  rf[q] = rf[q] * 100f;
232  gf[q] = gf[q] * 100f;
233  bf[q] = bf[q] * 100f;
234 //WAH - these are the D65 values per BruceLindbloom, so I decided to stick with D65
235  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
236  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
237  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
238 
239  c1[q] = X;
240  c2[q] = Y;
241  c3[q] = Z;
242  }
243  }
244 
245  public void getYxy(){
246  // @ARTICLE{TrussellHJ95colour:art,
247  // author = {H. J. Trussell and E. Saber and M. Vrhel},
248  // title = {Color image processing [basics and special issue overview]},
249  // journal = {IEEE Signal Processing Magazine},
250  // year = {2005},
251  // volume = {22},
252  // pages = {14 - 22},
253  // number = {1},
254  // month = {January},
255  //}
256  for(int q=0; q<size; q++){
257  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
258  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
259  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
260 
261  rf[q] = rf[q] * 100f;
262  gf[q] = gf[q] * 100f;
263  bf[q] = bf[q] * 100f;
264 
265  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
266  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
267  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
268 
269  float xx = (X == 0f && Y == 0f && Z == 0f)? 0f : (X / ((X + Y + Z)));
270  float yy = (X == 0f && Y == 0f && Z == 0f)? 0f : (Y / ((X + Y + Z)));
271 
272  c1[q] = Y;
273  c2[q] = xx;
274  c3[q] = yy;
275  }
276  }
277 
278  public void getYUV(){
279  //@ARTICLE{ChengHD00:art,
280  // author = {H.D. Cheng and X.H. Jiang and Y. Sun and J.L. Wang},
281  // title = {Color Image Segmentation: Advances and Prospects},
282  // journal = {Pattern Recognition},
283  // year = {2000},
284  // volume = {34},
285  // pages = {2259-2281},
286  // month = {September},
287  //}
288  for(int q=0; q<size; q++){
289  float Y = 0.299f * rf[q] + 0.587f * gf[q] + 0.114f * bf[q];
290  float U = -0.147f * rf[q] - 0.289f * gf[q] + 0.437f * bf[q];
291  float V = 0.615f * rf[q] - 0.515f * gf[q] - 0.100f * bf[q];
292 
293  c1[q] = Y;
294  c2[q] = U;
295  c3[q] = V;
296  }
297  }
298 
299  public void getYIQ(){
300  //@ARTICLE{ChengHD00:art,
301  // author = {H.D. Cheng and X.H. Jiang and Y. Sun and J.L. Wang},
302  // title = {Color Image Segmentation: Advances and Prospects},
303  // journal = {Pattern Recognition},
304  // year = {2000},
305  // volume = {34},
306  // pages = {2259-2281},
307  // month = {September},
308  //}
309  for(int q=0; q<size; q++){
310  float Y = 0.299f * rf[q] + 0.587f * gf[q] + 0.114f * bf[q];
311  float I = 0.596f * rf[q] - 0.274f * gf[q] - 0.322f * bf[q];
312  float Q = 0.211f * rf[q] - 0.253f * gf[q] - 0.312f * bf[q];
313 
314  c1[q] = Y;
315  c2[q] = I;
316  c3[q] = Q;
317  }
318  }
319 
320  public void getAC1C2(){
321  //@ARTICLE{FaugerasO79:art,
322  // author = {O. Faugeras},
323  // title = {Digital color image processing within the framework of a human visual model},
324  // journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
325  // year = {1979},
326  // volume = {27},
327  // pages = {380- 393},
328  // number = {4},
329  // month = {August},
330  //}
331  for(int q=0; q<size; q++){
332  float L, M, S;
333  float A, C1, C2;
334  L = 0.3634f * rf[q] + 0.6102f * gf[q] + 0.0264f * bf[q];
335  M = 0.1246f * rf[q] + 0.8138f * gf[q] + 0.0616f * bf[q];
336  S = 0.0009f * rf[q] + 0.0602f * gf[q] + 0.9389f * bf[q];
337 
338  L = new Double(Math.log(L)).floatValue();
339  M = new Double(Math.log(M)).floatValue();
340  S = new Double(Math.log(S)).floatValue();
341 
342  A = 13.8312f * L + 8.3394f * M + 0.4294f * S;
343  C1 = 64.0000f * L - 64.000f * M + 0.0000f * S;
344  C2 = 10.0000f * L + 0.0000f * M - 10.000f * S;
345 
346  c1[q] = A;
347  c2[q] = C1;
348  c3[q] = C2;
349  }
350  }
351 
352  public void getLuv(){
353  // http://www.easyrgb.com/math.html AND
354  // @INBOOK{RonnierLuoM98colour:chapterbook,
355  // chapter = {Colour science},
356  // pages = {27-65},
357  // title = {The Colour Image Processing Handbook},
358  // publisher = {Springer},
359  // year = {1998},
360  // editor = {R. E.N. Horne},
361  // author = {Ronnier Luo},
362  //}
363 
365  //X = 95.047, Y = 100.0, Z = 108.883;
366  float yn = 1f;
367 
369  // un' = 4X/(X + 15Y + 3Z)
370  float unp = 0.19784f;
371 
373  // vn = 9Y/(X + 15Y + 3Z)
374  float vnp = 0.4683f;
375 
376  for(int q=0; q<size; q++){
377  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
378  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
379  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
380 
381  rf[q] = rf[q] * 100f;
382  gf[q] = gf[q] * 100f;
383  bf[q] = bf[q] * 100f;
384 
385  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
386  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
387  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
388 
389  // As yn = 1.0, we will just consider Y value as yyn
390  //yyn = (Y/yn);
391  float f_yyn = Y / 100f;
392 
393  if (f_yyn > 0.008856f) {
394  f_yyn=new Double(Math.exp(Math.log(f_yyn)/3f)).floatValue();
395  } else {
396  f_yyn = ((7.787f * f_yyn) + (16f/116f));
397  }
398 
399  float up = (X == 0f && Y == 0f && Z == 0f)? 0f : (4f*X / ((X + 15f*Y + 3f*Z)));
400  float vp = (X == 0f && Y == 0f && Z == 0f)? 0f : (9f*Y / ((X + 15f*Y + 3f*Z)));
401 
402  float l = (116f *f_yyn)-16f;
403  float u = 13f * l * (up - unp);
404  float v = 13f * l * (vp - vnp);
405 
406  c1[q] = l;
407  c2[q] = u;
408  c3[q] = v;
409  }
410  }
411 
412  public void getLab(){
413  // http://www.easyrgb.com/math.html AND
414  // @INBOOK{RonnierLuoM98colour:chapterbook,
415  // chapter = {Colour science},
416  // pages = {27-65},
417  // title = {The Colour Image Processing Handbook},
418  // publisher = {Springer},
419  // year = {1998},
420  // editor = {R. E.N. Horne},
421  // author = {Ronnier Luo},
422  //}
423  for(int q=0; q<size; q++){
424  float l, a, b;
425  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055f)/1.055f)*2.4f))).floatValue():rf[q]/12.92f;
426  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055f)/1.055f)*2.4f))).floatValue():gf[q]/12.92f;
427  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055f)/1.055f)*2.4f))).floatValue():bf[q]/12.92f;
428 
429  rf[q] = rf[q] * 100f;
430  gf[q] = gf[q] * 100f;
431  bf[q] = bf[q] * 100f;
432 
433  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
434  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
435  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
436 
437  // XYZ to Lab
438  float fX, fY, fZ;
439  float La, aa, bb;
440  //WAH normalize to L*a*b* color space using D65 white reference
441  // from Color_Space_Converter code: public double[] D65 = {95.0429, 100.0, 108.8900};
442 
443  X = X / 95.0429f;
444  Y = Y / 100.0f;
445  Z = Z / 108.89f;
446 
447  if ( X > 0.008856f )
448  fX = (new Double(Math.exp(Math.log(X)/3f))).floatValue();
449  else
450  fX = ((7.787f * X) + (16f/116f));
451 
452  if ( Y > 0.008856f )
453  fY = (new Double(Math.exp(Math.log(Y)/3f))).floatValue();
454  else
455  fY = ((7.787f * Y) + (16f/116f));
456 
457  if ( Z > 0.008856f )
458  fZ = (new Double(Math.exp(Math.log(Z)/3f))).floatValue();
459  else
460  fZ = ((7.787f * Z) + (16f/116f));
461 
462  l = ( 116f * fY ) - 16f;
463  a = 500f * ( fX - fY );
464  b = 200f * ( fY - fZ );
465 
466  c1[q] = l;
467  c2[q] = a;
468  c3[q] = b;
469  }
470  }
471 
472  public void getI1I2I3(){
473  // @ARTICLE{Ohta80:art,
474  // author = {Y. Ohta and T. Kanade and T. Sakai},
475  // title = {Color Information for Region Segmentation},
476  // journal = {Computer Graphics and Image Processing},
477  // year = {1980},
478  // volume = {13},
479  // pages = {222 - 241},
480  // number = {3},
481  // month = {July},
482  //}
483  for(int q=0; q<size; q++){
484  float I1 = (rf[q] + gf[q] + bf[q])/3f;
485  float I2 = (rf[q] - bf[q])/2f;
486  float I3 = (2f * gf[q] - rf[q] - bf[q])/4f;
487  c1[q] = I1;
488  c2[q] = I2;
489  c3[q] = I3;
490  }
491  }
492 
493  public void getYuv(){
494  // @ARTICLE{LittmanE97colour:art,
495  // author = {E. Littmann and H. Ritter},
496  // title = {Adaptive Color Segmentation - A comparison of Neural and Statistical Methods},
497  // journal = {IEEE Transactions on neural networks},
498  // year = {1997},
499  // volume = {8},
500  // pages = {175-185},
501  // number = {1},
502  // month = {January},
503  //}
504  for(int q=0; q<size; q++){
505  float u, v;
506  float Y = (rf[q] + gf[q] + bf[q])/3f;
507  if(Y != 0f){
508  u = 3f*(rf[q] - bf[q])/2f*Y;
509  v = (new Double(Math.sqrt(3.0)).floatValue())*(2f * gf[q] - rf[q] - bf[q])/2f*Y;
510  }
511  else{
512  u = 0f;
513  v = 0f;
514  }
515  c1[q] = Y;
516  c2[q] = u;
517  c3[q] = v;
518  }
519  }
520 
521  public void getYQ1Q2(){
522  // @ARTICLE{LittmanE97colour:art,
523  // author = {E. Littmann and H. Ritter},
524  // title = {Adaptive Color Segmentation - A comparison of Neural and Statistical Methods},
525  // journal = {IEEE Transactions on neural networks},
526  // year = {1997},
527  // volume = {8},
528  // pages = {175-185},
529  // number = {1},
530  // month = {January},
531  //}
532  for(int q=0; q<size; q++){
533  float Y = (rf[q] + gf[q] + bf[q])/3f;
534  float Q1 = ((rf[q] + gf[q]) != 0f)?rf[q]/(rf[q] + gf[q]):0f;
535  float Q2 = ((rf[q] + bf[q]) != 0f)?rf[q]/(rf[q] + bf[q]):0f;
536  c1[q] = Y;
537  c2[q] = Q1;
538  c3[q] = Q2;
539  }
540  }
541 
542  public void getHSI(){
543  // @BOOK{MalacaraD01:book,
544  // title = {Color Vision and Colorimetry, Theory and Applications},
545  // publisher = {SPIE International Society for Optical Engineering},
546  // year = {2001},
547  // author = {D. Malacara},
548  // address = {Bellingham, Washington USA},
549  //}
550  for(int q=0; q<size; q++){
551  float var_Min = Math.min(rf[q], gf[q]); //Min. value of RGB
552  var_Min = Math.min(var_Min, bf[q]);
553  float var_Max = Math.max(rf[q], gf[q]); //Max. value of RGB
554  var_Max = Math.max(var_Max, bf[q]);
555  float del_Max = var_Max - var_Min; //Delta RGB value
556 
557  c3[q] = (rf[q] + gf[q] + bf[q])/3f;
558 
559  if ( del_Max == 0f ){ //This is a gray, no chroma...
560  c1[q] = 0f; //HSL results = 0 � 1
561  c2[q] = 0f;
562  }
563  else{ //Chromatic data...
564  c2[q] = 1 - (var_Min / c3[q]);
565 
566  float del_R = ( ( ( var_Max - rf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
567  float del_G = ( ( ( var_Max - gf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
568  float del_B = ( ( ( var_Max - bf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
569 
570  if ( rf[q] == var_Max ) c1[q] = del_B - del_G;
571  else if ( gf[q] == var_Max ) c1[q] = ( 1f / 3f ) + del_R - del_B;
572  else if ( bf[q] == var_Max ) c1[q] = ( 2f / 3f ) + del_G - del_R;
573 
574  if ( c1[q] < 0 ) c1[q] += 1;
575  if ( c1[q] > 1 ) c1[q] -= 1;
576  }
577  }
578  }
579 
580  public void getHSL(){
581  // http://www.easyrgb.com/math.html
582  for(int q=0; q<size; q++){
583  float H=0, S=0, L=0;
584  float var_Min = Math.min(rf[q], gf[q]); //Min. value of RGB
585  var_Min = Math.min(var_Min, bf[q]);
586  float var_Max = Math.max(rf[q], gf[q]); //Max. value of RGB
587  var_Max = Math.max(var_Max, bf[q]);
588  float del_Max = var_Max - var_Min; //Delta RGB value
589 
590  L = (var_Max + var_Min)/2;
591 
592  if ( del_Max == 0f){ //This is a gray, no chroma...
593  H = 0f; //HSL results = 0 � 1
594  S = 0f;
595  }
596  else{ //Chromatic data...
597  if ( L < 0.5f ) S = del_Max / ( var_Max + var_Min );
598  else S = del_Max / ( 2f - var_Max - var_Min );
599 
600  float del_R = ( ( ( var_Max - rf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
601  float del_G = ( ( ( var_Max - gf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
602  float del_B = ( ( ( var_Max - bf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
603 
604  if ( rf[q] == var_Max ) H = del_B - del_G;
605  else if ( gf[q] == var_Max ) H = ( 1f / 3f ) + del_R - del_B;
606  else if ( bf[q] == var_Max ) H = ( 2f / 3f ) + del_G - del_R;
607 
608  if ( H < 0f ) H += 1f;
609  if ( H > 1f ) H -= 1f;
610  }
611  c1[q] = H;
612  c2[q] = S;
613  c3[q] = L;
614  }
615  }
616 
617  public void getHSV(){ // HSV_Stack Plugin (HSV colour space is also known as HSB where B means brightness)
618  // http://www.easyrgb.com/math.html
619  for(int q=0; q<size; q++){ // http://www.easyrgb.com/
620  float H=0, S=0, V=0;
621  float var_Min = Math.min(rf[q], gf[q]); //Min. value of RGB
622  var_Min = Math.min(var_Min, bf[q]);
623  float var_Max = Math.max(rf[q], gf[q]); //Max. value of RGB
624  var_Max = Math.max(var_Max, bf[q]);
625  float del_Max = var_Max - var_Min; //Delta RGB value
626 
627  V = var_Max*1f;
628  if ( del_Max == 0 ){ //This is a gray, no chroma...
629  H = 0f; //HSV results = 0 � 1
630  S = 0f;
631  }
632  else{ //Chromatic data...
633  S = del_Max / var_Max;
634  float del_R = ( ( ( var_Max - rf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
635  float del_G = ( ( ( var_Max - gf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
636  float del_B = ( ( ( var_Max - bf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
637 
638  if ( rf[q] == var_Max ) H = del_B - del_G;
639  else if ( gf[q] == var_Max ) H = ( 1f / 3f ) + del_R - del_B;
640  else if ( bf[q] == var_Max ) H = ( 2f / 3f ) + del_G - del_R;
641 
642  if ( H < 0 ) H += 1;
643  if ( H > 1 ) H -= 1;
644  }
645  c1[q] = H;
646  c2[q] = S;
647  c3[q] = V;
648  }
649 
650  }
651 
652  public void getLCHLuv(){
653  // @BOOK{MalacaraD01:book,
654  // title = {Color Vision and Colorimetry, Theory and Applications},
655  // publisher = {SPIE International Society for Optical Engineering},
656  // year = {2001},
657  // author = {D. Malacara},
658  // address = {Bellingham, Washington USA},
659  //}
661  //X = 95.047, Y = 100.0, Z = 108.883;
662  float yn = 1f;
663 
665  // un' = 4X/(X + 15Y + 3Z)
666  float unp = 0.19784f;
667 
669  // vn = 9Y/(X + 15Y + 3Z)
670  float vnp = 0.4683f;
671 
672  for(int q=0; q<size; q++){
673  float L=0f, C=0f, H=0f;
674  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
675  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
676  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
677 
678  rf[q] = rf[q] * 100f;
679  gf[q] = gf[q] * 100f;
680  bf[q] = bf[q] * 100f;
681 
682  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
683  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
684  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
685 
686  // As yn = 1.0, we will just consider Y value as yyn
687  //yyn = (Y/yn);
688  float f_yyn = Y / 100f;
689 
690  if (f_yyn > 0.008856f) {
691  f_yyn=new Double(Math.exp(Math.log(f_yyn)/3f)).floatValue();
692  } else {
693  f_yyn = ((7.787f * f_yyn) + (16f/116f));
694  }
695 
696  float up = (X == 0f && Y == 0f && Z == 0f)? 0f : (4f*X / ((X + 15f*Y + 3f*Z)));
697  float vp = (X == 0f && Y == 0f && Z == 0f)? 0f : (9f*Y / ((X + 15f*Y + 3f*Z)));
698 
699  float l = (116f *f_yyn)-16f;
700  float u = 13f * l * (up - unp);
701  float v = 13f * l * (vp - vnp);
702 
703  L = l;
704  C = new Double(Math.sqrt((u*u)+(v*v))).floatValue();
705 
706  if ( u == 0 ){ //This is a gray, no chroma...
707  H = 0f; //LCH results = 0 � 1
708  }
709  else{
710  if (u>=0f && v>=0f) H = new Double(Math.atan(v/u)).floatValue();
711  else if (u>=0f && v<0f) H = new Double(Math.atan(v/u) + Math.PI).floatValue();
712  else if (u<0f && v<0f) H = new Double(Math.atan(v/u) + Math.PI).floatValue();
713  else if (u<0f && v>=0f) H = new Double(Math.atan(v/u) + (2*Math.PI)).floatValue();
714  }
715  c1[q] = L;
716  c2[q] = C;
717  c3[q] = H;
718  }
719  }
720 
721  public void getLSHLuv(){
722  // @BOOK{MalacaraD01:book,
723  // title = {Color Vision and Colorimetry, Theory and Applications},
724  // publisher = {SPIE International Society for Optical Engineering},
725  // year = {2001},
726  // author = {D. Malacara},
727  // address = {Bellingham, Washington USA},
728  //}
730  //X = 95.047, Y = 100.0, Z = 108.883;
731  float yn = 1f;
732 
734  // un' = 4X/(X + 15Y + 3Z)
735  float unp = 0.19784f;
736 
738  // vn = 9Y/(X + 15Y + 3Z)
739  float vnp = 0.4683f;
740 
741  for(int q=0; q<size; q++){
742  float L=0f, S=0f, H=0f;
743  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
744  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
745  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
746 
747  rf[q] = rf[q] * 100f;
748  gf[q] = gf[q] * 100f;
749  bf[q] = bf[q] * 100f;
750 
751  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
752  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
753  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
754 
755  // As yn = 1.0, we will just consider Y value as yyn
756  //yyn = (Y/yn);
757  float f_yyn = Y / 100f;
758 
759  if (f_yyn > 0.008856f) {
760  f_yyn=new Double(Math.exp(Math.log(f_yyn)/3f)).floatValue();
761  } else {
762  f_yyn = ((7.787f * f_yyn) + (16f/116f));
763  }
764 
765  float up = (X == 0f && Y == 0f && Z == 0f)? 0f : (4f*X / ((X + 15f*Y + 3f*Z)));
766  float vp = (X == 0f && Y == 0f && Z == 0f)? 0f : (9f*Y / ((X + 15f*Y + 3f*Z)));
767 
768  float l = (116f *f_yyn)-16f;
769  float u = 13f * l * (up - unp);
770  float v = 13f * l * (vp - vnp);
771 
772  L = l;
773  S = (new Double(13*Math.sqrt(((u-up)*(u-up))+((v-vp)*(v-vp))))).floatValue();
774 
775  if ( u == 0 ){ //This is a gray, no chroma...
776  H = 0f; //LCH results = 0 � 1
777  }
778  else{
779  if (u>=0f && v>=0f) H = new Double(Math.atan(v/u)).floatValue();
780  else if (u>=0f && v<0f) H = new Double(Math.atan(v/u) + Math.PI).floatValue();
781  else if (u<0f && v<0f) H = new Double(Math.atan(v/u) + Math.PI).floatValue();
782  else if (u<0f && v>=0f) H = new Double(Math.atan(v/u) + (2*Math.PI)).floatValue();
783  }
784  c1[q] = L;
785  c2[q] = S;
786  c3[q] = H;
787  }
788  }
789 
790  public void getLCHLab(){
791  // @BOOK{MalacaraD01:book,
792  // title = {Color Vision and Colorimetry, Theory and Applications},
793  // publisher = {SPIE International Society for Optical Engineering},
794  // year = {2001},
795  // author = {D. Malacara},
796  // address = {Bellingham, Washington USA},
797  //}
798  for(int q=0; q<size; q++){
799  float L=0f, C=0f, H=0f;
800  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055f)/1.055f)*2.4f))).floatValue():rf[q]/12.92f;
801  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055f)/1.055f)*2.4f))).floatValue():gf[q]/12.92f;
802  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055f)/1.055f)*2.4f))).floatValue():bf[q]/12.92f;
803 
804  rf[q] = rf[q] * 100f;
805  gf[q] = gf[q] * 100f;
806  bf[q] = bf[q] * 100f;
807 
808  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
809  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
810  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
811 
812  float fX, fY, fZ;
813  // XYZ to Lab
814  //WAH normalize to L*a*b* color space using D65 white reference
815  // from Color_Space_Converter code: public double[] D65 = {95.0429, 100.0, 108.8900};
816 
817  X = X / 95.0429f;
818  Y = Y / 100.0f;
819  Z = Z / 108.89f;
820 
821  if ( X > 0.008856f )
822  fX = (new Double(Math.exp(Math.log(X)/3f))).floatValue();
823  else
824  fX = ((7.787f * X) + (16f/116f));
825 
826  if ( Y > 0.008856f )
827  fY = (new Double(Math.exp(Math.log(Y)/3f))).floatValue();
828  else
829  fY = ((7.787f * Y) + (16f/116f));
830 
831  if ( Z > 0.008856f )
832  fZ = (new Double(Math.exp(Math.log(Z)/3f))).floatValue();
833  else
834  fZ = ((7.787f * Z) + (16f/116f));
835 
836  float l = ( 116f * fY ) - 16f;
837  float a = 500f * ( fX - fY );
838  float b = 200f * ( fY - fZ );
839 
840  L = l;
841  C = new Double(Math.sqrt((a*a)+(b*b))).floatValue();
842 
843  if ( a == 0f ){ //This is a gray, no chroma...
844  H = 0f; //LCH results = 0 � 1
845  }
846  else{
847  if (a>=0f && b>=0f) H = new Double(Math.atan(b/a)).floatValue();
848  else if (a>=0f && b<0f) H = new Double(Math.atan(b/a) + Math.PI).floatValue();
849  else if (a<0f && b<0f) H = new Double(Math.atan(b/a) + Math.PI).floatValue();
850  else if (a<0f && b>=0f) H = new Double(Math.atan(b/a) + (2*Math.PI)).floatValue();
851  }
852  c1[q] = L;
853  c2[q] = C;
854  c3[q] = H;
855  }
856  }
857 
858 
859 
860 
861 
862  void showAbout() {
863  IJ.showMessage("About Colour_transform...",
864  "It converts an RGB image into a colour space stack.\n"
865  );
866  }
867 
868  void error() {
869  IJ.showMessage("Colour_transform", "This plugin converts an RGB image into \n"
870  +"a colour space stack.");
871  }
872 
873 }
Color_Transformer.run
void run(ImageProcessor ip)
Definition: Color_Transformer.java:78
-
Color_Transformer.getXYZ
void getXYZ()
Definition: Color_Transformer.java:224
-
Color_Transformer.getLab
void getLab()
Definition: Color_Transformer.java:412
-
Color_Transformer.getLCHLuv
void getLCHLuv()
Definition: Color_Transformer.java:652
-
Color_Transformer.getLSHLuv
void getLSHLuv()
Definition: Color_Transformer.java:721
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Color_Transformer.getAC1C2
void getAC1C2()
Definition: Color_Transformer.java:320
-
Color_Transformer.getYxy
void getYxy()
Definition: Color_Transformer.java:245
-
Color_Transformer.getLCHLab
void getLCHLab()
Definition: Color_Transformer.java:790
-
Color_Transformer.getYuv
void getYuv()
Definition: Color_Transformer.java:493
-
Color_Transformer
Definition: Color_Transformer.java:32
-
Color_Transformer.getYIQ
void getYIQ()
Definition: Color_Transformer.java:299
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Color_Transformer.getHSV
void getHSV()
Definition: Color_Transformer.java:617
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Color_Transformer.showDialog
boolean showDialog()
Definition: Color_Transformer.java:52
-
Color_Transformer.setup
int setup(String arg, ImagePlus imp)
Definition: Color_Transformer.java:45
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Color_Transformer.getI1I2I3
void getI1I2I3()
Definition: Color_Transformer.java:472
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Color_Transformer.getYUV
void getYUV()
Definition: Color_Transformer.java:278
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Color_Transformer.getYQ1Q2
void getYQ1Q2()
Definition: Color_Transformer.java:521
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Color_Transformer.getHSL
void getHSL()
Definition: Color_Transformer.java:580
- -
Color_Transformer.getHSI
void getHSI()
Definition: Color_Transformer.java:542
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Color_Transformer.getLuv
void getLuv()
Definition: Color_Transformer.java:352
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class  xmipp.viewer.models.ColumnInfo
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.models;
27 
28 import xmipp.jni.MDLabel;
29 import xmipp.jni.MetaData;
30 
32 public class ColumnInfo {
33 
34 
35  public int label;
36  public String labelName; //This is redundant, but for avoid a function call
37  public boolean visible;
38  public boolean render;
39  public boolean allowRender = false;
40  public boolean allowEdit = false;
41  public String comment;
42  public int type;
43 
46  public ColumnInfo(int label, String name, String comment, int type, boolean allowRender, boolean visible, boolean render, boolean allowEdit){
47  this.label = label;
48  this.labelName = name;
49  this.visible = visible;
50  this.render = render;
51  this.allowRender = allowRender;
52  this.comment = comment;
53  this.type = type;
54  this.allowEdit = allowEdit;
55  }
56 
57 
58  public ColumnInfo(int label, String name, String comment, int type, boolean allowRender,boolean allowEdit){
59  this(label, name, comment, type, allowRender, true, allowRender, allowEdit);
60  }
61 
62  public ColumnInfo(int label){
63  this(label, MetaData.getLabelName(label), MetaData.getLabelComment(label), MetaData.getLabelType(label), MetaData.isImage(label), true, false, true);
64  }
65 
66 
67  public ColumnInfo(int label, boolean visible){
68  this(label, MetaData.getLabelName(label), MetaData.getLabelComment(label), MetaData.getLabelType(label), MetaData.isImage(label), visible, false, true);
69  }
70 
71  public ColumnInfo(int label, boolean visible, boolean render){
72  this(label, MetaData.getLabelName(label), MetaData.getLabelComment(label), MetaData.getLabelType(label), MetaData.isImage(label), visible, render, true);
73  }
74 
78  public boolean updateInfo(ColumnInfo ci){
79  boolean result = labelName != ci.labelName || visible != ci.visible
80  || render != ci.render || allowEdit != ci.allowEdit;
81  visible = ci.visible;
82  render = ci.render;
83  allowEdit = ci.allowEdit;
84  labelName = ci.labelName;
85  return result;
86  }
87 
88  public String getLabelTypeString(){
89  try {
90 
91  return MetaData.getLabelTypeString(type);
92  }catch(Exception e){
93  e.printStackTrace();
94  }
95  return null;
96  }
97 
98 
99  public ColumnInfo clone(){
100  return new ColumnInfo(label, labelName, comment, type, allowRender, visible, render, allowEdit);
101  }
102 
103  @Override
104  public boolean equals(Object o){
105 
106  if (o == null) return false;
107  if (!getClass().equals(o.getClass())) return false;
108 
109  ColumnInfo col = (ColumnInfo)o;
110  return label == col.label &&
111  visible == col.visible &&
112  render == col.render;
113  }
114 
115  public boolean isEnable() {
116  return label == MDLabel.MDL_ENABLED || labelName.equals("enabled");
117  }
118 
119  public class ColumnExtraInfo {
120  public String color;
121  public String marker;
122  public String linestyle;
123  public boolean plot;
124 
125  public ColumnExtraInfo(String c){
126  color = c;
127  linestyle = "solid";
128  marker = "none";
129  plot = false;
130  }
131  }
132 
133  public String toString()
134  {
135  return labelName;
136  }
137 
138 
139 }//class ColumnInfo
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ColumnInfo(int label, boolean visible)
Definition: ColumnInfo.java:67
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static String getLabelName(int label)
Definition: MetaData.java:247
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ColumnInfo(int label, String name, String comment, int type, boolean allowRender, boolean allowEdit)
Definition: ColumnInfo.java:58
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static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
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boolean updateInfo(ColumnInfo ci)
Definition: ColumnInfo.java:78
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xmipp.viewer.models.ColumnInfo.ColumnInfo
ColumnInfo(int label, boolean visible, boolean render)
Definition: ColumnInfo.java:71
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xmipp.jni.MetaData.getLabelComment
static native String getLabelComment(int label)
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xmipp.jni.MetaData.getLabelTypeString
static String getLabelTypeString(int labelType)
Definition: MetaData.java:286
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xmipp.jni.MetaData.isImage
static native boolean isImage(int label)
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xmipp.jni.MetaData.getLabelType
static native int getLabelType(int label)
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xmipp.viewer.models.ColumnInfo.ColumnInfo
ColumnInfo(int label, String name, String comment, int type, boolean allowRender, boolean visible, boolean render, boolean allowEdit)
Definition: ColumnInfo.java:46
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class  xmipp.viewer.windows.ColumnsJDialog
 
class  xmipp.viewer.windows.ColumnsJDialog.ColumnsTableModel
 
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package  xmipp.viewer.windows
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import java.awt.Dimension;
29 import java.awt.GridBagConstraints;
30 import java.awt.GridBagLayout;
31 import java.awt.Insets;
32 import java.awt.event.ActionEvent;
33 import java.util.ArrayList;
34 import java.util.List;
35 
36 import javax.swing.BorderFactory;
37 import javax.swing.JButton;
38 import javax.swing.JPanel;
39 import javax.swing.JScrollPane;
40 import javax.swing.JTable;
41 import javax.swing.ListSelectionModel;
42 import javax.swing.event.ListSelectionEvent;
43 import javax.swing.event.ListSelectionListener;
44 import javax.swing.table.AbstractTableModel;
45 
46 import xmipp.ij.commons.XmippApplication;
47 import xmipp.jni.MetaData;
48 import xmipp.utils.XmippDialog;
49 import xmipp.utils.XmippWindowUtil;
50 import xmipp.viewer.models.ColumnInfo;
51 
52 public class ColumnsJDialog extends XmippDialog {
53  private static final long serialVersionUID = 1L;
54  private JTable tableColumns;
55  private JButton btnUp;
56  private JButton btnDown;
57  private ColumnsTableModel model;
58  // This will be used for check for results from the dialog
59  private List<ColumnInfo> rows;
60  boolean fireEvent = true;
61 
62  public ColumnsJDialog(GalleryJFrame parent) {
63  super(parent, "Columns", true);
64  initComponents();
65  }// constructor ColumnsJDialog
66 
67  public List<ColumnInfo> getColumnsResult() {
68  return rows;
69  }
70 
71  @Override
72  protected void createContent(JPanel panel){
73  setResizable(false);
74  panel.setLayout(new GridBagLayout());
75  GridBagConstraints gbc = new GridBagConstraints();
76  gbc.insets = new Insets(10, 10, 10, 10);
77  gbc.anchor = GridBagConstraints.WEST;
78 
79  JPanel groupstbpn = new JPanel();
80  JScrollPane sp = new JScrollPane();
81  groupstbpn.setBorder(BorderFactory
82  .createTitledBorder("Column properties"));
83  groupstbpn.add(sp);
84  sp.setOpaque(true);
85  model = new ColumnsTableModel(((GalleryJFrame)parent).getData().getLabelsInfo());
86  tableColumns = new JTable(model);
87  tableColumns
88  .setPreferredScrollableViewportSize(new Dimension(350, 200));
89  sp.setViewportView(tableColumns);
90  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 0));
91 
92  JPanel panelUpDown = new JPanel();
93  panelUpDown.setLayout(new GridBagLayout());
94  gbc.insets = new Insets(0, 0, 5, 5);
95  btnUp = XmippWindowUtil.getIconButton("up.gif", this);
96  panelUpDown.add(btnUp, XmippWindowUtil.getConstraints(gbc, 0, 0));
97  btnDown = XmippWindowUtil.getIconButton("down.gif", this);
98  panelUpDown.add(btnDown, XmippWindowUtil.getConstraints(gbc, 0, 1));
99  panel.add(panelUpDown, XmippWindowUtil.getConstraints(gbc, 1, 0));
100  // this buttons will be enabled after selection
101  enableUpDown(false);
102  // listen to selection changes (only one row selected)
103  tableColumns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
104  tableColumns.getSelectionModel().addListSelectionListener(
105  new ListSelectionListener() {
106  @Override
107  public void valueChanged(ListSelectionEvent e) {
108  enableUpDown(true);
109  }
110  });
111  formatTable();
112  }// function initComponents
113 
114  protected void formatTable() {
115  tableColumns.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
116  tableColumns.getColumnModel().getColumn(0).setPreferredWidth(200);
117  tableColumns.getColumnModel().getColumn(1).setPreferredWidth(50);
118  tableColumns.getColumnModel().getColumn(2).setPreferredWidth(50);
119  tableColumns.getColumnModel().getColumn(3).setPreferredWidth(50);
120 
121  }
122 
123  protected void enableUpDown(boolean value) {
124  btnUp.setEnabled(value);
125  btnDown.setEnabled(value);
126  }// function enableUpDown
127 
128  // move the selection on the table, -1 up, 0 down
129  protected void moveSelection(int deltha) {
130  int pos = tableColumns.getSelectedRow();
131  ColumnInfo ci = rows.remove(pos);
132  pos += deltha;
133  rows.add(pos, ci);
134  model.fireTableDataChanged();
135  tableColumns.setRowSelectionInterval(pos, pos);
136  }
137 
138  @Override
139  public void handleActionPerformed(ActionEvent evt){
140  JButton btn = (JButton) evt.getSource();
141 
142  if (btn == btnUp && tableColumns.getSelectedRow() > 0)
143  moveSelection(-1);
144  else if (btn == btnDown && tableColumns.getSelectedRow() < rows.size() - 1)
145  moveSelection(1);
146  }// function actionPerformed
147 
148  class ColumnsTableModel extends AbstractTableModel {
149  private static final long serialVersionUID = 1L;
150 
151  private String[] columns = { "Label", "Visible", "Render", "Edit" };
152 
153  public ColumnsTableModel(int[] labels) {
154  rows = new ArrayList<ColumnInfo>(labels.length);
155  for (int i = 0; i < labels.length; ++i)
156  rows.add(new ColumnInfo(labels[i]));
157  }
158 
159  public ColumnsTableModel(List<ColumnInfo> labelsInfo) {
160  int n = labelsInfo.size();
161  rows = new ArrayList<ColumnInfo>(n);
162  for (int i = 0; i < n; ++i)
163  rows.add(labelsInfo.get(i).clone());
164  }
165 
166  @Override
167  public Class getColumnClass(int column) {
168  return getValueAt(0, column).getClass();
169  }
170 
171  @Override
172  public String getColumnName(int columnIndex) {
173  return columns[columnIndex];
174  }
175 
176  @Override
177  public int getColumnCount() {
178  return columns.length;
179  }
180 
181  @Override
182  public int getRowCount() {
183  return rows.size();
184  // return frame.getParticlePicker().getFamilies().size();
185  }
186 
187  @Override
188  public boolean isCellEditable(int row, int column) {
189  try {
190  if (column == 2 && !rows.get(row).allowRender)
191  return false;
192  GalleryJFrame frame = (GalleryJFrame)parent;
193 
194  if (column == 3 && frame.data.isScipionInstance())
195  return false;
196  } catch (Exception e) {
197  e.printStackTrace();
198  }
199  return true;
200  }
201 
202  @Override
203  public void setValueAt(Object value, int row, int column) {
204  ColumnInfo col = rows.get(row);
205  switch (column) {
206  case 0:
207  col.labelName = ((String)value);
208  break;
209  case 1:
210  col.visible = (Boolean) value;
211  break;
212  case 2:
213  col.render = (Boolean) value;
214  break;
215  case 3:
216  col.allowEdit = (Boolean) value;
217  break;
218  }
219 
220  }
221 
222  @Override
223  public Object getValueAt(int row, int column) {
224  ColumnInfo col = rows.get(row);
225  switch (column) {
226  case 0:
227  return col.labelName;
228  case 1:
229  return col.visible;
230  case 2:
231  return col.render;
232  case 3:
233  return col.allowEdit;
234  }
235  return null;
236  }
237 
238  }// class ColumnsTableModel
239 
240 }// class ColumnsJDialog
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xmipp.viewer.windows.ColumnsJDialog.handleActionPerformed
void handleActionPerformed(ActionEvent evt)
Definition: ColumnsJDialog.java:139
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xmipp.viewer.windows.ColumnsJDialog.ColumnsJDialog
ColumnsJDialog(GalleryJFrame parent)
Definition: ColumnsJDialog.java:62
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xmipp.utils.XmippWindowUtil.getIconButton
static JButton getIconButton(String icon, ActionListener listener)
Definition: XmippWindowUtil.java:124
- -
xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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package  xmipp.viewer.ctf
 
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.viewer.ctf;
6 
7 import xmipp.utils.DEBUG;
8 import ij.IJ;
9 import java.io.BufferedReader;
10 import java.io.InputStreamReader;
11 import java.util.ArrayList;
12 
19 public class CommandTask implements Runnable {
20 
21  protected ArrayList<String> commands;
22  protected int row = -1;
23  protected iTaskCompletionListener commandsListener;
24 
25  public CommandTask(String command, int row,
26  iTaskCompletionListener commandsListener) {
27  this(command, commandsListener);
28  this.row = row;
29  }
30 
31  public CommandTask(String command, iTaskCompletionListener commandsListener) {
32  this(command);
33  this.commandsListener = commandsListener;
34  }
35 
36  public CommandTask(String command) {
37  //System.out.println(command);
38  commands = new ArrayList<String>();
39  addCommand(command);
40  }
41 
42  public void start() {
43  Thread t = new Thread(this);
44  t.start();
45  }
46 
47  public void run() {
48  try {
49  runTask();
50  } catch (Exception ex) {
51  IJ.error("Error running command: " + ex.getMessage());
52  } finally {
53  if (commandsListener != null) {
54  commandsListener.done(this);
55  }
56  }
57  }
58 
59  public void addCommand(String command){
60  commands.add(command);
61  }
62 
63  private void runTask() throws Exception {
64  for (String command : commands) {
65  DEBUG.printMessage(">> " + command);
66  Process p = Runtime.getRuntime().exec(command);
67 
68  BufferedReader stdInput = new BufferedReader(new InputStreamReader(
69  p.getInputStream()));
70 
71  // read the output from the command
72  String s;
73  while ((s = stdInput.readLine()) != null) {
74  DEBUG.printMessage(s);
75  }
76  }
77  }
78 }
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xmipp.viewer.ctf.CommandTask.CommandTask
CommandTask(String command, int row, iTaskCompletionListener commandsListener)
Definition: CommandTask.java:25
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iTaskCompletionListener commandsListener
Definition: CommandTask.java:23
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ArrayList< String > commands
Definition: CommandTask.java:21
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void addCommand(String command)
Definition: CommandTask.java:59
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static void printMessage(String message)
Definition: DEBUG.java:18
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CommandTask(String command, iTaskCompletionListener commandsListener)
Definition: CommandTask.java:31
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enum  xmipp.utils.CompoundIcon.Axis
 
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1 package xmipp.utils;
2 
3 import java.awt.Component;
4 import java.awt.Graphics;
5 
6 import javax.swing.Icon;
7 
8 
21 public class CompoundIcon implements Icon
22 {
23  public enum Axis
24  {
25  X_AXIS,
26  Y_AXIS,
27  Z_AXIS;
28  }
29 
30  public final static float TOP = 0.0f;
31  public final static float LEFT = 0.0f;
32  public final static float CENTER = 0.5f;
33  public final static float BOTTOM = 1.0f;
34  public final static float RIGHT = 1.0f;
35 
36  private Icon[] icons;
37 
38  private Axis axis;
39 
40  private int gap;
41 
42  private float alignmentX = CENTER;
43  private float alignmentY = CENTER;
44 
52  public CompoundIcon(Icon... icons)
53  {
54  this(Axis.X_AXIS, icons);
55  }
56 
65  public CompoundIcon(Axis axis, Icon... icons)
66  {
67  this(axis, 0, icons);
68  }
69 
79  public CompoundIcon(Axis axis, int gap, Icon... icons)
80  {
81  this(axis, gap, CENTER, CENTER, icons);
82  }
83 
96  public CompoundIcon(Axis axis, int gap, float alignmentX, float alignmentY, Icon... icons)
97  {
98  this.axis = axis;
99  this.gap = gap;
100  this.alignmentX = alignmentX > 1.0f ? 1.0f : alignmentX < 0.0f ? 0.0f : alignmentX;
101  this.alignmentY = alignmentY > 1.0f ? 1.0f : alignmentY < 0.0f ? 0.0f : alignmentY;
102 
103  for (int i = 0; i < icons.length; i++)
104  {
105  if (icons[i] == null)
106  {
107  String message = "Icon (" + i + ") cannot be null";
108  throw new IllegalArgumentException( message );
109  }
110  }
111 
112  this.icons = icons;
113  }
114 
120  public Axis getAxis()
121  {
122  return axis;
123  }
124 
130  public int getGap()
131  {
132  return gap;
133  }
134 
140  public float getAlignmentX()
141  {
142  return alignmentX;
143  }
144 
150  public float getAlignmentY()
151  {
152  return alignmentY;
153  }
154 
160  public int getIconCount()
161  {
162  return icons.length;
163  }
164 
172  public Icon getIcon(int index)
173  {
174  return icons[ index ];
175  }
176 //
177 // Implement the Icon Interface
178 //
184  @Override
185  public int getIconWidth()
186  {
187  int width = 0;
188 
189  // Add the width of all Icons while also including the gap
190 
191  if (axis == Axis.X_AXIS)
192  {
193  width += (icons.length - 1) * gap;
194 
195  for (Icon icon : icons)
196  width += icon.getIconWidth();
197  }
198  else // Just find the maximum width
199  {
200  for (Icon icon : icons)
201  width = Math.max(width, icon.getIconWidth());
202  }
203 
204  return width;
205  }
206 
212  @Override
213  public int getIconHeight()
214  {
215  int height = 0;
216 
217  // Add the height of all Icons while also including the gap
218 
219  if (axis == Axis.Y_AXIS)
220  {
221  height += (icons.length - 1) * gap;
222 
223  for (Icon icon : icons)
224  height += icon.getIconHeight();
225  }
226  else // Just find the maximum height
227  {
228  for (Icon icon : icons)
229  height = Math.max(height, icon.getIconHeight());
230  }
231 
232  return height;
233  }
234 
243  @Override
244  public void paintIcon(Component c, Graphics g, int x, int y)
245  {
246  if (axis == Axis.X_AXIS)
247  {
248  int height = getIconHeight();
249 
250  for (Icon icon : icons)
251  {
252  int iconY = getOffset(height, icon.getIconHeight(), alignmentY);
253  icon.paintIcon(c, g, x, y + iconY);
254  x += icon.getIconWidth() + gap;
255  }
256  }
257  else if (axis == Axis.Y_AXIS)
258  {
259  int width = getIconWidth();
260 
261  for (Icon icon : icons)
262  {
263  int iconX = getOffset(width, icon.getIconWidth(), alignmentX);
264  icon.paintIcon(c, g, x + iconX, y);
265  y += icon.getIconHeight() + gap;
266  }
267  }
268  else // must be Z_AXIS
269  {
270  int width = getIconWidth();
271  int height = getIconHeight();
272 
273  for (Icon icon : icons)
274  {
275  int iconX = getOffset(width, icon.getIconWidth(), alignmentX);
276  int iconY = getOffset(height, icon.getIconHeight(), alignmentY);
277  icon.paintIcon(c, g, x + iconX, y + iconY);
278  }
279  }
280  }
281 
282  /*
283  * When the icon value is smaller than the maximum value of all icons the
284  * icon needs to be aligned appropriately. Calculate the offset to be used
285  * when painting the icon to achieve the proper alignment.
286  */
287  private int getOffset(int maxValue, int iconValue, float alignment)
288  {
289  float offset = (maxValue - iconValue) * alignment;
290  return Math.round(offset);
291  }
292 }
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Definition: CompoundIcon.java:31
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CompoundIcon(Axis axis, Icon... icons)
Definition: CompoundIcon.java:65
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Definition: CompoundIcon.java:52
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static final float TOP
Definition: CompoundIcon.java:30
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static final float BOTTOM
Definition: CompoundIcon.java:33
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static final float CENTER
Definition: CompoundIcon.java:32
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Definition: CompoundIcon.java:96
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void paintIcon(Component c, Graphics g, int x, int y)
Definition: CompoundIcon.java:244
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static final float RIGHT
Definition: CompoundIcon.java:34
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Definition: CompoundIcon.java:79
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.viewer.particlepicker.training;
8 
9 import java.util.logging.Level;
10 import xmipp.jni.MDRow;
11 import xmipp.jni.Particle;
12 import xmipp.jni.PickingClassifier;
13 import xmipp.utils.XmippDialog;
14 import xmipp.utils.XmippWindowUtil;
15 import xmipp.viewer.particlepicker.ParticlePicker;
16 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame;
17 import xmipp.viewer.particlepicker.training.model.MicrographState;
18 import xmipp.viewer.particlepicker.training.model.Mode;
19 import xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker;
20 import xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph;
21 
22 import javax.swing.*;
23 
28 public class CorrectAndAutopickRunnable implements Runnable
29  {
30 
31  private final MDRow[] manualRows;
32  private final MDRow[] automaticRows;
33  private Particle[] autopickRows;
34 
35  private SupervisedPickerMicrograph next;
36  private SupervisedPickerJFrame frame;
37  private final SupervisedParticlePicker picker;
38  private final PickingClassifier classifier;
39 
40 
41  public CorrectAndAutopickRunnable(SupervisedPickerJFrame frame, MDRow[] manualRows, MDRow[] automaticRows,
42  SupervisedPickerMicrograph next)
43  {
44  this.frame = frame;
45  this.manualRows = manualRows;
46  this.automaticRows = automaticRows;
47  this.next = next;
48  this.picker = frame.getParticlePicker();
49  this.classifier = (PickingClassifier)picker.getClassifier();
50  }
51 
52  public void run()
53  {
54  try
55  {
56  classifier.correct(manualRows, automaticRows);
57 
58  if (picker.getMode() == Mode.Supervised && next.getState() == MicrographState.Supervised)
59  {
60  next.getAutomaticParticles().clear();
61  next.setAutopickpercent(picker.getAutopickpercent());
62  autopickRows = classifier.autopick(next.getFile(), next.getAutopickpercent());
63  picker.loadParticles(next, autopickRows);
64  picker.saveData(next);
65  // Runs inside of the Swing UI thread
66  SwingUtilities.invokeLater(new Runnable() {
67  public void run() {
68  frame.setChanged(false);
69  }
70  });
71 
72  }
73 
74 
75  // Runs inside of the Swing UI thread
76  SwingUtilities.invokeLater(new Runnable() {
77  public void run() {
78  // Select the worse particle as active
79  frame.getCanvas().refreshActive(null);
80  frame.getCanvas().repaint();
81  frame.getCanvas().setEnabled(true);
82  XmippWindowUtil.releaseGUI(frame.getRootPane());
83  frame.updateMicrographsModel(true);
84  }
85  });
86 
87  }
88  catch(Exception e)
89  {
90 
91  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
92  SwingUtilities.invokeLater(new Runnable() {
93  public void run() {
94  XmippDialog.showError(frame, "Classifier error");
95  }
96  });
97 
98  }
99  }
100  }
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void loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
Definition: SupervisedParticlePicker.java:1102
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static void releaseGUI(JRootPane panel)
Definition: XmippWindowUtil.java:242
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boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.viewer.particlepicker.ParticlePickerCanvas.refreshActive
abstract void refreshActive(PickerParticle p)
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xmipp.viewer.particlepicker.training.CorrectAndAutopickRunnable.CorrectAndAutopickRunnable
CorrectAndAutopickRunnable(SupervisedPickerJFrame frame, MDRow[] manualRows, MDRow[] automaticRows, SupervisedPickerMicrograph next)
Definition: CorrectAndAutopickRunnable.java:41
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xmipp.jni.PickingClassifier.autopick
synchronized native Particle [] autopick(String micrograph, int percent)
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1 package xmipp.viewer.particlepicker;
2 
3 public class CtfInfo {
4 
5  public String psd;
6  public String ctf;
7  public Float voltage;
8  public Float defocusU;
9  public Float resolution;
10  public Float fitQuality;
11 }
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.utils;
10 public class DEBUG {
11 
12  private static boolean DEBUG = false;
13 
14  public static void enableDebug(boolean enable) {
15  DEBUG = enable;
16  }
17 
18  public static void printMessage(String message) {
19  if (DEBUG) {
20  System.out.println(message);
21  }
22  }
23 
24  public static void printFormat(String format, Object...objects){
25  if (DEBUG){
26  System.out.format(format+"\n", objects);
27  }
28  }
29 
30  public static void printException(Exception ex) {
31  if (DEBUG) {
32  ex.printStackTrace();
33  }
34  }
35 
36  public static void printStackTrace() {
37  if (DEBUG){
38  Exception ex = new Exception();
39  ex.printStackTrace();
40  }
41  }
42 
43  public static boolean hasScipionDebug() {
44  String debug = System.getenv("SCIPION_DEBUG");
45  return (debug != null && debug.equals("1"));
46  }
47 
48  //Timing
49  public static long millisecs;
50 
51  public static long tic(){
52  millisecs = System.currentTimeMillis();
53  return millisecs;
54  }
55 
56  public static long toc(){
57  long current = System.currentTimeMillis();
58  long result = current - millisecs;
59  millisecs = current;
60  System.out.format("took: %d milliseconds %n", result);
61  return result;
62  }
63 
64 }
xmipp.utils.DEBUG.millisecs
static long millisecs
Definition: DEBUG.java:49
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static long toc()
Definition: DEBUG.java:56
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static boolean hasScipionDebug()
Definition: DEBUG.java:43
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static void printFormat(String format, Object...objects)
Definition: DEBUG.java:24
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Definition: DEBUG.java:30
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static long tic()
Definition: DEBUG.java:51
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static void printStackTrace()
Definition: DEBUG.java:36
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Definition: DEBUG.java:14
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Definition: DEBUG.java:18
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1 import java.io.*;
2 import java.util.*; // for the Vector and Hashtable classes
3 import java.awt.*;
4 import ij.*;
5 import ij.plugin.*;
6 import ij.process.*;
7 import ij.io.*;
8 import ij.measure.*;
9 //import ij.IJ.*;
10 
11 // ------------------------------------------
12 // DM3_Reader.java
13 // ------------------------------------------
14 // This plugin will read DM3 files produced by Gatan Digital Micrograph
15 // Decoding is based on info gleaned from the EMAN project based at Baylor
16 // Made a start using the Analyze_Reader plugin by Guy Williams and
17 // the Biorad_Reader as a base, but not that much remains.
18 // The guts were significantly inspired by the GatanDM3.C and
19 // GatanDM3.h files of the EMAN project source code:
20 // http://ncmi.bcm.tmc.edu/~stevel/EMAN/doc/
21 // ------------------------------------
22 // Greg Jefferis,
23 // Dept Biological Sciences,
24 // Stanford University
25 // jefferis@stanford.edu
26 // -------------------------------------------
27 // as of v1.0.1 030615
28 // -------------------------------------------
29 // - reads 16 bit images only,
30 // - correctly parses all simple tags
31 // - Places tags in File/Show Info
32 // including acquisition time / sample date etc.
33 // - allows spatial calibration of images
34 // - sets minimum and maximum intensity
35 // ------------------------------------
36 // as of v1.1 030615
37 // - went back to making it an ImagePlus extension
38 // ------------------------------------
39 // as of v1.2.6 030618
40 // - Corrected a bad bug - The offset for the image data was off
41 // by +1
42 // - AND I never told the image opener whether the image data was
43 // in little endian format or not.
44 // - So what I was doing was reading one byte from pixel n and one from pixel n+1!
45 // (which looked more or less like the correct number in big-endian)
46 // - Added my best guess for what ImageJ image type should be set for
47 // the standard data types
48 // - Changed load(), parseDM3() and getDM3FileInfo functions to receive
49 // directory and FileName as parameters - that way load() can be called
50 // directly bypassing the run() function.
51 // ------------------------------------
52 // v 1.2.7 030621
53 // - Most functions were previously defined as public, now restricted
54 // to those that might actually get an external call
55 // - read through code once making a few small tidies and improving comments
56 // ------------------------------------
57 // v 1.2.8 030624
58 // - Improved ability to set min/max brightness of image according to information
59 // in the Gatan file after bug report from Charles Daghlian at Dartmouth.
60 // This takes place at the end of the load()function.
61 // ------------------------------------
62 // v 1.2.9 030625
63 // - Fixed handling of signed 16 bit and 32 bit images by using the
64 // FileInfo.GRAY16_SIGNED and FileInfo.GRAY32_INT constants
65 // & keeping the Calibration object generated by ImageJ when the image
66 // is loaded rather than creating my own from scratch - I had been
67 // throwing away the brightness calibration which ImageJ does on
68 // 16 bit signed images as a result.
69 // & supplying _raw_ values of loVal and hiVal to setMinAndMax()
70 // ------------------------------------
71 // v 1.3.0 030625
72 // - Removed calls to functions introduced since Java 1.1 to allow
73 // plugin to run on OS9 Macs with Java 1.1.7
74 // - However as far as I can see there is a bug in MRJ that prevents
75 // UTF-16 conversion from occurring so unicode strings in the
76 // DM3 tags don't import. Instead there will be a string saying
77 // "couldn't read string blah". This is annoying because the
78 // calibration units are given as a unicode string.
79 // ------------------------------------
80 // v 1.3.1 030625
81 // - Fixed UTF-16 conversion bug in MRJ by writing a quick and dirty unicode
82 // reader to be used if the UTF-16 conversion fails. Now correctly
83 // sets the spatial calibration on OS9
84 // - Another thing that I noticed was that it seemed to be important to
85 // compile with v1.3.1 if one wanted to use the class with v1.1.7
86 // ------------------------------------
87 // v 1.3.2 030808
88 // - Fixed a bug in getDM3FileInfo which meant that the last rather than
89 // the largest image in the DM3 file was chosen
90 // - Fixed a bug in getDM3CalibrationInfo which caused a failure to
91 // recognise "nm" as a valid calibration unit - the problem was caused
92 // by doing (unit == "nm") instead of (unit.equals("nm"))
93 // ------------------------------------
94 // v 1.3.3 030821
95 // - Fixed a remaining bug in the image selection routine which now
96 // works for all files that I have available to test.
97 // ------------------------------------
98 // v 1.3.4 040506
99 // - Fixed a bug reading in USHORT image data. The problem was that
100 // USHORT data and strings are hard to tell apart. Although Image Data
101 // can be identified categorically, other lumps of data (e.g. LUTs)
102 // scattered throughout the file are harder to spot and will cause problems
103 // if read as a string. Have compromised by reading as string if:
104 // + it isn't image data
105 // + but is an unsigned short array
106 // + of less than 256 bytes
107 // ------------------------------------
108 // v 1.3.4 051213 (Yes the 2nd v1.3.4 - hadn't noticed a branch!)
109 // - Fixed a bug which prevented units other than µm or nm being passed to
110 // calibration object. Occasioned by a file with units 1/nm
111 // ------------------------------------
112 // v 1.3.5 051213
113 // - Adding handling of DIFFRACTION mode images (ie reciprocal space) by
114 // setting FHT property and copying
115 // calibration object. Occasioned by a file with units 1/nm
116 // ------------------------------------
117 // v 1.3.6 060904
118 // - Added storing of struct fields to tag list
119 // They are displayed as tag= {1,2,3,4}
120 // This means that Digital Micrograph selection rectangles
121 // can now be identified from Show Info
122 // ------------------------------------
123 // v 1.3.7 070831
124 // - debugLevel is now set according to IJ.debugMode
125 // (accesible from Edit ... Options ... Misc)
126 // - Can now open data type 23 (RGBA_UINT8_3_DATA) images
127 // ------------------------------------
128 // v 1.3.8 080326
129 // - Fixed a bug in which tag hashes were not cleared when reading a new file
130 // - Small speed improvement by converting tags to String via StringBuffer
131 // - Both thanks to report by Eric Olson at UIUC
132 
133 public class DM3_Reader extends ImagePlus implements PlugIn
134 {
135  // Decide whether to use Gatan's information for determining the min
136  // and maximum brightness thresholds for display or leave to ImageJ
137  // I find Gatan more reliable
138  public boolean useGatanMinMax = true;
139 
140  private boolean littleEndian = true; // default for .dm3 files
141  // nb all tags are written big-endian, it is only the actual data
142  // attached to each tag that may be little-endian (and will be for PC files)
143  //private String directory;
144  //private String fileName;
145  private RandomAccessFile f; // This stream will be used for reading by parseDM3()
146 
147  private FileInfo fi;
148 
149  private String notes = ""; // I will store interesting file info in here
150 
151  // 0=none, 1-3=basic, 4-5=simple, 6-10 verbose
152  private static final int debugLevel = IJ.debugMode?10:0;
153 
154  // the number of the chosen image in the DM3 file
155  // since there apparently may be several - usually at least a thumbnail
156  // I will select the largest image. If there are multiple images
157  // of the same size, the first will be chosen.
158  private int chosenImage = 1;
159 
160  private int curGroupLevel=-1; // Track how deep is the group we are currently reading
161  private static final int MAXDEPTH = 64; // Maximum number of levels of tags
162  private int[] curGroupAtLevelX=new int[MAXDEPTH]; // To track group at current level
163  private String[] curGroupNameAtLevelX=new String[MAXDEPTH]; // To track group name at current level
164 
165  private int[] curTagAtLevelX=new int[MAXDEPTH]; // To track tag number at current level
166  private String curTagName = ""; // the name of the current tag data item
167 
168  // Will use these to store tags
169  private Vector storedTags = new Vector();
170  private Hashtable tagHash = new Hashtable();
171 
172  // Set up constants for the different encoded data types used in DM3 files
173  private static final int SHORT = 2;
174  private static final int LONG = 3;
175  private static final int USHORT = 4;
176  private static final int ULONG = 5;
177  private static final int FLOAT = 6;
178  private static final int DOUBLE = 7;
179  private static final int BOOLEAN = 8;
180  private static final int CHAR = 9;
181  private static final int OCTET = 10;
182  private static final int STRUCT = 15;
183  private static final int STRING = 18;
184  private static final int ARRAY = 20;
185 
186  // This the lhs of Image list tags
187  private static final String IMGLIST = "root.ImageList.";
188  // This is the lhs for Document Object List Tags
189  // root.DocumentObjectList.0.AnnotationGroupList.0.AnnotationType = 31
190  private static final String OBJLIST = "root.DocumentObjectList.";
191 
192  public void run(String arg) {
193  String directory = "";
194  String fileName = arg;
195  //if (debugLevel>5);
196 
197  if (debugLevel>5) IJ.write("IN:dir = "+directory+", file="+fileName);
198  if ((arg==null) || (arg==""))
199  { // Choose a file since none specified
200  OpenDialog od = new OpenDialog("Load DM3 File...", arg);
201  fileName = od.getFileName();
202  if (fileName==null)
203  return;
204  directory = od.getDirectory();
205  if (debugLevel>5) IJ.write("IF:dir = "+directory+", file="+fileName);
206  }
207  else
208  { // we were sent a filename to open
209  File dest = new File(arg);
210  directory = dest.getParent();
211  fileName = dest.getName();
212  if (debugLevel>5) IJ.write("ELSE:dir = "+directory+", file="+fileName);
213  }
214 
215  // Load in the image
216  ImagePlus imp = load(directory, fileName);
217  if (imp==null) return;
218 
219  // Attach the Image Processor
220  setProcessor(fileName, imp.getProcessor());
221  // Copy the scale info over
222  copyScale(imp);
223  // Copy the Show Info field over
224  setProperty("Info",imp.getProperty("Info"));
225  // and the FHT property (to handle diffraction mode images)
226  if(imp.getProperty("FHT")!=null) setProperty("FHT", imp.getProperty("FHT"));
227 
228  // Show the image if it was selected by the file
229  // chooser, don't if an argument was passed ie
230  // some other ImageJ process called the plugin
231  if (arg.equals("")) show();
232  }
233 
234  public ImagePlus load(String directory, String fileName) /*throws IOException*/ {
235 
236  if ((fileName == null) || (fileName == "")) return null;
237 
238  if (!directory.endsWith(File.separator)) directory += File.separator;
239 
240  IJ.showStatus("Loading DM3 File: " + directory + fileName);
241 
242  // Clear the lists of tags in which additional info will be stored
243  tagHash.clear();
244  storedTags.clear();
245  // Try calling the parse routine
246  try{ parseDM3(directory, fileName);}
247  catch (Exception e) {
248  IJ.showStatus("parseDM3() error");
249  IJ.showMessage("DM3_Reader", ""+e);
250  return null;
251  }
252 
253  // Make a blank file information object
254  fi = new FileInfo();
255 
256  // Go and fetch the DM3 specific file Information
257  try {fi=getDM3FileInfo(directory, fileName);}
258  // This is in case of trouble parsing the tag table
259  catch (Exception e) {
260  IJ.showStatus("");
261  IJ.showMessage("DM3_Reader", "gDM3:"+e);
262  return null;
263  }
264 
265  // Write out Calculated Offset if reqd
266  if(debugLevel>1) IJ.write("Calculated offset = "+fi.offset);
267  if(debugLevel>1) IJ.write("Chosen image = "+chosenImage);
268 
269  // Open the image!
270  FileOpener fo = new FileOpener(fi);
271  ImagePlus imp = fo.open(false);
272  //if(debugLevel>5) if(imp==null) IJ.write("Image load failed!");
273 
274  // Write out the contents of the storedTags list
275  // and set the value of notes
276  StringBuffer notesBuffer=new StringBuffer();
277  for (int i = 0; i<storedTags.size();i++){
278  // Can decide whether I want to do this
279  //IJ.log((String) storedTags.elementAt(i));
280  notesBuffer.append( (String) storedTags.elementAt(i) + "\n");
281  }
282  notes=notesBuffer.toString();
283  if (!notes.equals("")) imp.setProperty("Info", notes);
284 
285  // Set (spatial) calibration
286  // nb pass the current calibration in case that contains useful info
287  // already (such as a brightness calibration)
288  try {
289  imp.setCalibration(getDM3CalibrationInfo(imp.getCalibration()));
290  }
291  catch (Exception e) {
292  IJ.showStatus("No Calibration info in "+fileName);
293  }
294  // If this is a diffraction (ie reciprocal space) image then set the
295  // FHT property so that ImageJ displays inverse scale
296  String imagingMode = (String) tagHash.get(IMGLIST+chosenImage+".ImageTags.Microscope Info.Imaging Mode");
297  if (imagingMode!=null && imagingMode.toUpperCase().equals("DIFFRACTION")){
298  imp.setProperty("FHT", "Dummy FHT");
299  }
300 
301 
302  // Set the min and max brightness for display purposes
303  // from DM3 header info if required - ImageJ can do this
304  // but is less robust
305  if(useGatanMinMax) {
306  // now searches through all tags
307  // after bug report by <Charles.P.Daghlian@Dartmouth.EDU>
308  double hiVal=0.0, loVal=0.0;
309  // Iterate over components of the taglist
310  // looking for the image brightness tag
311  // all this because I don't know how to partially match a hash key
312  for (Enumeration e = tagHash.keys() ; e.hasMoreElements() ;) {
313  String thisElementString = (String) e.nextElement();
314 
315  if( (thisElementString).endsWith("ImageDisplayInfo.HighLimit"))
316  hiVal = ((Float) tagHash.get(thisElementString)).doubleValue();
317  if( (thisElementString).endsWith("ImageDisplayInfo.LowLimit"))
318  loVal = ((Float) tagHash.get(thisElementString)).doubleValue();
319  }
320 
321  // If we found at least one, then set the min max brightness
322  if (hiVal!=0.0 || loVal!=0.0) {
323  // min,max are set through the image processor, so get it
324  ImageProcessor ip = imp.getProcessor();
325  // set them - nb setMinMax expects raw pixel values
326  // if a brightness calibration is in force then getRawValue()
327  // does the appropriate conversion
328  ip.setMinAndMax(imp.getCalibration().getRawValue(loVal),imp.getCalibration().getRawValue(hiVal));
329  }
330  }
331 
332  return imp;
333  }
334 
335  void parseDM3(String directory, String fileName) throws IOException {
336  // This reads through the DM3 file, extracting useful tags
337  // which allow one to determine the data offset etc.
338 
339  // alternative way to read from file - allows seeks!
340  // and therefore keeps track of position (use long getFilePointer())
341  // also has DataInput Interface allowing
342  // reading of specific types
343  f = new RandomAccessFile(directory+fileName,"r");
344  if(debugLevel>0) IJ.write("Directory = "+directory);
345  if(debugLevel>0) IJ.write("File = "+fileName);
346 
347  // Get the first 3 4byte ints from Header to find out
348  // FileVersion (which must be 3)
349  int fileVersion = f.readInt();
350  if (fileVersion!=3) throw new IOException("This does not seem to be a DM3 file");
351 
352  if(debugLevel>5) IJ.write("File Version"+fileVersion);
353 
354  // ... file size
355  int FileSize=f.readInt();
356  int lE=f.readInt();
357 
358  if(debugLevel>5) IJ.write("lE "+lE);
359 
360  // ... and whether it was written in little endian (PC) format or not
361  // (Mac and Java output are big endian)
362  if(lE==1) {
363  littleEndian=true;
364  }
365  else {
366  if(lE==0) littleEndian=false;
367  else {
368  throw new IOException("This does not seem to be a DM3 file");
369  }
370  }
371 
372  // The DM3 file has an unnamed root group which contains everything in the file
373  curGroupNameAtLevelX[0] = "root"; // Set the name of the root group
374 
375  // Now go read it (and all of its sub groups.
376  readTagGroup();
377 
378  // Close the input stream
379  f.close();
380  }
381 
382  FileInfo getDM3FileInfo(String directory, String fileName) throws IOException {
383  // this gets the basic file information using the contents of the tag
384  // tables created by parseDM3()
385 
386  // Set the basic file information
387  FileInfo fi = new FileInfo();
388  fi.fileFormat = fi.RAW;
389  fi.fileName = fileName;
390  fi.directory = directory;
391  // Originally forgot to do this - tells ImageJ what endian form the actual
392  // image data is in
393  fi.intelByteOrder=littleEndian;
394 
395  chosenImage = 0;
396  // Look for largest Image and assume that is the one we want
397  int i=0; // nb the first image is image = 0
398  long largestDataSizeSoFar=0;
399 
400  // Iterate over images keeping a note of the largest image so far
401  while (true) {
402  // The specific part of the key we are looking for
403  String rString=".ImageData.Data.Size";
404  if(debugLevel>1) IJ.write("Looking for:"+IMGLIST+i+rString);
405 
406  // Can we find information for image i
407  if(tagHash.containsKey(IMGLIST+i+rString)) {
408  if(debugLevel>1) IJ.write("Found:"+IMGLIST+i+rString);
409  // how big is this image?
410  long dataSize = ((Long) tagHash.get(IMGLIST+i+rString)).longValue();
411  if(debugLevel>1) IJ.write("Current Data Size"+dataSize);
412 
413  // Is it the largest so far?
414  if(dataSize>largestDataSizeSoFar) {
415  // Choose this image
416  largestDataSizeSoFar=dataSize;
417  if(debugLevel>1) IJ.write("New Largest Data Size:"+largestDataSizeSoFar);
418  chosenImage=i;
419  if(debugLevel>1) IJ.write("New Chosen Image:"+chosenImage);
420  }
421 
422  i++; // move on to the next image
423  } else {
424  break; // we ran out of images
425  }
426  }
427 
428  /* Here are the ImageData.DataType definitions from GatanDM3.h
429  class DataType {
430  public:
431  enum Type {
432  0= NULL_DATA,
433  1= SIGNED_INT16_DATA,
434  ... REAL4_DATA,
435  COMPLEX8_DATA,
436  OBSELETE_DATA,
437  PACKED_DATA,
438  UNSIGNED_INT8_DATA,
439  SIGNED_INT32_DATA,
440  RGB_DATA,
441  SIGNED_INT8_DATA,
442  UNSIGNED_INT16_DATA,
443  UNSIGNED_INT32_DATA,
444  REAL8_DATA,
445  COMPLEX16_DATA,
446  BINARY_DATA,
447  RGB_UINT8_0_DATA,
448  RGB_UINT8_1_DATA,
449  RGB_UINT16_DATA,
450  RGB_FLOAT32_DATA,
451  RGB_FLOAT64_DATA,
452  RGBA_UINT8_0_DATA,
453  RGBA_UINT8_1_DATA,
454  RGBA_UINT8_2_DATA,
455  RGBA_UINT8_3_DATA,
456  RGBA_UINT16_DATA,
457  RGBA_FLOAT32_DATA,
458  RGBA_FLOAT64_DATA,
459  POINT2_SINT16_0_DATA,
460  POINT2_SINT16_1_DATA,
461  POINT2_SINT32_0_DATA,
462  POINT2_FLOAT32_0_DATA,
463  RECT_SINT16_1_DATA,
464  RECT_SINT32_1_DATA,
465  RECT_FLOAT32_1_DATA,
466  RECT_FLOAT32_0_DATA,
467  SIGNED_INT64_DATA,
468  UNSIGNED_INT64_DATA,
469  LAST_DATA
470  };
471 
472  };
473  */
474  // OK pick the DataType
475  int dataType = ((Integer) tagHash.get(IMGLIST+chosenImage+".ImageData.DataType")).intValue();
476 
477  // I have made my best guess for types 1-14
478  // ie SIGNED_INT16_DATA to BINARY_DATA
479  // but I don't know how to implement the remainder
480  switch(dataType){
481  case 1: // SIGNED_INT16_DATA
482  fi.fileType=FileInfo.GRAY16_SIGNED;
483  break;
484  case 10: // UNSIGNED_INT16_DATA
485  fi.fileType=FileInfo.GRAY16_UNSIGNED;
486  break;
487 
488  case 2: // REAL4_DATA
489  fi.fileType=FileInfo.GRAY32_FLOAT;
490  break;
491 
492  //case 9: // or SIGNED_INT8_DATA
493  // NB ImageJ only handles unsigned ints - initially was treating
494  // these as unsigned, but in the end decided to remove for safety
495 
496  case 6: // UNSIGNED_INT8_DATA
497  fi.fileType=FileInfo.GRAY8;
498  break;
499 
500  case 7: // SIGNED_INT32_DATA
501  fi.fileType=FileInfo.GRAY32_INT;
502  break;
503  case 11: // UNSIGNED_INT32_DATA
504  fi.fileType=FileInfo.GRAY32_UNSIGNED;
505  break;
506 
507  case 8: // RGB_DATA
508  fi.fileType=FileInfo.RGB;
509  break;
510 
511  case 14: // BINARY_DATA
512  fi.fileType=FileInfo.BITMAP;
513  break;
514  case 23: // RGBA_UINT8_3_DATA
515  // NB it is uncertain if this data type corresponds exactly to ImageJ's ARGB
516  // A definitely comes first but the RGB values could be scrambled
517  // (since they were all equal on my test image)
518  fi.fileType=FileInfo.ARGB;
519  break;
520 
521  default:
522  throw new IOException("Unimplemented ImageData dataType="+dataType+" in DM3 file. See getDM3FileInfo() for details");
523  }
524 
525  // Get the dimensions of the image for the chosen image
526  // I'm assuming they are ordered width then height
527  fi.width = ((Integer) tagHash.get(IMGLIST+chosenImage+".ImageData.Dimensions.0")).intValue();
528  fi.height = ((Integer) tagHash.get(IMGLIST+chosenImage+".ImageData.Dimensions.1")).intValue();
529 
530  // Get the offset of the Image Data for chosen image
531  fi.offset = ((Long) tagHash.get(IMGLIST+chosenImage+".ImageData.Data.Offset")).intValue();
532 
533  return fi;
534  }
535 
536  Calibration getDM3CalibrationInfo(Calibration cal){
537  // get the spatial calibration information
538  // could also do brightness
539  // (actually a calibration fn is applied by ImageJ according
540  // to the image Type - GRAY16_SIGNED has 32768 removed in calibration
541 
542  // Figure out what the units are - need to check if nm is correct and
543  // if other units are likely
544  // also will µm get corrupted? may be necessary to do a unicode comparison
545  String unit = (String) tagHash.get(IMGLIST+chosenImage+".ImageData.Calibrations.Dimension.0.Units");
546 
547  // Reciprocal space images - return the original unit - reciprocal
548  // space will be handled by setting the FHT image property
549  if (unit.startsWith("1/")) unit=unit.substring(2);
550 
551  if (unit.equals("µm")){
552  cal.setUnit("micron");
553  } else {
554  cal.setUnit(unit);
555  }
556  if(debugLevel>0) IJ.write("Calibration unit: "+unit);
557 
558  cal.pixelWidth = ((Float) tagHash.get(IMGLIST+chosenImage+".ImageData.Calibrations.Dimension.0.Scale")).doubleValue();
559  cal.pixelHeight = ((Float) tagHash.get(IMGLIST+chosenImage+".ImageData.Calibrations.Dimension.1.Scale")).doubleValue();
560  // not yet implemented stacks - if they exist
561  //cal.pixelDepth =
562  return cal;
563  }
564 
565  int readTagGroup() throws IOException {
566  curGroupLevel+=1; // Go down a level since this is a new group
567  curGroupAtLevelX[curGroupLevel]++; // Increment the group counter at this level
568  // Set the number of current tag at this level to -1
569  // since the readTagEntry routine pre-increments
570  // ie the first tag will be labelled tag 0
571  curTagAtLevelX[curGroupLevel]=-1;
572 
573  if(debugLevel>5) IJ.write("rTG: Current Group Level: "+curGroupLevel);
574 
575  int isSorted=f.readByte();
576  int isOpen=f.readByte();
577  int nTags=f.readInt();
578 
579  if(debugLevel>5) IJ.write("rTG: Iterating over the "+nTags+" tag entries in this group");
580  // Iterate over the number of Tag Entries in this group
581  for( int i = 0; i<nTags;i++) {
582  readTagEntry();
583  }
584 
585  // Go back up a level now that we've finished reading this group
586  curGroupLevel-=1;
587 
588  return 1;
589  };
590 
591  String makeGroupString() {
592  // Produces a string which is the concatenation of the current group levels
593  String tString = new String(""+curGroupAtLevelX[0]);
594 
595  for (int i=1; i<=curGroupLevel;i++){
596  tString += "."+curGroupAtLevelX[i];
597  }
598 
599  return tString;
600  }
601 
602  int readTagEntry() throws IOException {
603  int isData=f.readByte();
604 
605  // Record that we've found a new tag at this level
606  curTagAtLevelX[curGroupLevel]++;
607 
608  //Get the tag label if one exists
609  int lenTagLabel=f.readShort();
610  String tagLabel;
611  if(lenTagLabel!=0){
612  tagLabel=readString(lenTagLabel);
613  } else {
614  tagLabel=new String(""+curTagAtLevelX[curGroupLevel]);
615  }
616 
617  // For debugging
618  if(debugLevel>5) {
619  IJ.write(curGroupLevel+"|"+makeGroupString()+": Tag label = "+tagLabel);
620  } else if (debugLevel>0){
621  IJ.write(curGroupLevel+": Tag label = "+tagLabel);
622  }
623 
624  // Figure out if the tag was data or a new group
625  if (isData==21) {
626  // this tag entry is data
627 
628  // OK settle what this piece of data will be called
629  curTagName = new String(makeGroupNameString()+"."+tagLabel);
630 
631  // now get it
632  readTagType();
633  } else {
634  //this tag entry is a tag group
635 
636  // Slightly ugly that this can't be done in readTagGroup
637  curGroupNameAtLevelX[curGroupLevel+1]=tagLabel; // Store the name of the group at the new level
638  readTagGroup(); // which will actually increment curGroupLevel
639  }
640  return 1;
641  };
642 
643  String makeGroupNameString() {
644  // A utility function:
645  // Produces a string which is the concatenation of the current group names
646  String tString = new String(curGroupNameAtLevelX[0]);
647 
648  for (int i=1; i<=curGroupLevel;i++){
649  tString += "."+curGroupNameAtLevelX[i];
650  }
651 
652  return tString;
653  }
654 
655  int readTagType() throws IOException {
656  int Delim=f.readInt();
657  // Should always start with %%%%
658  if (Delim!=0x25252525) throw new IOException("Tag Type delimiter not %%%%");
659 
660  // This is redundant info, so just ignore it.
661  int nInTag=f.readInt();
662 
663  readAnyData();
664 
665  return 1;
666  };
667 
668  int readAnyData() throws IOException {
669  // Higher level function which dispatches to functions
670  // handling specific data types
671 
672  // This specifies what kind of type we are dealing with
673  // eg short, long, struct, array etc.
674  int encodedType = f.readInt();
675 
676  // Figure out the size of the encodedType
677  int etSize = encodedTypeSize(encodedType);
678  if(debugLevel>5) IJ.write("rAnD, "+hexPosition()+": Tag Type = "+encodedType+", Tag Size = "+etSize);
679 
680  if(etSize>0){
681  // must be a regular data type, so read it and store a tag for ir
682  storeTag( curTagName,readNativeData(encodedType,etSize) );
683  }
684  // OK then, perhaps it's an array, struct or string.
685  else if (encodedType==STRING) // String
686  {
687  // nb readStringData will also store tags internally
688  int stringSize = f.readInt();
689  readStringData(stringSize);
690  }
691  else if (encodedType==STRUCT) // Struct
692  {
693  // This now stores fields (in curly braces) but does not store
694  // field names. In fact the code will be break for non-zero
695  // field names.
696  Vector structTypes = readStructTypes();
697  readStructData(structTypes);
698  }
699  else if (encodedType==ARRAY) // Array
700  {
701  // This only stores a tag which I defined myself
702  // to indicate the size of data chunks that are skipped
703  Vector arrayTypes=readArrayTypes();
704  readArrayData(arrayTypes);
705  }
706  else {
707  throw new IOException("rAnD, 0x"+hexPosition()+": Can't understand encoded type");
708  }
709  return 1;
710  }
711 
712  Object readNativeData(int encodedType,int etSize) throws IOException {
713  // Does the actual reading of ordinary data types
714 
715  // since it starts as an object, it is not tied to a particular
716  // data type
717  Object val=null;
718 
719  if(encodedType==SHORT){ //short
720  val = new Short(blreadShort());
721  }
722  else if(encodedType==LONG){ //long
723  val = new Integer(blreadInt());
724  }
725  else if(encodedType==USHORT){ //u short
726  val = new Short(blreadUShort());
727  }
728  else if(encodedType==ULONG){ //u long
729  val = new Integer(blreadInt());
730  }
731  else if(encodedType==FLOAT){ //float
732  val = new Float(blreadFloat());
733  }
734  else if(encodedType==DOUBLE){ //double
735  val = new Double(blreadDouble());
736  }
737  else if(encodedType==BOOLEAN){ //boolean
738  if (f.readByte()==0){
739  val = new Boolean(false);
740  } else {
741  val = new Boolean(true);
742  }
743  }
744  else if(encodedType==CHAR){ //char
745  val = new Character( (char) f.readByte() );
746  }
747  else if(encodedType==OCTET){ //octet
748  // what's the difference?
749  val = new Byte( f.readByte() );
750  } else {
751  // Not a known data type
752  throw new IOException("rND, 0x"+hexPosition()+": Unknown data type "+encodedType);
753  }
754 
755  // Print out the value if necessary
756  if(debugLevel>3){
757  IJ.write("rND, 0x"+hexPosition()+": "+val);
758  } else if(debugLevel>0) {
759  IJ.write(""+val);
760  }
761 
762  return val;
763  }
764  String readStringData(int stringSize) throws IOException {
765  // Does the actual reading of string data types
766  // These should be written as Unicode which can be directly
767  // converted by the String constructor
768  if(stringSize<=0) return new String("");
769 
770  // Read the string data into a temporary byte buffer.
771  byte[] temp = new byte[stringSize];
772  f.read(temp,0,stringSize);
773 
774  // Now convert these unicode bytes into a real string
775  String rString;
776 
777  // Note that I can't get UTF encoding to work on MRJ 2.2.5 =
778  // JDK 1.1.7 even though I think it should
779  // so I have put together a kludge
780  if(littleEndian){
781  // Use UTF-16LE encoding (this seems to fail with MacOS 9 Java 1.1.7)
782  try {
783  rString=new String(temp,"UTF-16LE");
784  }
785  catch (Exception e) {
786  // Manual conversion of the string if the above fails
787  rString="";
788  for(int i=0;i<stringSize;i+=2) {
789  rString+=new Character((char)((temp[i+1]&0xFF) <<8 | (temp[i] & 0xFF)));
790  }
791  }
792 
793  }else{
794  // use UTF-16BE encoding (this seems to fail with MacOS 9 Java 1.1.7)
795  try {
796  rString=new String(temp,"UTF-16BE");
797  }
798  catch (Exception e) {
799  // Manual conversion of the string if the above fails
800  rString="";
801  for(int i=0;i<stringSize;i+=2) {
802  rString+=new Character((char)((temp[i]&0xFF) <<8 | (temp[i+1] & 0xFF)));
803  }
804  }
805 
806  }
807 
808  if(debugLevel>0) IJ.write("StringVal: "+rString);
809 
810  // Store the value of this tag
811  storeTag(curTagName,rString);
812 
813  return rString;
814  }
815 
816  Vector readArrayTypes() throws IOException {
817  // Figures out the data types in an array data type
818  // complicated by the fact that the array type could be a struct!
819 
820  // Don't know if this will behave for arrays of strings or arrays
821 
822 
823  int arrayType=f.readInt();
824 
825  Vector itemTypes = new Vector();
826  if (arrayType==STRUCT) { // ie a Struct
827  itemTypes = readStructTypes();
828  }
829  else if (arrayType==ARRAY) { // ie a sub array
830  itemTypes = readArrayTypes();
831  // not sure if this will work!
832  }
833  else {
834  // assume its an array of simple types
835  // add changed to addElement for Java 1.1.7 compatibility
836  itemTypes.addElement(new Integer(arrayType));
837  }
838 
839  return itemTypes;
840  }
841  int readArrayData(Vector arrayTypes) throws IOException {
842  // Reads in array data
843 
844  // First thing to do is get number of array elements
845  int arraySize=f.readInt();
846  if(debugLevel>3) IJ.write("rArD, 0x"+hexPosition()+": Reading array of size = "+arraySize);
847 
848  // Now figure out the total width of each element in the array
849  // nb these elements can have subelements if the array is an array
850  // of STRUCTS etc.
851  int itemSize=0;
852 
853  // Iterate over every type in arrayTypes - there may be more than
854  // one type if this is an array of structs or arrays.
855  int encodedType=0;
856  for (int i = 0; i < arrayTypes.size(); i++) {
857  // cast the ith Vector element to Integer and then get a regular int
858  encodedType = ((Integer) arrayTypes.elementAt(i)).intValue();
859  int etSize=encodedTypeSize(encodedType);
860  // Now add that size to our running total
861  itemSize+=etSize;
862  // For debugging
863  if(debugLevel>5) IJ.write("rArD: Tag Type = "+encodedType+", Tag Size = "+etSize);
864  //readNativeData(encodedType,etSize);
865  }
866  if(debugLevel>5) IJ.write("rArD: Array Item Size = "+itemSize);
867 
868  // OK now figure out what to do with this array
869  // this would be the buffer size needed to accommodate ot
870  long bufSize = (long) arraySize * (long) itemSize;
871 
872  // If this isn't image data but is an unsigned short array
873  // of less than 256 bytes then it is probably a string
874  if(!curTagName.endsWith("ImageData.Data") && arrayTypes.size() == 1
875  && encodedType == USHORT && arraySize <256) {
876  // read in as string
877  String val = readStringData((int) bufSize);
878  }
879  else { // treat as binary data
880  // Make up my own tags to indicate data size
881  storeTag(curTagName+".Size",new Long(bufSize));
882  // and current offset
883  // nb for a while I had offset + 1but this was wrong!
884  // and gave a peculiar staircase histogram because what I had
885  // ended up doing was reading one byte each from a pair of pixels
886  // rather than 2 bytes from a single pixel. Ugh!
887  storeTag(curTagName+".Offset",new Long(f.getFilePointer()));
888 
889  // then go ahead and skip bufSize bytes from current position
890  // without trying to read this data
891  f.seek( f.getFilePointer()+bufSize);
892  }
893  return 1;
894  }
895 
896  Vector readStructTypes() throws IOException {
897  // Figures out the data types in a struct
898  if(debugLevel>3) IJ.write("Reading Struct Types at Pos = "+f.getFilePointer()+", 0x"+hexPosition());
899 
900  // nb GatanDM3 has longs - I think C++ long = 4 bytes, so use Java int
901  int structNameLength=f.readInt();
902  int nFields=f.readInt();
903 
904  if(debugLevel>5) IJ.write("nFields = "+nFields);
905 
906  if (nFields>100) throw new IOException("Too many fields");
907 
908  Vector fieldTypes = new Vector();
909  int nameLength = 0;
910  for (int i = 0; i<nFields; i++) {
911  nameLength=f.readInt();
912  if(debugLevel>10) IJ.write(i+"th namelength = "+nameLength);
913  int fieldType=f.readInt();
914 
915  // add changed to addElement for Java 1.1.7 compatibility
916  fieldTypes.addElement(new Integer(fieldType));
917  }
918 
919  return fieldTypes;
920  }
921 
922  int readStructData(Vector structTypes) throws IOException {
923  // Reads in struct data based on the type info in structTypes
924  String structAsString="";
925 
926  for (int i = 0; i < structTypes.size(); i++) {
927  Integer iTagType = (Integer) structTypes.elementAt(i);
928 
929  int encodedType = iTagType.intValue();
930  int etSize=encodedTypeSize(encodedType);
931  // For debugging
932  if(debugLevel>5) IJ.write("Tag Type = "+encodedType+", Tag Size = "+etSize);
933 
934  // OK now get the data
935  structAsString+=readNativeData(encodedType,etSize);
936  // Add a comma to separate values unless this is the last entry
937  if(i+1!=structTypes.size()) structAsString+=",";
938  }
939  storeTag(curTagName,"{"+structAsString+"}");
940  return 1;
941  }
942 
943 
944  int encodedTypeSize(int encodedType){
945  // returns the size in bytes of the data type
946  // 030614 Replaced type numbers based on GatanDM3.h
947 
948  // so -1 will be the value returned for an unrecognised type
949  // (which could include ARRAYs, STRUCTs, STRINGs)
950  int width=-1;
951 
952  switch(encodedType){
953  case 0: // blank field? Do I need this?
954  width = 0; break;
955 
956  case BOOLEAN: // boolean: data size = 1
957  case CHAR: // char: data size = 1
958  case OCTET: // octet: data size = 1
959  width=1; break;
960 
961  case SHORT: // 1. short: data size = 2
962  case USHORT: // 3. unsigned short: data size = 2
963  width=2; break;
964 
965  case LONG: // 2. long: data size = 4
966  case ULONG: // 4. unsigned long: data size = 4
967  case FLOAT: // 5. float: data size = 4
968  width=4; break;
969 
970  case DOUBLE: // double: data size = 8
971  width=8; break;
972  }
973  return(width);
974  }
975 
976  // Store the value and key of the tag that we have just
977  // read in a table
978  void storeTag( String tagName, Object tagValue){
979  // add changed to addElement for Java 1.1.7 compatibility
980  storedTags.addElement(new String(tagName+" = "+tagValue));
981  tagHash.put(tagName,tagValue);
982  }
983 
984 
985  // ********************************************************
986  // the bl methods will check value of littleEndian and read
987  // from the RandomAccessFile f accordingly.
988  // (bl for big/little - ie can cope with either endian format)
989  // ********************************************************
990 
991  short blreadShort() throws IOException
992  {
993  if (!littleEndian) return f.readShort();
994  byte b1 = f.readByte();
995  byte b2 = f.readByte();
996  return ( (short) (((b2 & 0xff) << 8) | (b1 & 0xff)) );
997  }
998  short blreadUShort() throws IOException
999  // Identical to blreadShort - is this correct?
1000  // not really - java uses signed shorts, but I think it's
1001  // too complicated to try and implement unsigned
1002  // In principle, one should add 65536 to negative values
1003  // to convert, but then they would have to be stored as 4 byte ints
1004  // or something.
1005  {
1006  if (!littleEndian) return (short) f.readUnsignedShort();
1007  byte b1 = f.readByte();
1008  byte b2 = f.readByte();
1009  return ( (short) (((b2 & 0xff) << 8) | (b1 & 0xff)) );
1010  }
1011 
1012  int blreadInt() throws IOException
1013  {
1014  if (!littleEndian) return f.readInt();
1015  byte b1 = f.readByte();
1016  byte b2 = f.readByte();
1017  byte b3 = f.readByte();
1018  byte b4 = f.readByte();
1019  return ( (((b4 & 0xff) << 24) | ((b3 & 0xff) << 16) | ((b2 & 0xff) << 8) | (b1 & 0xff)) );
1020  }
1021 
1022 
1023  long blreadLong() throws IOException
1024  // New fn, not quite sure if the little endian version is correct
1025  // OK Corrected now as far as I can tell
1026  {
1027  if (!littleEndian) return f.readLong();
1028  int i1=blreadInt();
1029  int i2=blreadInt();
1030 
1031  // need to convert intermediates to long explicitly since the standard
1032  // is presumably just to work with them as int
1033  return ( ((long) (i2 & 0xffffffff) << 32) | (long) (i1 & 0xffffffff) );
1034 
1035  }
1036 
1037  double blreadDouble() throws IOException
1038  // new fn to read 8 byte doubles using blreadLong as a base
1039  {
1040  if (!littleEndian) return f.readDouble();
1041 
1042  long orig = blreadLong();
1043  return (Double.longBitsToDouble(orig));
1044  }
1045 
1046  float blreadFloat() throws IOException
1047  {
1048  if (!littleEndian) return f.readFloat();
1049 
1050  int orig = blreadInt();
1051  return (Float.intBitsToFloat(orig));
1052  }
1053 
1054  // used to read in field labels
1055  String readString(int n) throws IOException{
1056  // not sure if this readString limit is sensible or necessary
1057  if(n>2000) throw new IOException("Can't handle strings longer than 2000 chars, n = "+n+" at pos = "+f.getFilePointer());
1058 
1059  byte[] temp = new byte[n];
1060  f.read(temp,0,n);
1061 
1062  return new String(temp);
1063 
1064  }
1065 
1066  String hexPosition() throws IOException {
1067  // Utility fn to return current file position in hex
1068  return ( Long.toHexString( f.getFilePointer() ) );
1069  }
1070 
1071 }
DM3_Reader
Definition: DM3_Reader.java:133
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DM3_Reader.run
void run(String arg)
Definition: DM3_Reader.java:192
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DM3_Reader.load
ImagePlus load(String directory, String fileName)
Definition: DM3_Reader.java:234
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boolean useGatanMinMax
Definition: DM3_Reader.java:138
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.ij.commons;
8 
9 import ij.IJ;
10 import ij.ImagePlus;
11 import ij.gui.Roi;
12 import ij.gui.Toolbar;
13 import ij.process.FloatProcessor;
14 
15 import java.awt.Color;
16 import java.awt.FlowLayout;
17 import java.awt.GridBagConstraints;
18 import java.awt.GridBagLayout;
19 import java.awt.Insets;
20 import java.awt.event.ActionEvent;
21 import java.awt.event.ActionListener;
22 import java.text.NumberFormat;
23 import java.util.HashMap;
24 import java.util.logging.Level;
25 import java.util.logging.Logger;
26 
27 import javax.swing.JButton;
28 import javax.swing.JCheckBox;
29 import javax.swing.JFormattedTextField;
30 import javax.swing.JFrame;
31 import javax.swing.JPanel;
32 import javax.swing.JToggleButton;
33 import javax.swing.JToolBar;
34 
35 import xmipp.jni.ImageGeneric;
36 import xmipp.utils.ScipionParams;
37 import xmipp.utils.XmippWindowUtil;
38 
43 public class DesignMaskJFrame extends JFrame implements ActionListener{
44  protected ImagePlus mask;
45  private ImageJPanel imagepn;
46  private JButton registerbt;
47  protected int width, height;
48  private ImagePlus imp;
49  private JCheckBox invertbt;
50  private JCheckBox addbt;
51  private final XmippImageWindow iw;
52  private JToggleButton smoothbt;
53  private JFormattedTextField smoothtf;
54  private JButton refreshbt;
55 
56  public DesignMaskJFrame(XmippImageWindow iw)
57  {
58  this.iw = iw;
59  createMask();
60  XmippUtil.showImageJ(Tool.VIEWER);
61  IJ.setTool(Toolbar.OVAL);
62  initComponents();
63  }
64 
65  protected void initComponents()
66  {
67  setTitle("Design Mask");
68  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
69 
70  GridBagConstraints constraints = new GridBagConstraints();
71  constraints.insets = new Insets(0, 5, 0, 5);
72  constraints.anchor = GridBagConstraints.WEST;
73  setLayout(new GridBagLayout());
74  JToolBar optionspn = new JToolBar();
75 
76  optionspn.setFloatable(false);
77  add(optionspn, XmippWindowUtil.getConstraints(constraints, 0, 0));
78  refreshbt = XmippWindowUtil.getIconButton("fa-refresh.png", new ActionListener()
79  {
80 
81  @Override
82  public void actionPerformed(ActionEvent e)
83  {
84  refreshMask();
85 
86  }
87  });
88  optionspn.add(refreshbt);
89  invertbt = new JCheckBox("Invert:");
90  invertbt.addActionListener(this);
91  optionspn.add(invertbt);
92 
93  smoothbt = new JCheckBox("Smooth:");
94  smoothbt.addActionListener(this);
95  optionspn.add(smoothbt);
96  smoothtf = new JFormattedTextField(NumberFormat.getIntegerInstance());
97  smoothtf.setColumns(2);
98  smoothtf.setValue(2);
99  smoothtf.addActionListener(this);
100  smoothtf.setEnabled(false);
101  optionspn.add(smoothtf);
102  imagepn = new ImageJPanel(mask, width, height);
103  add(imagepn, XmippWindowUtil.getConstraints(constraints, 0, 1));
104 
105 
106  JPanel commandspn = new JPanel(new FlowLayout(FlowLayout.RIGHT));
107  add(commandspn, XmippWindowUtil.getConstraints(constraints, 0, 2, 1, 1, GridBagConstraints.HORIZONTAL));
108 
109 
110  registerbt = XmippWindowUtil.getScipionIconButton("Create Mask");
111  registerbt.addActionListener(new ActionListener() {
112 
113  @Override
114  public void actionPerformed(ActionEvent ae) {
115  registerMask();
116  }
117 
118  });
119 
120  commandspn.add(registerbt);
121  registerbt.setVisible(XmippApplication.isScipion());
122  pack();
123  setVisible(true);
124 
125  }
126 
127  protected void registerMask() {
128  HashMap<String, String> msgfields = new HashMap<String, String>();
129  String field = "Run name:";
130  msgfields.put(field, "create mask");
131  InputFieldsMessageDialog dlg = new InputFieldsMessageDialog(this, "Question", "Are you sure you want to register mask?", msgfields);
132  int create = dlg.action;
133  boolean register = (create == InputFieldsMessageDialog.OK_OPTION);
134  if (register)
135  try {
136  String path = "mask.spi";
137  ImageGeneric ig = XmippImageConverter.convertToImageGeneric(mask);
138  ig.write(path);
139  ScipionParams params = (ScipionParams)iw.getParams();
140  String label = dlg.getFieldValue(field);
141  String command = String.format("run protocol ProtCreateMask inputObj=%s maskFile='%s' label='%s'", params.inputid, path, label);
142  XmippWindowUtil.runCommand(command, params.port);
143 // String[] command = new String[]{params.python, params.getRegisterMaskScript(), params.projectid, params.inputid, path, label};
144 // String output = XmippWindowUtil.executeCommand(command, true);
145 // System.out.println(output);
146  } catch (Exception ex) {
147  ex.printStackTrace();
148  Logger.getLogger(DesignMaskJFrame.class.getName()).log(Level.SEVERE, null, ex);
149  }
150  }
151 
152 
153 
154  private void createMask() {
155  imp = IJ.getImage();
156 
157  width = imp.getCanvas().getWidth();
158  height = imp.getCanvas().getHeight();
159 
160  if (imp != null) {
161  Roi roi = imp.getRoi();
162 
163  if (roi != null) {
164  if (mask == null || !mask.isVisible()) {
165  createDefaultMask();
166  }
167 
168  mask.getProcessor().setColor(Color.WHITE);
169  mask.getProcessor().fill(roi);
170  if(isInvert())
171  mask.getProcessor().invert();
172  if(isSmooth())
173  mask.getProcessor().blurGaussian(((Number) smoothtf.getValue()).intValue());
174 
175  } else
176  createDefaultMask();
177 
178  mask.getProcessor().multiply(1/mask.getProcessor().getMax());
179  mask.getProcessor().setMinAndMax(0, 1);
180  mask.updateAndDraw();
181 
182  } else {
183  IJ.error("There are no images open.");
184  }
185  }
186 
187  public boolean isInvert()
188  {
189  if(invertbt == null)
190  return false;
191  return invertbt.isSelected();
192  }
193 
194  public boolean isSmooth()
195  {
196  if(smoothbt == null)
197  return false;
198  return smoothbt.isSelected();
199  }
200 
201  public boolean isAddRoi()
202  {
203  if(addbt == null)
204  return false;
205  return addbt.isSelected();
206  }
207 
208  protected void createDefaultMask()
209  {
210  FloatProcessor processor = new FloatProcessor(imp.getWidth(), imp.getHeight());
211  mask = new ImagePlus("Mask", processor);
212 
213 
214  }
215 
216  public void refreshMask()
217  {
218  createMask();
219  imagepn.setMask(mask, width, height);
220  pack();
221  }
222 
223  @Override
224  public void actionPerformed(ActionEvent ae) {
225  smoothtf.setEnabled(isSmooth());
226  createMask();
227  imagepn.setMask(mask, width, height);
228 
229  }
230 
231 
232 
233 
234 
235 }
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xmipp.ij.commons.ImageJPanel.setMask
void setMask(ImagePlus mask, int width, int height)
Definition: ImageJPanel.java:46
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static ImageGeneric convertToImageGeneric(ImagePlus imp)
Definition: XmippImageConverter.java:297
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Definition: XmippUtil.java:28
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Definition: XmippWindowUtil.java:124
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Definition: XmippWindowUtil.java:105
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class  xmipp.viewer.windows.EditLabelsJDialog.ColumnsTableModel
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import java.awt.Dimension;
29 import java.awt.GridBagConstraints;
30 import java.awt.GridBagLayout;
31 import java.awt.event.ActionEvent;
32 import java.util.ArrayList;
33 import java.util.List;
34 
35 import javax.swing.BorderFactory;
36 import javax.swing.JButton;
37 import javax.swing.JPanel;
38 import javax.swing.JScrollPane;
39 import javax.swing.JTable;
40 import javax.swing.ListSelectionModel;
41 import javax.swing.event.ListSelectionEvent;
42 import javax.swing.event.ListSelectionListener;
43 import javax.swing.table.AbstractTableModel;
44 
45 import xmipp.utils.XmippDialog;
46 import xmipp.utils.XmippWindowUtil;
47 import xmipp.viewer.models.ColumnInfo;
48 import xmipp.viewer.models.ImageGalleryTableModel;
49 
50 public class EditLabelsJDialog extends XmippDialog {
51  private static final long serialVersionUID = 1L;
52  private JTable tableColumns;
53  private JButton btnAdd, btnDelete, btnFill, btnOpen;
54  private List<ColumnInfo> rows;
55  private ColumnsTableModel model;
56  // This will be used for check for results from the dialog
57  boolean fireEvent = true;
58  GridBagConstraints gbc = new GridBagConstraints();
59  ImageGalleryTableModel gallery;
60  JPanel panelButtons;
61 
62  public EditLabelsJDialog(GalleryJFrame parent) {
63  super(parent, "Edit labels", true);
64  this.rows = parent.getData().getLabelsInfo();
65  this.gallery = parent.gallery;
66  btnOkText = "Close";
67  btnCancelDisplay = false;
68  initComponents();
69  enableDelete(false);
70  enableFill(false);
71  }// constructor ColumnsJDialog
72 
73  private JButton createButton(String icon, String tip) {
74  JButton btn = XmippWindowUtil.getIconButton(icon, this);
75  btn.setToolTipText(tip);
76  btn.setFocusable(false);
77  panelButtons.add(btn);
78  return btn;
79  }
80 
81  protected void createToolbarButtons() {
82  panelButtons = new JPanel();
83  btnAdd = createButton("add.gif", "Add new label");
84  btnDelete = createButton("delete.gif", "Delete label");
85  btnFill = createButton("fill.png", "Fill label");
86  }
87 
88  @Override
89  protected void createContent(JPanel panel) {
90  setResizable(false);
91  panel.setLayout(new GridBagLayout());
92  gbc.anchor = GridBagConstraints.EAST;
93 
94  JPanel groupstbpn = new JPanel();
95  JScrollPane sp = new JScrollPane();
96  groupstbpn.setBorder(BorderFactory.createTitledBorder("Labels"));
97  groupstbpn.add(sp);
98  sp.setOpaque(true);
99  model = new ColumnsTableModel();
100  tableColumns = new JTable(model);
101  tableColumns
102  .setPreferredScrollableViewportSize(new Dimension(350, 200));
103  sp.setViewportView(tableColumns);
104  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
105  createToolbarButtons();
106  panel.add(panelButtons, XmippWindowUtil.getConstraints(gbc, 1, 0));
107 
108  // listen to selection changes (only one row selected)
109  // tableColumns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
110  tableColumns.getSelectionModel().addListSelectionListener(
111  new ListSelectionListener() {
112  @Override
113  public void valueChanged(ListSelectionEvent e) {
114  int n = getSelectedRows().length;
115  enableDelete(n > 0);
116  enableFill(n == 1);
117  }
118  });
119  }// function initComponents
120 
121  private void enableDelete(boolean value) {
122  btnDelete.setEnabled(value);
123  }
124 
125  private void enableFill(boolean value) {
126  btnFill.setEnabled(value);
127  }
128 
129  private void rowsChanged() {
130  this.rows = ((GalleryJFrame) parent).getData().getLabelsInfo();
131  model.fireTableDataChanged();
132  }
133 
134  private void showAddFillDialog(AddFillLabelsJDialog dlg) throws Exception {
135 
136  if (dlg.showDialog()) {
137  ((GalleryJFrame) parent).fillLabel(dlg.getLabel(),
138  dlg.getFillMode(), dlg.getValues());
139  rowsChanged();
140  }
141 
142  }
143 
144  @Override
145  public void handleActionPerformed(ActionEvent evt) {
146  try {
147  JButton btn = (JButton) evt.getSource();
148  if (btn == btnAdd) {
149  showAddFillDialog(new AddFillLabelsJDialog(
150  (GalleryJFrame) parent, rows));
151  } else if (btn == btnDelete) {
152  System.out.println("Here testing java...");
153  if (showWarning("Are you sure to remove this label?")) {
154  int [] rows = getSelectedRows();
155  System.out.println("Rows: " + Integer.toString(rows.length));
156  for (int row: rows) {
157  ((GalleryJFrame) parent).removeLabel(rowToLabel(row));
158  }
159  rowsChanged();
160  }
161  } else if (btn == btnFill) {
162  int [] rows = getSelectedRows();
163  showAddFillDialog(new AddFillLabelsJDialog(
164  (GalleryJFrame) parent, rowToLabel(rows[0])));
165  }
166  } catch (Exception e) {
167  showException(e);
168  }
169  }// function actionPerformed
170 
171  public int[] getSelectedRows() {
172  return tableColumns.getSelectedRows();
173  }
174 
175  // Get the label corresponding to a given row
176  public int rowToLabel(int row) {
177  return rows.get(row).label;
178  }
179 
180  class ColumnsTableModel extends AbstractTableModel {
181  private static final long serialVersionUID = 1L;
182 
183  private String[] columns = { "Label", "Type" };
184 
185  @Override
186  public Class getColumnClass(int column) {
187  return getValueAt(0, column).getClass();
188  }
189 
190  @Override
191  public String getColumnName(int columnIndex) {
192  return columns[columnIndex];
193  }
194 
195  @Override
196  public int getColumnCount() {
197  return columns.length;
198  }
199 
200  @Override
201  public int getRowCount() {
202  return rows.size();
203  // return frame.getParticlePicker().getFamilies().size();
204  }
205 
206  @Override
207  public boolean isCellEditable(int row, int column) {
208  return false;
209  }
210 
211  @Override
212  public void setValueAt(Object value, int row, int column) {
213  }
214 
215  @Override
216  public Object getValueAt(int row, int column) {
217  ColumnInfo col = rows.get(row);
218  switch (column) {
219  case 0:
220  return col.labelName;
221  case 1:
222  return col.getLabelTypeString();
223  }
224  return null;
225  }
226 
227  }// class ColumnsTableModel
228 
229 }// class ColumnsJDialog
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List< ColumnInfo > getLabelsInfo()
Definition: GalleryData.java:1495
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boolean showException(Exception e)
Definition: XmippDialog.java:217
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boolean showWarning(String message)
Definition: XmippDialog.java:205
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static JButton getIconButton(String icon, ActionListener listener)
Definition: XmippWindowUtil.java:124
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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class  xmipp.jni.EllipseCTF
 
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package  xmipp.jni
 
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.jni;
6 
7 import ij.process.EllipseFitter;
8 import java.util.ArrayList;
9 import java.util.List;
10 import java.util.Locale;
11 
12 
17 public class EllipseCTF {
18 
19  private double Q0, Cs, Ts, kV, lambda, lowFreq, highFreq, downsampleFactor;
20  int D;
21  double mddefU, mddefV;
22  private double defocusU, defocusV;
23  private long id;
24  private EllipseFitter ellipseFitter;
25  private double defocusAngle;
26 
27  public void setEllipseFitter(EllipseFitter ellipseFitter) {
28  this.ellipseFitter = ellipseFitter;
29  defocusAngle = ellipseFitter.angle;
30  }
31 
32  public double getDefocusAngle() {
33  return defocusAngle;
34  }
35 
36  public EllipseCTF(long id, double Q0, double Cs, double downsampleFactor, double Ts, double kV, double mddefU, double mddefV, double defocusAngle, int D)
37  {
38  this.id = id;
39  this.D = D;
40  this.Q0 = Q0;
41  this.Cs = Cs;
42  this.downsampleFactor = downsampleFactor;
43  this.Ts = Ts;
44  this.kV = kV;
45  this.lambda = EllipseCTF.lambda(kV);
46  this.mddefU = mddefU;
47  this.mddefV = mddefV;
48  this.defocusAngle = defocusAngle;
49  }
50 
51  public long getId()
52  {
53  return id;
54  }
55 
56  public static double lambda(double Kv) {
57  double local_kV = Kv * 1.0e3;
58 
59  return 12.3 / Math.sqrt(local_kV * (1. + local_kV * 1e-6));
60  }
61 
62 
63  public double getDefocusU() {
64  return defocusU;
65  }
66 
67  public double getDefocusV() {
68  return defocusV;
69  }
70 
72  public void setFreqRange(double lowFreq, double highFreq){
73  this.lowFreq = lowFreq;
74  this.highFreq = highFreq;
75  }
76 
77  public double getLowFreq(){
78  return lowFreq;
79  }
80 
81  public double getHighFreq(){
82  return highFreq;
83  }
84 
85  public double getQ0(){
86  return Q0;
87  }
88 
89  // Calculates defocus U and V according to ellipse parameters.
90  public void calculateDefocus(double minor, double major) {
91  defocusU = defocus(minor, Q0, lambda, Cs, D, Ts * downsampleFactor);
92  defocusV = defocus(major, Q0, lambda, Cs, D, Ts * downsampleFactor);
93  }
94 
95 
96 
97  private double defocus(double r, double Q0, double lambda, double Cs, double D, double Ts) {
98  double R = r / (D * Ts);
99 
100  double a = lambda * R * R;
101  double defocus = Math.atan(-Q0) / (Math.PI * a) - 1 / a - 0.5 * (Cs * a * lambda);
102 
103  return -defocus;
104  }
105 
106  public double getSamplingRate() {
107  return Ts;
108  }
109 
110  public double getVoltage() {
111  return kV;
112  }
113 
114  public double getSphericalAberration() {
115  return Cs;
116  }
117 
118 
119  public String toString2() {
120  return "---------------------------------------------------\n"
121  + "Q0: " + Q0 + "\n"
122  + "Cs: " + Cs + "\n"
123  + "D: " + D + "\n"
124  + "Ts: " + Ts + "\n"
125  + "Kv: " + kV + "\n"
126  + "lambda: " + lambda + "\n"
127  + "---------------------------------------------------\n"
128  + "defocusU: " + defocusU + " > (file: " + mddefU + ")\n"
129  + "defocusV: " + defocusV + " > (file: " + mddefV + ")\n"
130  + "---------------------------------------------------\n";
131  }
132 
133  @Override
134  public String toString()
135  {
136  String format = "%10.2f%10.2f%10.2f%10.2f%10.2f";
137  return String.format(Locale.ENGLISH, format, getDefocusU(), getDefocusV(), getDefocusAngle(), getLowFreq(), getHighFreq());
138  }
139 
140  public int getD()
141  {
142  return D;
143  }
144 
145  public MetaData getCTFMd()
146  {
147  MetaData md = new MetaData();
148  md.setColumnFormat(true);
149  long id = md.addObject();
150  md.setValueDouble(MDLabel.MDL_CTF_Q0, Q0, id);
151  md.setValueDouble(MDLabel.MDL_CTF_CS, Cs, id);
152  md.setValueDouble(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED, downsampleFactor, id);
153  md.setValueDouble(MDLabel.MDL_SAMPLINGRATE, Ts,id);
154  md.setValueDouble(MDLabel.MDL_CTF_VOLTAGE, kV, id);
155  md.setValueDouble(MDLabel.MDL_CTF_DEFOCUSU, mddefU, id);
156  md.setValueDouble(MDLabel.MDL_CTF_DEFOCUSV, mddefV, id);
157  md.setValueDouble(MDLabel.MDL_CTF_DEFOCUS_ANGLE, defocusAngle, id);
158  //md.print();
159  return md;
160  }
161 
162  public double getDownsamplingFactor() {
163  return downsampleFactor;
164  }
165 
166  public void setDefocus(double defU, double defV, double angle) {
167  this.defocusU = defU;
168  this.defocusV = defV;
169  this.defocusAngle = angle;
170  }
171 
172 
173 
174 
175 }
xmipp.jni.EllipseCTF.EllipseCTF
EllipseCTF(long id, double Q0, double Cs, double downsampleFactor, double Ts, double kV, double mddefU, double mddefV, double defocusAngle, int D)
Definition: EllipseCTF.java:36
-
xmipp.jni.MetaData.addObject
native long addObject()
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUSU
static final int MDL_CTF_DEFOCUSU
< average defocus (Angtroms)
Definition: MDLabel.java:86
-
xmipp.jni.MDLabel.MDL_SAMPLINGRATE
static final int MDL_SAMPLINGRATE
rfactor
Definition: MDLabel.java:331
-
xmipp.jni.MetaData.setColumnFormat
native void setColumnFormat(boolean format)
-
xmipp.jni.EllipseCTF.lambda
static double lambda(double Kv)
Definition: EllipseCTF.java:56
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xmipp.jni.EllipseCTF.getSphericalAberration
double getSphericalAberration()
Definition: EllipseCTF.java:114
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xmipp.jni.EllipseCTF.getDefocusAngle
double getDefocusAngle()
Definition: EllipseCTF.java:32
-
xmipp.jni.EllipseCTF.calculateDefocus
void calculateDefocus(double minor, double major)
Definition: EllipseCTF.java:90
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUSV
static final int MDL_CTF_DEFOCUSV
< Defocus U (Angstroms)
Definition: MDLabel.java:87
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xmipp.jni.MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED
static final int MDL_CTF_DOWNSAMPLE_PERFORMED
< Iceness of the micrograph
Definition: MDLabel.java:155
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xmipp.jni.EllipseCTF.setFreqRange
void setFreqRange(double lowFreq, double highFreq)
Definition: EllipseCTF.java:72
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xmipp.jni.MDLabel.MDL_CTF_VOLTAGE
static final int MDL_CTF_VOLTAGE
< Sampling rate in Z direction
Definition: MDLabel.java:84
-
xmipp.jni.EllipseCTF.setDefocus
void setDefocus(double defU, double defV, double angle)
Definition: EllipseCTF.java:166
-
xmipp.jni.MetaData.setValueDouble
native boolean setValueDouble(int label, double value, long objId)
-
xmipp.jni.EllipseCTF.setEllipseFitter
void setEllipseFitter(EllipseFitter ellipseFitter)
Definition: EllipseCTF.java:27
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xmipp.jni.EllipseCTF.getDownsamplingFactor
double getDownsamplingFactor()
Definition: EllipseCTF.java:162
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_ANGLE
static final int MDL_CTF_DEFOCUS_ANGLE
< Defocus = A*x+B*y+C
Definition: MDLabel.java:102
-
xmipp.jni.MDLabel.MDL_CTF_CS
static final int MDL_CTF_CS
< Defocus angle (degrees)
Definition: MDLabel.java:103
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xmipp.jni.MDLabel.MDL_CTF_Q0
static final int MDL_CTF_Q0
< Transversal displacemente
Definition: MDLabel.java:113
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package  xmipp.viewer.ctf
 
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.viewer.ctf;
6 
7 import xmipp.jni.EllipseCTF;
8 
9 
14 public class EstimateFromCTFTask extends CommandTask {
15 
16  private final static String XMIPP_CTF_ESTIMATE_FROM_PSD = "xmipp_ctf_estimate_from_psd";
17 
18  public EstimateFromCTFTask(EllipseCTF ellipseCTF, double angle, String PSDFilename, int modelSize,
19  iTaskCompletionListener commandsListener, int row, String sortFn) {
20  super(XMIPP_CTF_ESTIMATE_FROM_PSD
21  + " --sampling_rate " + ellipseCTF.getSamplingRate()
22  + " --downSamplingPerformed " + ellipseCTF.getDownsamplingFactor()
23  + " --kV " + ellipseCTF.getVoltage()
24  + " --Cs " + ellipseCTF.getSphericalAberration()
25  + " --defocusU " + ellipseCTF.getDefocusU()
26  + " --defocusV " + ellipseCTF.getDefocusV()
27  + " --azimuthal_angle " + angle
28  + " --psd " + PSDFilename
29  + " --ctfmodelSize " + modelSize
30  + " --min_freq " + ellipseCTF.getLowFreq()
31  + " --max_freq " + ellipseCTF.getHighFreq()
32  + " --Q0 " + ellipseCTF.getQ0()
33  + " --defocus_range 5000"
34 
35  ,//+ " ; " + getSortCmd(sortFn),
36  row,
37  commandsListener);
38 
39  addCommand(getSortCmd(sortFn));
40  }
41 
42  public static String getSortCmd(String filename){
43  return String.format("xmipp_ctf_sort_psds -i %s -o %s", filename, filename);
44  }
45 }
xmipp.viewer.ctf.EstimateFromCTFTask.EstimateFromCTFTask
EstimateFromCTFTask(EllipseCTF ellipseCTF, double angle, String PSDFilename, int modelSize, iTaskCompletionListener commandsListener, int row, String sortFn)
Definition: EstimateFromCTFTask.java:18
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xmipp.jni.EllipseCTF.getSphericalAberration
double getSphericalAberration()
Definition: EllipseCTF.java:114
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static String getSortCmd(String filename)
Definition: EstimateFromCTFTask.java:42
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iTaskCompletionListener commandsListener
Definition: CommandTask.java:23
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xmipp.jni.EllipseCTF.getDownsamplingFactor
double getDownsamplingFactor()
Definition: EllipseCTF.java:162
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xmipp.viewer.ctf.CommandTask.addCommand
void addCommand(String command)
Definition: CommandTask.java:59
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1 import ij.*;
2 import ij.gui.*;
3 import ij.plugin.PlugIn;
4 import java.awt.*;
5 
10 public class Example_Plot implements PlugIn {
11 
12  public void run(String arg) {
13  if (IJ.versionLessThan("1.27t"))
14  return;
15 
16  float[] x = {0.1f, 0.25f, 0.35f, 0.5f, 0.61f,0.7f,0.85f,0.89f,0.95f}; // x-coordinates
17  float[] y = {2f,5.6f,7.4f,9f,9.4f,8.7f,6.3f,4.5f,1f}; // x-coordinates
18  float[] e = {.8f,.6f,.5f,.4f,.3f,.5f,.6f,.7f,.8f}; // error bars
19 
20  PlotWindow plot = new PlotWindow("Example Plot","x-axis","y-axis",x,y);
21  plot.setLimits(0, 1, 0, 10);
22  plot.addErrorBars(e);
23 
24  // add a second curve
25  float x2[] = {.4f,.5f,.6f,.7f,.8f};
26  float y2[] = {4,3,3,4,5};
27  plot.setColor(Color.red);
28  plot.addPoints(x2,y2,PlotWindow.X);
29  plot.addPoints(x2,y2,PlotWindow.LINE);
30 
31  plot.setColor(Color.blue);
32  plot.draw();
33  }
34 }
Example_Plot
Definition: Example_Plot.java:10
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Definition: Example_Plot.java:12
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.viewer.windows;
8 
9 import java.awt.GridBagConstraints;
10 import java.awt.GridBagLayout;
11 import java.awt.Insets;
12 import java.awt.event.ActionEvent;
13 import java.awt.event.ActionListener;
14 import java.io.File;
15 import java.util.ArrayList;
16 import java.util.Arrays;
17 import java.util.List;
18 
19 import javax.swing.JButton;
20 import javax.swing.JCheckBox;
21 import javax.swing.JDialog;
22 import javax.swing.JLabel;
23 import javax.swing.JPanel;
24 import javax.swing.JTextField;
25 
26 import xmipp.ij.commons.XmippApplication;
27 import xmipp.ij.commons.XmippUtil;
28 import xmipp.jni.Filename;
29 import xmipp.jni.MDLabel;
30 import xmipp.jni.MetaData;
31 import xmipp.utils.XmippDialog;
32 import xmipp.utils.XmippFileChooser;
33 import xmipp.utils.XmippWindowUtil;
34 
39 public class ExportImagesJDialog extends JDialog{
40 
41  private int label;
42  private String path;
43  private XmippFileChooser fc;
44  private JButton savebt;
45  private JButton cancelbt;
46  private final String note1 = "<html><b>Note 1:</b> Only enabled images will be saved";
47  private final String note2 = "<html><b>Note 2:</b> Use extension stk, mrcs or img to save as SPIDER, MRC or IMAGIC stacks";
48  private JButton browsebt;
49  private JTextField pathtf;
50  private JCheckBox applygeochb;
51 
52  private GalleryJFrame frame;
53 
54  public ExportImagesJDialog(GalleryJFrame parent)
55  {
56  super(parent);
57  this.frame = parent;
58 
59  path = parent.data.getFileName();
60  if(path == null)
61  path = "images";
62  path = Filename.removeExtension(path) + "_export.stk";
63  label = parent.data.getRenderLabel();
64  initComponents();
65  }
66 
67  private void initComponents() {
68  setTitle("Export Images ...");
69 
70  setLayout(new GridBagLayout());
71  GridBagConstraints c = new GridBagConstraints();
72  c.anchor = GridBagConstraints.WEST;
73  c.insets = new Insets(5, 5, 5, 5);
74  add(new JLabel("Path:"), XmippWindowUtil.getConstraints(c, 0, 0));
75 
76 
77  pathtf = new JTextField(path);
78  pathtf.setColumns(50);
79  add(pathtf, XmippWindowUtil.getConstraints(c, 1, 0));
80  fc = new XmippFileChooser(path);
81  if(path.contains(File.separator))
82  {
83  int index = path.lastIndexOf(File.separator);//-1 if separator does not exists
84  String dir = path.substring(0, index);
85  fc.setCurrentDirectory(new File(dir));
86  }
87  browsebt = XmippWindowUtil.getIconButton("folderopen.gif", new ActionListener() {
88 
89  @Override
90  public void actionPerformed(ActionEvent ae) {
91  int returnVal = fc.showOpenDialog(null);
92 
93  if (returnVal == XmippFileChooser.APPROVE_OPTION)
94  {
95  File file = fc.getSelectedFile();
96  String text = file.getPath();
97  pathtf.setText(text);
98  }
99  }
100  });
101  add(browsebt, XmippWindowUtil.getConstraints(c, 2, 0));
102  JLabel applygeolb = new JLabel("Apply Geometry:");
103  add(applygeolb, XmippWindowUtil.getConstraints(c, 0, 1));
104 
105 
106  applygeochb = new JCheckBox();
107  applygeochb.setSelected(frame.data.useGeo());
108  applygeochb.setEnabled(frame.data.containsGeometryInfo());
109  applygeolb.setEnabled(frame.data.containsGeometryInfo());
110  add(applygeochb, XmippWindowUtil.getConstraints(c, 1, 1));
111  add(new JLabel(note1), XmippWindowUtil.getConstraints(c, 0, 2, GridBagConstraints.HORIZONTAL));
112  add(new JLabel(note2), XmippWindowUtil.getConstraints(c, 0, 3, GridBagConstraints.HORIZONTAL));
113  JPanel actionspn = new JPanel();
114  cancelbt = XmippWindowUtil.getTextButton("Cancel", new ActionListener() {
115 
116  @Override
117  public void actionPerformed(ActionEvent ae) {
118  close();
119  }
120  });
121  actionspn.add(cancelbt);
122 
123  savebt = XmippWindowUtil.getTextButton("Export", new ActionListener() {
124 
125  @Override
126  public void actionPerformed(ActionEvent ae) {
127  saveImages();
128  close();
129  }
130  });
131  actionspn.add(savebt);
132  add(actionspn, XmippWindowUtil.getConstraints(c, 0, 4, GridBagConstraints.HORIZONTAL));
133  pack();
134  XmippWindowUtil.setLocation(0.5, 0.5, this);
135  setVisible(true);
136  }
137 
138  private void close()
139  {
140  setVisible(false);
141  dispose();
142  }
143 
144  private void saveImages()
145  {
146  XmippWindowUtil.blockGUI(frame, "Exporting images..", true);
147  new Thread(new Runnable() {
148 
149  @Override
150  public void run() {
151 
152  try {
153  path = pathtf.getText();
154  if(path.endsWith(".mrcs"))
155  path += ":mrcs";
156  int label = frame.data.getRenderColumn().label;
157  MetaData md;
158  if(frame.data.isScipionInstance())
159  {
160  md = frame.data.getImagesMd();//reads only enabled objects
161  label = MDLabel.MDL_IMAGE;
162  }
163  else
164  md = frame.data.getMd();
165 
166  // Relion rlnAnglePsi is inverse as how we expect it in Xmipp
167  // that's why we need to invert the angle before exporting particles
168  System.out.println("Exporting metadata to: " + path);
169 
170  if (md.containsLabel(MetaData.GEOMETRY_RELION_LABELS))
171  {
172  // Since we need to modify the metadata, let's make a copy
173  // Since the copy constructor is not ported to the binding
174  // I will use this dirty way with unionAll
175  MetaData md2 = new MetaData();
176  md2.unionAll(md);
177  md = md2;
178  md.operate("rlnAnglePsi=rlnAnglePsi*-1");
179  md.renameColumn(MDLabel.RLN_ORIENT_ORIGIN_X, MDLabel.MDL_SHIFT_X);
180  md.renameColumn(MDLabel.RLN_ORIENT_ORIGIN_Y, MDLabel.MDL_SHIFT_Y);
181  md.renameColumn(MDLabel.RLN_ORIENT_PSI, MDLabel.MDL_ANGLE_PSI);
182  }
183 
184  md.writeMdToStack(path, applygeochb.isSelected(), frame.data.isWrap(), label);
185 
186  } catch (Exception ex) {
187 
188  XmippDialog.showException(frame,ex);
189  } finally {
190  XmippWindowUtil.releaseGUI(frame.getRootPane());
191  }
192 
193  }
194  }).start();
195  }
196 
197 
198 
199 
200 }
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static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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xmipp.jni.MDLabel.MDL_ANGLE_PSI
static final int MDL_ANGLE_PSI
Special label to be used when gathering MDs in MpiMetadataPrograms.
Definition: MDLabel.java:8
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static final int MDL_SHIFT_Y
< difference in Shift along X axis (double)
Definition: MDLabel.java:367
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boolean showException(Exception e)
Definition: XmippDialog.java:217
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static final int RLN_ORIENT_ORIGIN_X
Definition: MDLabel.java:662
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xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Y
static final int RLN_ORIENT_ORIGIN_Y
Definition: MDLabel.java:664
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xmipp.jni.MetaData.GEOMETRY_RELION_LABELS
static final int GEOMETRY_RELION_LABELS[]
Definition: MetaData.java:80
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xmipp.jni.MetaData.unionAll
native void unionAll(MetaData mdIn)
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xmipp.utils.XmippWindowUtil.releaseGUI
static void releaseGUI(JRootPane panel)
Definition: XmippWindowUtil.java:242
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native void writeMdToStack(String filename, boolean applyGeo, boolean wrap, int label)
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static final int MDL_SHIFT_X
< A collection of micrographs, e.g. a tilt serie (std::string)
Definition: MDLabel.java:363
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xmipp.jni.Filename.removeExtension
static String removeExtension(String path)
Definition: Filename.java:465
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xmipp.utils.XmippWindowUtil.getTextButton
static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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xmipp.jni.MDLabel.MDL_IMAGE
static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
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native void operate(String operateStr)
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static final int RLN_ORIENT_PSI
Definition: MDLabel.java:672
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static JButton getIconButton(String icon, ActionListener listener)
Definition: XmippWindowUtil.java:124
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native void renameColumn(int oldLabel, int newLabel)
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xmipp.viewer.models.GalleryData.getMd
MetaData getMd(List< Long > ids)
Definition: GalleryData.java:1626
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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package  xmipp.viewer.particlepicker.extract
 
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1 package xmipp.viewer.particlepicker.extract;
2 
3 import java.awt.Color;
4 import java.awt.Graphics2D;
5 import java.awt.event.MouseEvent;
6 
7 import javax.swing.SwingUtilities;
8 
9 import xmipp.jni.Particle;
10 import xmipp.viewer.particlepicker.*;
11 
12 public class ExtractCanvas extends ParticlePickerCanvas
13 {
14 
15  public ExtractCanvas(ExtractPickerJFrame frame)
16  {
17  super(frame);
18  active = getLastParticle();
19  }
20 
21  @Override
22  public void refreshActive(PickerParticle p)
23  {
24  active = p;
25  repaint();
26 
27  }
28 
29  @Override
30  public ExtractParticle getActive()
31  {
32  return (ExtractParticle) active;
33  }
34 
35  @Override
36  public ExtractMicrograph getMicrograph()
37  {
38  return (ExtractMicrograph)micrograph;
39  }
40 
41  @Override
42  protected void doCustomPaint(Graphics2D g2)
43  {
44  Color color;
45  double score;
46  for (ExtractParticle p : getMicrograph().getParticles())
47  {
48  score = p.getScore(getFrame().getColorHelper().getId());
49  color = getFrame().getColorHelper().getColor(score);
50  if (p.isEnabled())
51  drawShape(g2, p.getX(), p.getY(), getFrame().getParticlePicker().getSize(), false, continuousst, color);
52  else
53  drawShape(g2, p.getX(), p.getY(), getFrame().getParticlePicker().getSize(), false, dashedst, color);
54  }
55  if (active != null)
56  {
57  score = getActive().getScore(getFrame().getColorHelper().getId());
58  color = getFrame().getColorHelper().getColor(score);
59  drawShape(g2, active.getX(), active.getY(), frame.getParticlePicker().getSize(), true, activest, color);
60  }
61  }
62 
63  protected ExtractParticle getLastParticle()
64  {
65  if (getMicrograph().getParticles().isEmpty())
66  return null;
67  return getMicrograph().getParticles().get(getMicrograph().getParticles().size() - 1);
68  }
69 
70  public void mousePressed(MouseEvent e)
71  {
72  super.mousePressed(e);
73  int x = super.offScreenX(e.getX());
74  int y = super.offScreenY(e.getY());
75 
76  if (frame.isPickingAvailable(e))
77  {
78  if (frame.isEraserMode(null))
79  {
80  getMicrograph().removeParticles(x, y, picker);
81  active = getLastParticle();
82  refresh();
83 
84  return;
85  }
86  ExtractParticle p = getMicrograph().getParticle(x, y, picker.getSize());
87 
88  if (p != null)
89  {
90  if (SwingUtilities.isLeftMouseButton(e))
91  {
92  if (e.isShiftDown())
93  p.setEnabled(!p.isEnabled());
94  active = p;
95  }
96  getFrame().refreshActiveOnGallery(getActive());
97  }
98 
99  refresh();
100  }
101  }
102 
103  @Override
104  public void mouseDragged(MouseEvent e)
105  {
106 
107  super.mouseDragged(e);
108  int x = super.offScreenX(e.getX());
109  int y = super.offScreenY(e.getY());
110  if (frame.isPickingAvailable(e))
111  {
112  if (frame.isEraserMode(e))
113  {
114  getMicrograph().removeParticles(x, y, picker);
115  active = getLastParticle();
116  refresh();
117  return;
118  }
119  if (active == null)
120  return;
121 
122  if (!micrograph.fits(x, y, picker.getSize()))
123  return;
124  moveActiveParticle(x, y);
125  getActive().setEnabled(true);// if it was disabled gets enabled
126  getFrame().refreshActiveOnGallery(getActive());// if enabled propagate info
127  frame.setChanged(true);
128  repaint();
129  }
130  }
131 
132 
133 
134  protected void moveActiveParticle(int x, int y)
135  {
136  getActive().setEnabled(true);
137  super.moveActiveParticle(x, y);
138  getFrame().refreshActiveOnGallery(getActive());
139  }
140 
141  @Override
142  protected void manageActive(int x, int y)
143  {
144  if(!activemoved)
145  return;
146  if (!micrograph.fits(x, y, picker.getSize()))
147  return;
148  moveActiveParticle(x, y);
149  setActiveMoved(false);
150 
151  }
152 
153  @Override
154  public ExtractPickerJFrame getFrame()
155  {
156  return (ExtractPickerJFrame)frame;
157  }
158 
159  @Override
160  protected void removeParticle(PickerParticle particleToRemove) {
161  getMicrograph().removeParticle((ExtractParticle) particleToRemove);
162  }
163 
164  @Override
165  public ExtractParticlePicker getParticlePicker()
166  {
167  return (ExtractParticlePicker)picker;
168  }
169 
170 }
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abstract void setChanged(boolean changed)
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ExtractParticle getParticle(int x, int y, int size)
Definition: ExtractMicrograph.java:64
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xmipp.viewer.particlepicker.extract.ExtractMicrograph.removeParticles
void removeParticles(int x, int y, ParticlePicker picker)
Definition: ExtractMicrograph.java:46
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void removeParticle(PickerParticle particleToRemove)
Definition: ExtractCanvas.java:160
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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package  xmipp.viewer.particlepicker.extract
 
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1 package xmipp.viewer.particlepicker.extract;
2 
3 import java.util.ArrayList;
4 import java.util.List;
5 
6 import xmipp.jni.Particle;
7 import xmipp.viewer.particlepicker.CtfInfo;
8 import xmipp.viewer.particlepicker.Micrograph;
9 import xmipp.viewer.particlepicker.ParticlePicker;
10 import xmipp.viewer.particlepicker.PickerParticle;
11 
12 public class ExtractMicrograph extends Micrograph
13 {
14 
15  private ArrayList<ExtractParticle> particles;
16 
17  public ExtractMicrograph(String file, CtfInfo ctfInfo)
18  {
19  super(file, ctfInfo);
20  particles = new ArrayList<ExtractParticle>();
21  }
22 
23  @Override
24  public boolean hasData()
25  {
26  return !particles.isEmpty();
27  }
28 
29  @Override
30  public List<? extends PickerParticle> getParticleList() {
31  return getParticles();
32  }
33 
34 
35  public void addParticle(ExtractParticle p)
36  {
37  particles.add(p);
38 
39  }
40 
41  public List<ExtractParticle> getParticles()
42  {
43  return particles;
44  }
45 
46  public void removeParticles(int x, int y, ParticlePicker picker)
47  {
48  List<ExtractParticle> removelist = new ArrayList<ExtractParticle>();
49 
50  for (ExtractParticle p : particles)
51  if (p.contains(x, y, picker.getSize()))
52  removelist.add(p);
53  for (ExtractParticle p : removelist)
54  removeParticle(p);
55 
56 
57  }
58 
59  public void removeParticle(ExtractParticle particle)
60  {
61  particle.setEnabled(false);
62  }
63 
64  public ExtractParticle getParticle(int x, int y, int size)
65  {
66  for(ExtractParticle p: particles)
67  if(p.contains(x, y, size))
68  return p;
69  return null;
70  }
71 
72 
73 }
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ExtractParticle getParticle(int x, int y, int size)
Definition: ExtractMicrograph.java:64
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void removeParticles(int x, int y, ParticlePicker picker)
Definition: ExtractMicrograph.java:46
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package  xmipp.viewer.particlepicker.extract
 
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1 package xmipp.viewer.particlepicker.extract;
2 
3 import java.util.ArrayList;
4 import java.util.List;
5 import java.util.logging.Level;
6 
7 import javax.swing.JFrame;
8 import javax.swing.JOptionPane;
9 
10 import xmipp.ij.commons.IJCommand;
11 import xmipp.ij.commons.XmippImageJ;
12 import xmipp.jni.MDLabel;
13 import xmipp.jni.MetaData;
14 import xmipp.utils.XmippDialog;
15 import xmipp.viewer.particlepicker.*;
16 import xmipp.viewer.particlepicker.training.model.Mode;
17 import xmipp.viewer.windows.GalleryJFrame;
18 
19 public class ExtractParticlePicker extends ParticlePicker
20 {
21 
22  private ArrayList<ExtractMicrograph> micrographs;
23  private ExtractMicrograph micrograph;
24  private ArrayList<ColorHelper> colorby;
25 
26 
27  public ExtractParticlePicker(String selfile, int size, ParticlePickerParams params)
28  {
29  super(selfile, params);
30  setSize(size);
31  loadParticles();
32  if (filters.isEmpty())
33  filters.add(new IJCommand(XmippImageJ.gaussianBlurFilter, "sigma=2"));
34  }
35 
36  public ExtractParticlePicker(String block, String selfile, int size, ParticlePickerParams params)
37  {
38  super(block, selfile, ".", params);
39  setSize(size);
40  loadParticles();
41  if (filters.isEmpty())
42  filters.add(new IJCommand(XmippImageJ.gaussianBlurFilter, "sigma=2"));
43  }
44 
45 
46 
47  @Override
48  public void loadEmptyMicrographs()
49  {
50  micrographs = new ArrayList<ExtractMicrograph>();
51  String path = (block == null)? selfile: block + "@" + selfile;
52  MetaData md = new MetaData(path);
53  String fileiter;
54  boolean exists;
55  ExtractMicrograph current = null;
56  boolean existspsd = md.containsLabel(MDLabel.MDL_PSD_ENHANCED);
57  boolean existsctf = md.containsLabel(MDLabel.MDL_CTF_MODEL);
58  String psd = null, ctf = null;
59  CtfInfo ctfInfo;
60 
61  for (long id : md.findObjects())
62  {
63  exists = false;
64  fileiter = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
65  for (ExtractMicrograph iter : micrographs)
66  if (iter.getFile().equals(fileiter))
67  {
68  exists = true;
69  current = iter;
70  break;
71  }
72  if (!exists)
73  {
74  ctfInfo = (existsctf || existspsd) ? new CtfInfo() : null;
75  if (existspsd)
76  ctfInfo.psd = md.getValueString(MDLabel.MDL_PSD_ENHANCED, id);
77  if (existsctf)
78  ctfInfo.ctf = md.getValueString(MDLabel.MDL_CTF_MODEL, id);
79  current = new ExtractMicrograph(fileiter, ctfInfo);
80 
81  micrographs.add(current);
82  }
83 
84  }
85  loadColumns(md);
86  md.destroy();
87 
88  }
89 
90  public void loadColumns(MetaData md)
91  {
92  colorby = new ArrayList<ColorHelper>();
93 
94  loadColumn(MDLabel.MDL_ZSCORE, "ZScore", md);
95  loadColumn(MDLabel.MDL_ZSCORE_SHAPE1, "ZScore-Shape1", md);
96  loadColumn(MDLabel.MDL_ZSCORE_SHAPE2, "ZScore-Shape2", md);
97  loadColumn(MDLabel.MDL_ZSCORE_SNR1, "ZScore-SNR1", md);
98  loadColumn(MDLabel.MDL_ZSCORE_SNR2, "ZScore-SNR2", md);
99  loadColumn(MDLabel.MDL_ZSCORE_HISTOGRAM, "ZScore-Hist", md);
100  if(colorby.isEmpty())
101  throw new IllegalArgumentException("No score available to sort particles");
102 
103  }
104 
105  public void loadColumn(int column, String name, MetaData md)
106  {
107  boolean exists = md.containsLabel(column);
108  if(exists)
109  {
110  colorby.add(new ColorHelper(column, name, md));
111  }
112  }
113 
114 
115 
116  public void loadParticles()
117  {
118  String path = (block == null)? selfile: block + "@" + selfile;
119  MetaData md = new MetaData(path);
120  ExtractParticle p;
121  int x, y;
122  String fileiter;
123  boolean enabled;
124  ExtractMicrograph current = null;
125  double zscore, zscore_shape1, zscore_shape2, zscore_snr1, zscore_snr2, zscore_hist;
126  for (long id : md.findObjects())
127  {
128  fileiter = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
129  for (ExtractMicrograph iter : micrographs)
130  if (iter.getFile().equals(fileiter))
131  {
132  current = iter;
133  break;
134  }
135 
136  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
137  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
138  enabled = (md.getValueInt(MDLabel.MDL_ENABLED, id) == 1) ? true : false;
139  zscore = md.getValueDouble(MDLabel.MDL_ZSCORE, id);
140  zscore_shape1 = md.getValueDouble(MDLabel.MDL_ZSCORE_SHAPE1, id);
141  zscore_shape2 = md.getValueDouble(MDLabel.MDL_ZSCORE_SHAPE2, id);
142  zscore_snr1 = md.getValueDouble(MDLabel.MDL_ZSCORE_SNR1, id);
143  zscore_snr2 = md.getValueDouble(MDLabel.MDL_ZSCORE_SNR2, id);
144  zscore_hist = md.getValueDouble(MDLabel.MDL_ZSCORE_HISTOGRAM, id);
145  p = new ExtractParticle(id, x, y, current, enabled, zscore, zscore_shape1, zscore_shape2, zscore_snr1, zscore_snr2, zscore_hist);
146  current.addParticle(p);
147 
148  }
149  md.destroy();
150  }
151 
152  @Override
153  public List<ExtractMicrograph> getMicrographs()
154  {
155  return micrographs;
156  }
157 
158  public void saveData()
159  {
160  if (isChanged())
161  for(ExtractMicrograph m: micrographs)
162  saveData(m);
163  }
164 
165  @Override
166  public void saveData(Micrograph m)
167  {
168  long id;
169  micrograph = (ExtractMicrograph)m;
170  try
171  {
172  MetaData md = new MetaData();
173 
174  for (ExtractParticle p : micrograph.getParticles())
175  {
176  id = p.getId();
177  md.setValueInt(MDLabel.MDL_XCOOR, p.getX(), id);
178  md.setValueInt(MDLabel.MDL_YCOOR, p.getY(), id);
179  md.setValueInt(MDLabel.MDL_ENABLED, p.isEnabled()? 1: -1, id);
180  }
181  String path = (block == null)? selfile: block + "@" + selfile;
182  md.write(path);
183  md.destroy();
184 
185  }
186  catch (Exception e)
187  {
188  getLogger().log(Level.SEVERE, e.getMessage(), e);
189  throw new IllegalArgumentException(e.getMessage());
190  }
191 
192  }
193 
194  @Override
195  public ExtractMicrograph getMicrograph()
196  {
197  return micrograph;
198  }
199 
200  @Override
201  public void setMicrograph(Micrograph m)
202  {
203  micrograph = (ExtractMicrograph) m;
204 
205  }
206 
207  @Override
208  public void saveConfig()
209  {
210  // TODO Auto-generated method stub
211 
212  }
213 
214  @Override
215  public void loadConfig()
216  {
217  setMicrograph(micrographs.get(0));
218  }
219 
220  public static ExtractPickerJFrame open(String block, String filename, int size, GalleryJFrame galleryfr)
221  {
222  try
223 
224  {
225  ExtractParticlePicker picker = new ExtractParticlePicker(block, filename, size, new ParticlePickerParams(Mode.Extract));
226  return new ExtractPickerJFrame(picker, galleryfr);
227  }
228  catch(Exception e)
229  {
230  XmippDialog.showError(null,e.getMessage());
231  return null;
232  }
233  }
234 
235  @Override
236  public int getParticlesCount()
237  {
238  int particles = 0;
239  for (ExtractMicrograph m : micrographs)
240  particles += m.getParticles().size();
241  return particles;
242  }
243 
244 
245 
246  public ColorHelper[] getColumns()
247  {
248  return colorby.toArray(new ColorHelper[]{});
249  }
250 
251  @Override
252  public boolean isValidSize(JFrame parent, int size)
253  {
254  for (ExtractParticle p : getMicrograph().getParticles())
255  if (!getMicrograph().fits(p.getX(), p.getY(), size))
256  return false;
257  return true;
258  }
259 
260 
261 
262 
263 
264 }
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xmipp.jni.MetaData.containsLabel
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xmipp.viewer.particlepicker.extract.ExtractParticlePicker.ExtractParticlePicker
ExtractParticlePicker(String selfile, int size, ParticlePickerParams params)
Definition: ExtractParticlePicker.java:27
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xmipp.jni.MetaData.write
native void write(String filename)
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xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MDLabel.MDL_ZSCORE_SNR1
static final int MDL_ZSCORE_SNR1
< Z Score (double)
Definition: MDLabel.java:444
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xmipp.jni.MDLabel.MDL_CTF_MODEL
static final int MDL_CTF_MODEL
< Parameters file for the CTF Model (std::string)
Definition: MDLabel.java:80
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE1
static final int MDL_ZSCORE_SHAPE1
< Z Score of the covariance matrix of the residuals (double)
Definition: MDLabel.java:442
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.jni.MDLabel.MDL_PSD_ENHANCED
static final int MDL_PSD_ENHANCED
< A Power Spectrum Density file name (std::string)
Definition: MDLabel.java:309
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xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE2
static final int MDL_ZSCORE_SHAPE2
< Z Score (double)
Definition: MDLabel.java:443
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xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
-
xmipp.jni.MDLabel.MDL_ZSCORE_SNR2
static final int MDL_ZSCORE_SNR2
< Z Score (double)
Definition: MDLabel.java:445
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.viewer.particlepicker.extract.ExtractParticlePicker.ExtractParticlePicker
ExtractParticlePicker(String block, String selfile, int size, ParticlePickerParams params)
Definition: ExtractParticlePicker.java:36
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xmipp.jni.MDLabel.MDL_ZSCORE_HISTOGRAM
static final int MDL_ZSCORE_HISTOGRAM
< Z Score (double)
Definition: MDLabel.java:438
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xmipp.viewer.particlepicker.extract.ExtractParticlePicker.open
static ExtractPickerJFrame open(String block, String filename, int size, GalleryJFrame galleryfr)
Definition: ExtractParticlePicker.java:220
-
xmipp.jni.MDLabel.MDL_ZSCORE
static final int MDL_ZSCORE
< Z component (int)
Definition: MDLabel.java:435
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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static final String gaussianBlurFilter
Definition: XmippImageJ.java:14
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class  xmipp.viewer.particlepicker.extract.ExtractParticle
 
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package  xmipp.viewer.particlepicker.extract
 
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1 package xmipp.viewer.particlepicker.extract;
2 
3 import java.awt.Color;
4 
5 import xmipp.jni.MDLabel;
6 import xmipp.viewer.particlepicker.ColorHelper;
7 import xmipp.viewer.particlepicker.Micrograph;
8 import xmipp.viewer.particlepicker.PickerParticle;
9 
10 public class ExtractParticle extends PickerParticle
11 {
12  private boolean enabled;
13  private long id;
14  private double zscore, zscore_shape1, zscore_shape2, zscore_snr1, zscore_snr2, zscore_hist;
15 
16  public ExtractParticle(long id, int x, int y, Micrograph m, boolean enabled, double zscore,
17  double zscore_shape1, double zscore_shape2, double zscore_snr1, double zscore_snr2, double zscore_hist)
18  {
19  super(x, y, m);
20  this.enabled = enabled;
21  this.id = id;
22  this.zscore = zscore;
23  this.zscore_hist = zscore_hist;
24  this.zscore_shape1 = zscore_shape1;
25  this.zscore_shape2 = zscore_shape2;
26  this.zscore_snr1 = zscore_snr1;
27  this.zscore_snr2 = zscore_snr2;
28 
29  }
30 
31  public long getId()
32  {
33  return id;
34  }
35 
36  public ExtractParticle(long id, int x, int y, Micrograph m, double zscore, double zscore_shape1, double zscore_shape2,
37  double zscore_snr1, double zscore_snr2, double zscore_hist)
38  {
39  this(id, x, y, m, true, zscore, zscore_shape1, zscore_shape2, zscore_snr1, zscore_snr2, zscore_hist);
40  }
41 
42  public boolean isEnabled()
43  {
44  return enabled;
45  }
46 
47 
48 
49  public double getZscore()
50  {
51  return zscore;
52  }
53 
54 
55 
56  public double getZscore_shape1()
57  {
58  return zscore_shape1;
59  }
60 
61  public double getZscore_shape2()
62  {
63  return zscore_shape2;
64  }
65 
66  public double getZscore_snr1()
67  {
68  return zscore_snr1;
69  }
70 
71 
72  public double getZscore_snr2()
73  {
74  return zscore_snr2;
75  }
76 
77 
78 
79  public double getZscore_hist()
80  {
81  return zscore_hist;
82  }
83 
84  public void setEnabled(boolean b)
85  {
86  enabled = b;
87 
88  }
89 
90 
91 
92 
93  public double getScore(int id)
94  {
95  if(id == MDLabel.MDL_ZSCORE)
96  return getZscore();
97  if(id == MDLabel.MDL_ZSCORE_SHAPE1)
98  return getZscore_shape1();
99  if(id == MDLabel.MDL_ZSCORE_SHAPE2)
100  return getZscore_shape2();
101  if(id == MDLabel.MDL_ZSCORE_SNR1)
102  return getZscore_snr1();
103  if(id == MDLabel.MDL_ZSCORE_SNR2)
104  return getZscore_snr2();
105  if(id == MDLabel.MDL_ZSCORE_HISTOGRAM)
106  return getZscore_hist();
107  return 0;
108  }
109 
110 
111 
112 
113 
114 
115 
116 
117 }
- - -
xmipp.viewer.particlepicker.extract.ExtractParticle.ExtractParticle
ExtractParticle(long id, int x, int y, Micrograph m, boolean enabled, double zscore, double zscore_shape1, double zscore_shape2, double zscore_snr1, double zscore_snr2, double zscore_hist)
Definition: ExtractParticle.java:16
-
xmipp.jni.MDLabel.MDL_ZSCORE_SNR1
static final int MDL_ZSCORE_SNR1
< Z Score (double)
Definition: MDLabel.java:444
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xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE1
static final int MDL_ZSCORE_SHAPE1
< Z Score of the covariance matrix of the residuals (double)
Definition: MDLabel.java:442
-
xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE2
static final int MDL_ZSCORE_SHAPE2
< Z Score (double)
Definition: MDLabel.java:443
-
xmipp.jni.MDLabel.MDL_ZSCORE_SNR2
static final int MDL_ZSCORE_SNR2
< Z Score (double)
Definition: MDLabel.java:445
- -
xmipp.jni.MDLabel.MDL_ZSCORE_HISTOGRAM
static final int MDL_ZSCORE_HISTOGRAM
< Z Score (double)
Definition: MDLabel.java:438
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xmipp.jni.MDLabel.MDL_ZSCORE
static final int MDL_ZSCORE
< Z component (int)
Definition: MDLabel.java:435
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xmipp.viewer.particlepicker.extract.ExtractParticle.ExtractParticle
ExtractParticle(long id, int x, int y, Micrograph m, double zscore, double zscore_shape1, double zscore_shape2, double zscore_snr1, double zscore_snr2, double zscore_hist)
Definition: ExtractParticle.java:36
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class  xmipp.viewer.particlepicker.extract.ExtractPickerJFrame
 
class  xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.ExtractMicrographsTableModel
 
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package  xmipp.viewer.particlepicker.extract
 
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ExtractPickerJFrame.java
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1 package xmipp.viewer.particlepicker.extract;
2 
3 import java.awt.Dimension;
4 import java.awt.FlowLayout;
5 import java.awt.GridBagConstraints;
6 import java.awt.GridBagLayout;
7 import java.awt.Insets;
8 import java.awt.event.ActionEvent;
9 import java.awt.event.ActionListener;
10 import java.awt.event.MouseEvent;
11 import java.util.List;
12 
13 import javax.swing.BorderFactory;
14 import javax.swing.JButton;
15 import javax.swing.JComboBox;
16 import javax.swing.JLabel;
17 import javax.swing.JMenu;
18 import javax.swing.JMenuBar;
19 import javax.swing.JPanel;
20 import javax.swing.JScrollPane;
21 import javax.swing.JTable;
22 import javax.swing.ListSelectionModel;
23 import javax.swing.table.AbstractTableModel;
24 
25 import xmipp.utils.XmippDialog;
26 import xmipp.utils.XmippWindowUtil;
27 import xmipp.viewer.ctf.CTFAnalyzerJFrame;
28 import xmipp.viewer.particlepicker.ColorHelper;
29 import xmipp.viewer.particlepicker.Format;
30 import xmipp.viewer.particlepicker.Micrograph;
31 import xmipp.viewer.particlepicker.ParticlePicker;
32 import xmipp.viewer.particlepicker.ParticlePickerCanvas;
33 import xmipp.viewer.particlepicker.ParticlePickerJFrame;
34 import xmipp.viewer.particlepicker.ParticlesDialog;
35 import xmipp.viewer.particlepicker.PickerParticle;
36 import xmipp.viewer.particlepicker.training.model.Mode;
37 import xmipp.viewer.windows.GalleryJFrame;
38 
39 public class ExtractPickerJFrame extends ParticlePickerJFrame
40 {
41 
42  private ExtractParticlePicker picker;
43  private JMenuBar mb;
44  private JPanel micrographpn;
45  private JButton iconbt;
46  private ExtractMicrographsTableModel micrographsmd;
47  private JLabel particleslb;
48  private int index;
49  private ExtractCanvas canvas;
50  private ColorHelper[] colorby;
51  private JComboBox scorescb;
52  private GalleryJFrame galleryfr;
53  private JLabel minlb;
54  private JLabel maxlb;
55  private ExtractParticle active;
56  private JPanel colorlegendpn;
57 
58  public ExtractPickerJFrame(ParticlePicker picker, GalleryJFrame galleryfr)
59  {
60  super(picker);
61  this.picker = (ExtractParticlePicker)picker;
62  this.galleryfr = galleryfr;
63  initComponents();
64  // TODO Auto-generated constructor stub
65  }
66 
67  private void initComponents()
68  {
69  setResizable(false);
70  setTitle();
71  initMenuBar();
72  setJMenuBar(mb);
73  savemi.setEnabled(false);
74 
75  GridBagConstraints constraints = new GridBagConstraints();
76  constraints.insets = new Insets(0, 5, 0, 5);
77  constraints.anchor = GridBagConstraints.WEST;
78  setLayout(new GridBagLayout());
79 
80  initToolBar();
81  add(tb, XmippWindowUtil.getConstraints(constraints, 0, 1, 2, 1, GridBagConstraints.NONE));
82 
83  add(new JLabel("Color By:"), XmippWindowUtil.getConstraints(constraints, 0, 3));
84  initColorLegendPane();
85  add(colorlegendpn, XmippWindowUtil.getConstraints(constraints, 1, 3));
86  initMicrographsPane();
87 
88  initMicrographsPane();
89  add(micrographpn, XmippWindowUtil.getConstraints(constraints, 0, 4, 3));
90 
91  pack();
92  float positionx = 0.995f;
93  XmippWindowUtil.setLocation(positionx, 0.25f, this);
94  setVisible(true);
95  }
96 
97 
98  public boolean isPickingAvailable(MouseEvent e)
99  {
100  return false;
101  }
102 
103  private void initColorLegendPane()
104  {
105 
106  colorlegendpn = new JPanel(new FlowLayout(FlowLayout.LEFT));
107 
108  colorlegendpn.add(new JLabel("Color by:"));
109  colorby = picker.getColumns();
110  scorescb = new JComboBox(colorby);
111 
112  scorescb.addActionListener(new ActionListener()
113  {
114 
115  @Override
116  public void actionPerformed(ActionEvent arg0)
117  {
118  getCanvas().repaint();
119  minlb.setText(String.format("%.2f", getColorHelper().getMin()));
120  maxlb.setText(String.format("%.2f", getColorHelper().getMax()));
121  }
122  });
123  colorlegendpn.add(scorescb);
124  minlb = new JLabel(String.format("%.2f", getColorHelper().getMin()));
125  maxlb = new JLabel(String.format("%.2f", getColorHelper().getMax()));
126 
127 
128  colorlegendpn.add(minlb);
129  colorlegendpn.add(ColorHelper.getColorMap());
130  colorlegendpn.add(maxlb);
131 
132  index = picker.getMicrographIndex();
133 
134  }
135 
136  ColorHelper getColorHelper()
137  {
138 
139  return (ColorHelper)scorescb.getSelectedItem();
140  }
141 
142  private void initMicrographsPane()
143  {
144  GridBagConstraints constraints = new GridBagConstraints();
145  constraints.insets = new Insets(0, 5, 0, 5);
146  constraints.anchor = GridBagConstraints.NORTHWEST;
147  micrographpn = new JPanel(new GridBagLayout());
148  micrographpn.setBorder(BorderFactory.createTitledBorder("Micrograph"));
149  JScrollPane sp = new JScrollPane();
150  iconbt = new JButton(Micrograph.getNoImageIcon());
151  iconbt.setToolTipText("Load CTF Profile");
152  iconbt.setBorderPainted(false);
153  iconbt.setContentAreaFilled(false);
154  iconbt.setFocusPainted(false);
155  iconbt.setOpaque(false);
156  iconbt.setMargin(new Insets(0, 0, 0, 0));
157  iconbt.addActionListener(new ActionListener()
158  {
159 
160  @Override
161  public void actionPerformed(ActionEvent arg0)
162  {
163  String psd = getMicrograph().getPSD();
164  String ctf = getMicrograph().getCTF();
165  if (psd != null && ctf != null)
166  new CTFAnalyzerJFrame(psd, ctf, psd);
167  }
168  });
169  micrographsmd = new ExtractMicrographsTableModel();
170  micrographstb.setModel(micrographsmd);
171  micrographstb.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
172  micrographstb.getColumnModel().getColumn(0).setPreferredWidth(35);
173  micrographstb.getColumnModel().getColumn(1).setPreferredWidth(345);
174  micrographstb.getColumnModel().getColumn(2).setPreferredWidth(70);
175  micrographstb.getColumnModel().getColumn(3).setPreferredWidth(70);
176  micrographstb.setPreferredScrollableViewportSize(new Dimension(520, 304));
177  micrographstb.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
178  if (index != -1)
179  micrographstb.setRowSelectionInterval(index, index);
180 
181  sp.setViewportView(micrographstb);
182  micrographpn.add(sp, XmippWindowUtil.getConstraints(constraints, 0, 0, 1));
183  micrographpn.add(iconbt, XmippWindowUtil.getConstraints(constraints, 1, 0, 1));
184  JPanel infopn = new JPanel();
185  particleslb = new JLabel(Integer.toString(picker.getParticlesCount()));
186 
187  infopn.add(new JLabel("Particles:"));
188  infopn.add(particleslb);
189  micrographpn.add(infopn, XmippWindowUtil.getConstraints(constraints, 0, 1, 1));
190  JPanel buttonspn = new JPanel(new FlowLayout(FlowLayout.LEFT));
191 
192  buttonspn.add(resetbt);
193  buttonspn.add(usezoombt);
194  micrographpn.add(buttonspn, XmippWindowUtil.getConstraints(constraints, 0, 2, 2));
195 
196  }
197 
198  private void initMenuBar()
199  {
200  mb = new JMenuBar();
201 
202 
203  JMenu windowmn = new JMenu("Window");
204  JMenu helpmn = new JMenu("Help");
205  mb.add(filemn);
206  mb.add(filtersmn);
207  mb.add(windowmn);
208  mb.add(helpmn);
209  // importffilemi.setText("Import from File...");
210 
211  windowmn.add(pmi);
212  windowmn.add(ijmi);
213  helpmn.add(hcontentsmi);
214 
215  }
216 
217 
218  @Override
219  protected void loadMicrograph()
220  {
221  if (micrographstb.getSelectedRow() == -1)
222  return;// Probably from fireTableDataChanged raised
223  // is same micrograph??
224  if (index == micrographstb.getSelectedRow() && canvas != null && canvas.getIw().isVisible())
225  return;
226  if (picker.isChanged())
227  picker.saveData(getMicrograph());// Saving changes when switching
228  index = micrographstb.getSelectedRow();
229  picker.setMicrograph(picker.getMicrographs().get(index));
230  setChanged(false);
231  initializeCanvas();
232  iconbt.setIcon(picker.getMicrograph().getCTFIcon());
233 
234  pack();
235  }
236 
237  private void initializeCanvas()
238  {
239  if (canvas == null)
240  canvas = new ExtractCanvas(this);
241  else
242  canvas.updateMicrograph();
243 
244  }
245 
246  @Override
247  protected void openHelpURl()
248  {
249  XmippDialog.showInfo(this, "Not available yet");
250  }
251 
252  @Override
253  protected void resetMicrograph()
254  {
255  picker.getMicrograph().getParticles().clear();
256  canvas.refreshActive(null);
257  updateMicrographsModel();
258 
259  }
260 
261 
262 
263 
264 
265  @Override
266  public ParticlePickerCanvas getCanvas()
267  {
268  return canvas;
269  }
270 
271  @Override
272  public void updateMicrographsModel(boolean all)
273  {
274  if (particlesdialog != null)
275  loadParticles(false);
276 
277  if (all)
278  micrographsmd.fireTableRowsUpdated(0, micrographsmd.getRowCount() - 1);
279  else
280  micrographsmd.fireTableRowsUpdated(index, index);
281 
282  micrographstb.setRowSelectionInterval(index, index);
283  particleslb.setText(Integer.toString(picker.getParticlesCount()));
284 
285  }
286 
287  @Override
288  public ExtractMicrograph getMicrograph()
289  {
290  return picker.getMicrograph();
291  }
292 
293  @Override
294  public List<? extends PickerParticle> getAvailableParticles()
295  {
296  return getMicrograph().getParticles();
297  }
298 
299 
300 
301  @Override
302  public ExtractParticlePicker getParticlePicker()
303  {
304  return picker;
305  }
306 
307  @Override
308  public void setChanged(boolean changed)
309  {
310  picker.setChanged(changed);
311  }
312 
313 
314 
315  @Override
316  public String importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
317  {
318  throw new UnsupportedOperationException();
319 
320  }
321 
322  class ExtractMicrographsTableModel extends AbstractTableModel
323  {
324  private String[] columns = new String[]{"", "Name", "Particles", "State"};
325 
326  @Override
327  public int getColumnCount()
328  {
329  return columns.length;
330  }
331 
332  @Override
333  public String getColumnName(int c)
334  {
335  return columns[c];
336  }
337 
338 
339  @Override
340  public int getRowCount()
341  {
342  return picker.getMicrographs().size();
343  }
344 
345  @Override
346  public Object getValueAt(int row, int column)
347  {
348  ExtractMicrograph m = (ExtractMicrograph)picker.getMicrographs().get(row);
349  if(column == 0)
350  return row + 1;
351  if(column == 1)
352  return m.getName();
353  if(column == 2)
354  return m.getParticles().size();
355  if(column == 3)
356  return Mode.Extract;
357 
358  return null;
359 
360  }
361 
362  }
363  @Override
364  public ParticlesDialog initParticlesJDialog()
365  {
366  return new ParticlesDialog(this);
367  }
368 
369  public void refreshActive(long id, boolean b)
370  {
371  int index = 0;
372  active = null;
373  List<ExtractMicrograph> micrographs = picker.getMicrographs();
374  for(int i = 0; i < micrographs.size(); i ++)
375  for(ExtractParticle p: micrographs.get(i).getParticles())
376  if(p.getId() == id)
377  {
378  index = i;
379  active = p;
380  active.setEnabled(b);
381  break;
382 
383  }
384  if(index != this.index)
385  micrographstb.setRowSelectionInterval(index, index);
386  if(active != null)
387  {
388  canvas.refreshActive(active);
389  canvas.moveTo(active);
390  active = null;
391  }
392 
393  }
394 
395  public void refreshActiveOnGallery(ExtractParticle active)
396  {
397  if(galleryfr != null)
398  galleryfr.refreshActive(active.getId(), active.isEnabled());
399 
400  }
401 
402 }
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static String getName(String file, int level)
Definition: Micrograph.java:140
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void refreshActive(long id, boolean enabled)
Definition: GalleryJFrame.java:2271
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String importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: ExtractPickerJFrame.java:316
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boolean showInfo(String message)
Definition: XmippDialog.java:199
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ExtractPickerJFrame(ParticlePicker picker, GalleryJFrame galleryfr)
Definition: ExtractPickerJFrame.java:58
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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1 package xmipp.viewer.windows;
2 
3 import xmipp.utils.DEBUG;
4 import xmipp.utils.XmippWindowUtil;
5 import xmipp.utils.XmippLabel;
6 import xmipp.viewer.models.GalleryData;
7 
8 import java.awt.BorderLayout;
9 import java.awt.Button;
10 import java.awt.Panel;
11 import java.awt.event.ActionEvent;
12 import java.awt.event.ActionListener;
13 import java.util.Arrays;
14 import java.util.List;
15 
16 import javax.swing.JFrame;
17 import org.jfree.chart.ChartFactory;
18 import org.jfree.chart.ChartPanel;
19 import org.jfree.chart.ChartUtilities;
20 import org.jfree.chart.JFreeChart;
21 import org.jfree.chart.axis.NumberAxis;
22 import org.jfree.chart.axis.ValueAxis;
23 import org.jfree.chart.plot.PlotOrientation;
24 import org.jfree.chart.plot.XYPlot;
25 import org.jfree.chart.renderer.xy.StandardXYItemRenderer;
26 import org.jfree.data.xy.XYSeries;
27 import org.jfree.data.xy.XYSeriesCollection;
28 import xmipp.jni.MDLabel;
29 import xmipp.jni.MetaData;
30 
31 /*
32  * To change this template, choose Tools | Templates
33  * and open the template in the editor.
34  */
39 public class FSCJFrame extends JFrame {
40 
41  public FSCJFrame(GalleryData data, MetaData imagesmd, int label) {
42  super(XmippLabel.TITLE_FSC + data.getFileName());
43 
44  try {
45  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
46  setLayout(new BorderLayout());
47 
48  MetaData mdout = new MetaData();
49 
50  mdout.computeFourierStatistics(imagesmd, label);
51 
52  double xValues[] = mdout.getColumnValues(MDLabel.MDL_RESOLUTION_FREQ);
53  double y1s[] = mdout.getColumnValues(MDLabel.MDL_RESOLUTION_FRC);
54  double y2s[] = mdout.getColumnValues(MDLabel.MDL_RESOLUTION_DPR);
55 
56  //String labelX = MetaData.label2Str(MDLabel.MDL_RESOLUTION_FREQ);
57  String labelY1 = MetaData.label2Str(MDLabel.MDL_RESOLUTION_FRC);
58  String labelY2 = MetaData.label2Str(MDLabel.MDL_RESOLUTION_DPR);
59 
60  XYSeriesCollection dataset1 = new XYSeriesCollection(
61  createSeries(labelY1, xValues, y1s));
62  XYSeriesCollection dataset2 = new XYSeriesCollection(
63  createSeries(labelY2, xValues, y2s));
64 
65  JFreeChart chart = ChartFactory.createXYLineChart(
66  "", XmippLabel.LABEL_DIGITAL_FREQUENCY, "",
67  dataset1, PlotOrientation.VERTICAL,
68  true, true, false);
69 
70  // Sets second axis.
71  XYPlot plot = chart.getXYPlot();
72  ValueAxis axisDPR = plot.getRangeAxis();
73  axisDPR.setLabel(labelY1);
74 
75  NumberAxis axisFSC = new NumberAxis();
76  axisFSC.setLabel(labelY2);
77  axisFSC.setAutoRangeIncludesZero(false);
78 
79  plot.setRangeAxis(1, axisFSC);
80  plot.setDataset(1, dataset2);
81  plot.mapDatasetToRangeAxis(1, 1);
82 
83  // Sets a new renderer, so series color will be different.
84  plot.setRenderer(1, new StandardXYItemRenderer());
85 
86  add(createChartPanel(chart), BorderLayout.CENTER);
87  pack();
88  XmippWindowUtil.centerWindows(this);
89 
90  imagesmd.destroy();
91  mdout.destroy();
92 
93  } catch (Exception e) {
94  DEBUG.printException(e);
95  }
96  }
97 
98  private static ChartPanel createChartPanel(JFreeChart chart) {
99  XYPlot plot = (XYPlot) chart.getPlot();
100  plot.setDomainPannable(true);
101  plot.setRangePannable(true);
102  List<Integer> list = Arrays.asList(0, 1);
103  plot.mapDatasetToDomainAxes(0, list);
104  plot.mapDatasetToRangeAxes(0, list);
105  ChartUtilities.applyCurrentTheme(chart);
106 
107  return new ChartPanel(chart);
108  }
109 
110  private static XYSeries createSeries(String name, double[] xs, double[] values) {
111  XYSeries series = new XYSeries(name);
112 
113  for (int i = 0; i < xs.length; i++) {
114  series.add(xs[i], values[i]);
115  }
116 
117  return series;
118  }
119 }
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static final int MDL_RESOLUTION_DPR
<Resolution anisotropy used to store the significance of the Bingham Test (double) ...
Definition: MDLabel.java:318
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static final int MDL_RESOLUTION_FRC
<Error in l2 (double)
Definition: MDLabel.java:320
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native double [] getColumnValues(int label)
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xmipp.utils.XmippWindowUtil.centerWindows
static void centerWindows(Window w)
Definition: XmippWindowUtil.java:94
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synchronized native void destroy()
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static native String label2Str(int label)
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static final String LABEL_DIGITAL_FREQUENCY
Definition: XmippLabel.java:183
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xmipp.utils.DEBUG.printException
static void printException(Exception ex)
Definition: DEBUG.java:30
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static final String TITLE_FSC
Definition: XmippLabel.java:31
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static final int MDL_RESOLUTION_FREQ
<Fourier shell correlation noise (double)
Definition: MDLabel.java:322
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native void computeFourierStatistics(MetaData mdIn, int label)
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FSCJFrame(GalleryData data, MetaData imagesmd, int label)
Definition: FSCJFrame.java:41
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1 import ij.plugin.filter.ExtendedPlugInFilter;
2 import ij.plugin.filter.PlugInFilterRunner;
3 import ij.plugin.filter.RankFilters;
4 import ij.*;
5 import ij.gui.GenericDialog;
6 import ij.gui.DialogListener;
7 import ij.process.*;
8 import ij.measure.Calibration;
9 import java.awt.*;
10 import java.awt.event.*;
11 import java.util.*;
12 
107 public class Fast_Filters implements ExtendedPlugInFilter, DialogListener {
108  private final static String[] TYPES = new String[] {
109  "mean", "border-limited mean", "median", "minimum", "maximum", "eliminate maxima", "eliminate minima",
110  "background from minima", "background from maxima", "background from median"
111  };
112  private final static int MEAN=0, BORDER_LIMITED_MEAN=1, MEDIAN=2, MIN=3, MAX=4; //"elementary" filter types
113  //ELIM_MAX=5,ELIM_MIN=6,BACK_MIN=7, BACK_MAX=8, BACK_MEDIAN=9; //"composite filters" from > 1 elementary types
114  private final static int[][] taskLists = new int[][] { //what to do for the filter types
115  {MEAN},
116  {BORDER_LIMITED_MEAN},
117  {MEDIAN},
118  {MIN},
119  {MAX},
120  {MIN, MAX},
121  {MAX, MIN},
122  {MIN, MAX, BORDER_LIMITED_MEAN},
123  {MAX, MIN, BORDER_LIMITED_MEAN},
124  {MEDIAN, BORDER_LIMITED_MEAN}
125  };
126  private final static String[] PREPROCESSES = new String[] {
127  "none", "smooth", "median" //preprocessing types; 1 and 2 are the same as filter types 1 and 2 above
128  };
129  // F i l t e r p a r a m e t e r s
130  // Note that this makes it impossible to run the filter in parallel threads with different filter parameters!
131  private static int type = MEAN; // Filter type
132  private static int xRadius = 5; // The kernel radius in x direction
133  private static int yRadius = 5; // The kernel radius in x direction
134  private static boolean linkXY = true; // Whether to use the same radius in x&y
135  private static int preProcess = 0; // Preprocessing type
136  private static boolean subtract = false; // Whether output should be the original minus filtered
137  private static double[] offset = new double[] { // When subtracting, this will be added to the result.
138  128, 32768, 0, 128, 128 // Array for image types GRAY8, GRAY16, GRAY32, COLOR_256, COLOR_RGB
139  };
140  // F u r t h e r c l a s s v a r i a b l e s
141  private int flags = DOES_ALL|CONVERT_TO_FLOAT|SNAPSHOT|SUPPORTS_MASKING|KEEP_PREVIEW;
142  private int impType; // type of ImagePlus (GRAY_8, etc...)
143  private int nPasses = 1; // The number of passes (color channels * stack slices)
144  private int pass; // Current pass
145  // Multithreading-related
146  private int maxThreads = Runtime.getRuntime().availableProcessors(); // number of threads for filtering
147 
158  public int setup(String arg, ImagePlus imp) {
159  if (IJ.versionLessThan("1.38x")) // generates an error message for older versions
160  return DONE;
161  return flags;
162  }
163 
164  // Called by ImageJ after setup.
165  public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
166  impType = imp.getType();
167  int digits = (impType == ImagePlus.GRAY32) ? 2 : 0;
168  GenericDialog gd = new GenericDialog(command+"...");
169  gd.addChoice("Filter Type", TYPES, TYPES[type]);
170  gd.addNumericField("x Radius", xRadius, 0);
171  gd.addNumericField("y Radius", yRadius, 0);
172  gd.addCheckbox("Link x & y", linkXY);
173  gd.addChoice("Preprocessing", PREPROCESSES, PREPROCESSES[preProcess]);
174  gd.addCheckbox("Subtract Filtered", subtract);
175  gd.addNumericField("Offset (subtract only)", offset[impType], digits);
176  gd.addPreviewCheckbox(pfr); // passing pfr makes the filter ready for preview
177  gd.addDialogListener(this); // the DialogItemChanged method will be called on user input
178  gd.showDialog(); // display the dialog; preview runs in the background now
179  if (gd.wasCanceled()) return DONE;
180  IJ.register(this.getClass()); // protect static class variables (filter parameters) from garbage collection
181  Runtime.getRuntime().availableProcessors();
182  flags = IJ.setupDialog(imp, flags); // ask whether to process all slices of stack (if a stack)
183  // parallel processing of stacks is faster than prallel filtering of lines of one image.
184  if ((flags&DOES_STACKS)!=0) {
185  long bytesPerPixelNeeded = impType==ImagePlus.GRAY32 ? 4 : 8; // for conversion to float and snapshot
186  long bytesParallelNeeded = imp.getWidth()*imp.getHeight()*bytesPerPixelNeeded*Prefs.getThreads();
187  long freeMemory = Runtime.getRuntime().freeMemory();
188  if (freeMemory > bytesParallelNeeded*11/10) { //enough memory for stack parallelization?
189  flags |= PARALLELIZE_STACKS;
190  maxThreads = Math.max((int)Math.ceil(1.1*maxThreads/imp.getStackSize()), 1); //fewer threads for each image
191  }
192  //IJ.log("needed/free="+(bytesParallelNeeded/(1024L*1024L))+"/"+(freeMemory/(1024L*1024L))+"M");
193  //IJ.log("StackParall="+((flags&PARALLELIZE_STACKS)!=0)+" maxThreads="+maxThreads);
194  }
195  return flags;
196  }
197 
198  // Called after modifications to the dialog. Returns true if valid input.
199  public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
200  Vector numFields = gd.getNumericFields();
201  TextField xNumField = (TextField)numFields.get(0);
202  TextField yNumField = (TextField)numFields.get(1);
203  Checkbox linkCheckbox = (Checkbox)gd.getCheckboxes().get(0);
204  linkXY = gd.getNextBoolean();
205  if (linkXY && !xNumField.getText().equals(yNumField.getText())) {
206  if (e.getSource() == xNumField || e.getSource() == linkCheckbox)
207  yNumField.setText(xNumField.getText());
208  else if (e.getSource() == yNumField)
209  xNumField.setText(yNumField.getText());
210  }
211  type = gd.getNextChoiceIndex();
212  xRadius = (int)gd.getNextNumber();
213  yRadius = (int)gd.getNextNumber();
214  preProcess = gd.getNextChoiceIndex();
215  subtract = gd.getNextBoolean();
216  offset[impType] = gd.getNextNumber();
217  return (!gd.invalidNumber() && xRadius>=0 && yRadius>=0 && xRadius<1000000 && yRadius<1000000);
218  }
219 
220  // Process a FloatProcessor (with the CONVERT_TO_FLOAT flag,ImageJ does the conversion).
221  // Called by ImageJ for each stack slice (when processing a full stack); for RGB image also called once for each color.
222  public void run(ImageProcessor ip) {
223  int width = ip.getWidth();
224  int height = ip.getHeight();
225  Rectangle roiRect = ip.getRoi();
226  int[] taskList = taskLists[type];
227  int nTasks = taskList.length;
228  int extraX = xRadius*(nTasks-1); //out-of-roi margin that has to be processed for next steps
229  int extraY = yRadius*nTasks;
230  if (preProcess > 0) {
231  extraX += xRadius;
232  if (xRadius>0 && yRadius>0) {
233  filterFloat(ip, preProcess, 1, true, extraX, extraY+1, maxThreads);
234  filterFloat(ip, preProcess, 1, false, extraX, extraY, maxThreads);
235  extraY++;
236  } else if (xRadius>0) {
237  filterFloat(ip, preProcess, 2, true, extraX, extraY, maxThreads);
238  } else if (yRadius>0) {
239  filterFloat(ip, preProcess, 2, false, extraX, extraY, maxThreads);
240  }
241  }
242  for (int iTask=0; iTask<nTasks; iTask++) {
243  if (xRadius>0)
244  filterFloat(ip, taskList[iTask], xRadius, true, xRadius*(nTasks-iTask-1), yRadius*(nTasks-iTask), maxThreads);
245  if (yRadius>0)
246  filterFloat(ip, taskList[iTask], yRadius, false, xRadius*(nTasks-iTask-1), yRadius*(nTasks-iTask-1), maxThreads);
247  if (Thread.currentThread().isInterrupted()) return; // interruption for new parameters during preview?
248  }
249  if (subtract) {
250  float[] pixels = (float[])ip.getPixels();
251  float[] snapPixels = (float[])ip.getSnapshotPixels();
252  float fOffset = (float)offset[impType];
253  for (int y=roiRect.y; y<roiRect.y+roiRect.height; y++)
254  for (int x=roiRect.x, p=x+y*width; x<roiRect.x+roiRect.width; x++,p++)
255  pixels[p] = snapPixels[p] - pixels[p] + fOffset;
256  if (Thread.currentThread().isInterrupted()) return;
257  }
258  if (roiRect.height!=height || roiRect.width!=width)
259  resetOutOfRoi(ip, extraX, extraY); // reset out-of-Rectangle pixels above and below roi
260  showProgress(1.0);
261  return;
262  }
263 
266  private static void resetOutOfRoi (ImageProcessor ip, int extraX, int extraY) {
267  int width = ip.getWidth();
268  int height = ip.getHeight();
269  Rectangle roiRect = ip.getRoi();
270  Rectangle temp = (Rectangle)roiRect.clone();
271  temp.grow(extraX, extraY);
272  Rectangle outer = temp.intersection(new Rectangle(width, height));
273 
274  float[] pixels = (float[])ip.getPixels();
275  float[] snapPixels = (float[])ip.getSnapshotPixels();
276  for (int y=outer.y, p=y*width+outer.x; y<roiRect.y; y++, p+=width)
277  System.arraycopy(snapPixels, p, pixels, p, outer.width);
278  int leftWidth = roiRect.x - outer.x;
279  int rightWidth = outer.x+outer.width - (roiRect.x+roiRect.width);
280  for (int y=roiRect.y; y<roiRect.y+roiRect.height; y++) {
281  if (leftWidth > 0) {
282  int p = outer.x + y*width;
283  System.arraycopy(snapPixels, p, pixels, p, leftWidth);
284  }
285  if (rightWidth > 0) {
286  int p = roiRect.x+roiRect.width + y*width;
287  System.arraycopy(snapPixels, p, pixels, p, rightWidth);
288  }
289  }
290  for (int y=roiRect.y+roiRect.height, p=y*width+outer.x; y<outer.y+outer.height; y++, p+=width)
291  System.arraycopy(snapPixels, p, pixels, p, outer.width);
292 
293  }
294 
297  public void setNPasses (int nPasses) {
298  if (xRadius>0 && yRadius>0) nPasses *= 2;
299  this.nPasses = nPasses * taskLists[type].length;
300  pass = 0;
301  }
302 
304  private void showProgress(double percent) {
305  if (nPasses == 0) return;
306  percent = (double)pass/nPasses + percent/nPasses;
307  IJ.showProgress(percent);
308  }
309 
320  private void filterFloat(ImageProcessor ip, final int type, final int radius, boolean xDirection,
321  int extraX, int extraY, int maxThreads) {
322  final float sign = (type==MIN) ? -1 : 1;
323  final int width = ip.getWidth();
324  final int height = ip.getHeight();
325  Rectangle roiRect = (Rectangle)ip.getRoi().clone();
326  roiRect.grow(extraX, extraY);
327  Rectangle rect = roiRect.intersection(new Rectangle(width, height));
328 
329  final float[] pixels = (float[])ip.getPixels();
330  final int length = xDirection ? width : height; //number of points per line (line can be a row or column)
331  final int pointInc = xDirection ? 1 : width; //increment of the pixels array index to the next point in a line
332  final int lineInc = xDirection ? width : 1; //increment of the pixels array index to the next line
333  final int lineFrom = Math.max((xDirection ? rect.y : rect.x), 0); //the first line to process
334  int totalLines = (xDirection ? height:width);
335  final int lineTo = Math.min((xDirection ? rect.y+rect.height : rect.x+rect.width), totalLines); //the last line+1 to process
336  final int writeFrom = xDirection? rect.x : rect.y; //first point of a line that needs to be written
337  final int writeTo = xDirection ? rect.x+rect.width : rect.y+rect.height;
338  final int readFrom = (writeFrom-radius < 0) ? 0 : writeFrom-radius;
339  final int readTo = (writeTo+radius > length) ? length : writeTo+radius;
340 
341  int tmpMaxThreads = Math.min(((lineTo-lineFrom)*(writeTo-writeFrom))/100000+1, maxThreads); //avoid multithread overhead for small areas
342  final int numThreads = Math.min(tmpMaxThreads, lineTo-lineFrom);
343  final Thread[] lineThreads = new Thread[numThreads-1];
344  for (int t=0; t < numThreads-1; t++) {
345  final int ti = t+1; //this thread starts at lineFrom+0, the other (new) threads do the rest
346  final Thread thread = new Thread(
347  new Runnable() {
348  final public void run() { try {
349  filterLines(pixels, type, sign, radius, lineFrom+ti, lineTo, /*lineStep=*/numThreads,
350  length, readFrom, readTo, writeFrom, writeTo, pointInc, lineInc, /*isMainThread=*/false);
351  } catch(Exception ex) {IJ.handleException(ex);} }
352  },
353  "FastFilters-"+t);
354  thread.setPriority( Thread.currentThread().getPriority() );
355  lineThreads[t] = thread;
356  thread.start();
357  }
358  filterLines(pixels, type, sign, radius, lineFrom+0, lineTo, /*lineStep=*/numThreads,
359  length, readFrom, readTo, writeFrom, writeTo, pointInc, lineInc, /*isMainThread=*/true);
360 
361  try {
362  for ( final Thread thread : lineThreads )
363  if ( thread != null ) thread.join();
364  }
365  catch ( InterruptedException e ) {
366  for ( final Thread thread : lineThreads )
367  thread.interrupt();
368  try {
369  for ( final Thread thread : lineThreads )
370  thread.join();
371  }
372  catch ( InterruptedException f ) {}
373  Thread.currentThread().interrupt(); //set 'interrupted', which was cleared by handling InterruptedException
374  }
375  pass++;
376  }
377 
378  /* Filter the lines for one thread in one direction */
379  private void filterLines(float[] pixels, int type, float sign, int radius, int startLine, int lineTo, int lineStep,
380  int length, int readFrom, int readTo, int writeFrom, int writeTo, int pointInc, int lineInc, boolean isMainThread) {
381  float[] cache = new float[length]; //input for filter, hopefully in CPU cache
382  float[] vHi = (type == MEDIAN) ? new float[(2*xRadius+1)*(2*yRadius+1)] : null; //needed for median
383  float[] vLo = (type == MEDIAN) ? new float[(2*xRadius+1)*(2*yRadius+1)] : null; //needed for median
384  long lastTime = System.currentTimeMillis();
385  for (int line=startLine; line<lineTo; line+=lineStep) {
386  int pixel0 = line*lineInc + writeFrom*pointInc; //the first pixel to write in a line
387  long time = System.currentTimeMillis();
388  if (time - lastTime >110) {
389  if (isMainThread)
390  showProgress((double)(line-startLine)/(lineTo-startLine));
391  if (Thread.currentThread().isInterrupted()) return; // interruption for new parameters during preview?
392  lastTime = time;
393  }
394  int p = line*lineInc + readFrom*pointInc;
395  for (int i=readFrom; i<readTo; i++ ,p+=pointInc)
396  cache[i] = pixels[p]*sign;
397  switch (type) {
398  case MEAN:
399  lineMean (radius, cache, pixels, writeFrom, writeTo, pixel0, pointInc);
400  break;
401  case BORDER_LIMITED_MEAN:
402  lineBorderLimitedMean (radius, cache, pixels, writeFrom, writeTo, pixel0, pointInc);
403  break;
404  case MEDIAN:
405  lineMedian (radius, cache, pixels, writeFrom, writeTo, pixel0, pointInc, vLo, vHi);
406  break;
407  case MIN: case MAX:
408  lineMax(radius, sign, cache, pixels, writeFrom, writeTo, pixel0, pointInc);
409  }
410  }
411  }
412 
413  // Mean filter of a line.
414  // When trying to access out-of-border pixels it replaces them with the nearest border pixel.
415  // (this is the usual behavior of ImageJ filters)
416  // radius: Kernel width is 2*radius+1
417  // cache: Holds input data for one line, i.e., for one image row or column
418  // pixels: Image data are written to this point
419  // writeFrom: Index of first point of the line that should be written.
420  // writeTo: Last point + 1 of the line that should be written. Data will be read from 'cache'
421  // also outside the 'writeFrom', 'writeTo' range.
422  // pixel0: Index of the first value to be written in 'pixels'. Corresponds to index 'writeFrom' in 'cache'.
423  // pointInc: increment of index in 'pixels' from one point to the next (1 for image rows, width for columns).
424  private static void lineMean (int radius, float[] cache, float[] pixels, int writeFrom, int writeTo,
425  int pixel0, int pointInc) {
426  double sum = 0;
427  double factor = 1./(1 + 2*radius);
428  int length = cache.length;
429  float first = cache[0];
430  float last = cache[length-1];
431  int sumFrom = writeFrom-radius;
432  int sumTo = writeFrom+radius;
433  if (sumFrom < 0) {
434  sum = -sumFrom*first;
435  sumFrom = 0;
436  }
437  if (sumTo > length) {
438  sum += (sumTo-length)*last;
439  sumTo = length;
440  }
441  for (int i=sumFrom; i<sumTo; i++)
442  sum += cache[i];
443  for (int i = writeFrom, iMinus =i-radius, iPlus=i+radius, p=pixel0;
444  i<writeTo; i++,iMinus++,iPlus++,p+=pointInc) {
445  sum += (iPlus<length) ? cache[iPlus] : last;
446  if (Double.isNaN(sum))
447  sum = nanAwareSum (radius, cache, i, pixels, p); //writes pixel, returns NaN unless no NaNs
448  else
449  pixels[p] = (float)(sum*factor);
450  sum -= (iMinus>=0) ? cache[iMinus] : first;
451  }
452  }
453 
454  private static double nanAwareSum (int radius, float[] cache, int cachePos, float[] pixels, int p) {
455  int n = 0;
456  double sum = 0;
457  for (int i = cachePos-radius; i<=cachePos+radius; i++) {
458  float v = cache[i<0? 0 : (i>=cache.length ? cache.length-1 : i)];
459  if (v==v) {
460  sum += v;
461  n++;
462  }
463  }
464  if (n > 0) pixels[p] = (float)(sum/n);
465  return n==2*radius+1 ? sum : Double.NaN ;
466  }
467 
468  // Mean filter of a line; at the image borders it does not give extra weight to the border pixels.
469  private static void lineBorderLimitedMean (int radius, float[] cache, float[] pixels, int writeFrom, int writeTo,
470  int pixel0, int pointInc) {
471  double sum = 0;
472  int length = cache.length;
473  int sumFrom = (writeFrom-radius>0) ? writeFrom-radius : 0;
474  int sumTo = (writeFrom+radius<length) ? writeFrom+radius : length;
475  int kSize = sumTo - sumFrom;
476  for (int i=sumFrom; i<sumTo; i++)
477  sum += cache[i];
478  for (int i = writeFrom, iMinus =i-radius, iPlus=i+radius, p=pixel0;
479  i<writeTo; i++,iMinus++,iPlus++,p+=pointInc) {
480  if (iPlus<length) { sum += cache[iPlus]; kSize++; }
481  if (Double.isNaN(sum))
482  sum = nanAwareBLMean (radius, cache, i, kSize, pixels, p);
483  else
484  pixels[p] = ((float)sum)/kSize;
485  if (iMinus>=0) { sum -= cache[iMinus]; kSize--; }
486  }
487  }
488 
489  private static double nanAwareBLMean (int radius, float[] cache, int cachePos, int kSize, float[] pixels, int p) {
490  int n = 0;
491  double sum = 0;
492  for (int i = Math.max(cachePos-radius,0); i<=Math.min(cachePos+radius,cache.length-1); i++) {
493  float v = cache[i];
494  if (v==v) {
495  sum += v;
496  n++;
497  }
498  }
499  if (n > 0) pixels[p] = (float)(sum/n);
500  return n==kSize ? sum : Float.NaN;
501  }
502 
503  // Median filter of a line; at the image borders it does not give extra weight to the border pixels.
504  private static void lineMedian (int radius, float[] cache, float[] pixels, int writeFrom, int writeTo,
505  int pixel0, int pointInc, float[] vHi, float[] vLo) {
506  int length = cache.length;
507  float median = Float.isNaN(cache[writeFrom]) ? 0 : cache[writeFrom]; //a first guess
508  for (int i=writeFrom, iMinus=i-radius, iPlus=i+radius, p=pixel0;
509  i<writeTo; i++, iMinus++,iPlus++,p+=pointInc) {
510  int nHi = 0, nLo = 0;
511  int iStart = (iMinus>=0) ? iMinus : 0;
512  int iStop = (iPlus<length) ? iPlus : length-1;
513  int nEqual = 0;
514  for (int iRead=iStart; iRead <= iStop; iRead++) {
515  float v = cache[iRead];
516  if (v > median) vHi[nHi++] = v;
517  else if (v < median) vLo[nLo++] = v;
518  else if (v==v) nEqual++; //if (!isNaN(v))
519  }
520  int nPoints = nHi + nLo + nEqual;
521  if (nPoints == 0) {
522  pixels[p] = Float.NaN;
523  } else {
524  if (nPoints%2 == 0) { //avoid an even number of points: in case of doubt, leave it closer to original value
525  float v = cache[i];
526  if (v > median) vHi[nHi++] = v;
527  else if (v < median) vLo[nLo++] = v;
528  }
529  int half = nPoints/2;//>>1; //(nHi+nLo)/2, but faster
530  if (nHi>half)
531  median = RankFilters.findNthLowestNumber(vHi, nHi, nHi-half-1);
532  else if (nLo>half)
533  median = RankFilters.findNthLowestNumber(vLo, nLo, half);
534  pixels[p] = median;
535  }
536  }
537  }
538 
539  // Algorithm for finding maxima within a range of the input array 'cache':
540  // - When going to the next pixel, if the new pixel is > than the old maximum take it.
541  // - Get the maximum over the full range only if the pixel that is not in the range any more ('out')
542  // could be the one that has caused the current value of the maximum.
543  // - It is faster to start at a border than to end there: In the beginning, we need not care about
544  // pixels that get out of the range. Thus the algorithm starts from both borders; whenever a full
545  // determination of the maximum over the full range becomes necessary, the algorithm tries to avoid
546  // this by continuing at the other end.
547  private static void lineMax (int radius, float sign, float[] cache, float[] pixels, int writeFrom, int writeTo,
548  int pixel0, int pointInc) {
549  int length = cache.length;
550  int pUp = pixel0;
551  int pDn = pixel0 + (writeTo-writeFrom-1)*pointInc;
552  float maxUp = -Float.MAX_VALUE;
553  float maxDn = -Float.MAX_VALUE;
554  int iInUp = writeFrom + radius; //new in the range that we have to find the max of
555  int iOutUp = writeFrom - radius - 1; //not in the range any more
556  int iInDn = writeTo - radius -1;
557  int iOutDn = writeTo + radius;
558  boolean firstUp = true;
559  boolean firstDn = true;
560 
561  while (pUp<=pDn) {
562  boolean switchDirection = false;
563  for (; pUp<=pDn; pUp+=pointInc, iInUp++, iOutUp++) {
564  float oldmax = maxUp;
565  if (iInUp<length) {
566  if (firstUp || Float.isNaN(oldmax) || Float.isNaN(cache[iInUp])) {
567  maxUp = nanAwareMax (iOutUp+1, iInUp, cache, sign, pixels, pUp); //find max one-by-one with possible NaNs
568  firstUp = false;
569  continue;
570  }
571  if(maxUp<=cache[iInUp]) {
572  maxUp = cache[iInUp];
573  pixels[pUp] = maxUp*sign;
574  continue;
575  }
576  }
577  if (iOutUp>=0 && cache[iOutUp]==oldmax) { //full one-by-one determination
578  if (switchDirection)
579  break;
580  switchDirection = true;
581  int maxFrom = (iOutUp >= -1) ? iOutUp+1 : 0;
582  int maxTo = (iInUp < length) ? iInUp : length-1;
583  maxUp = cache[maxFrom];
584  for (int i=maxFrom+1; i<=maxTo; i++)
585  if (maxUp < cache[i]) maxUp = cache[i];
586  }
587  pixels[pUp] = maxUp*sign;
588  }
589  for (; pUp<=pDn; pDn-=pointInc, iInDn--, iOutDn--) {
590  switchDirection = false;
591  float oldmax = maxDn;
592  if (iInDn>=0) {
593  if (firstDn || Float.isNaN(oldmax) || Float.isNaN(cache[iInDn])) {
594  maxDn = nanAwareMax (iInDn, iOutDn-1, cache, sign, pixels, pDn);
595  firstDn = false;
596  continue;
597  }
598  if (maxDn<cache[iInDn]) {
599  maxDn = cache[iInDn];
600  pixels[pDn] = maxDn*sign;
601  continue;
602  }
603  }
604  if (iOutDn<length && cache[iOutDn]==oldmax) { //full one-by-one determination
605  if (switchDirection)
606  break;
607  switchDirection = true;
608  int maxFrom = (iOutDn <=length) ? iOutDn-1 : length-1;
609  int maxTo = (iInDn > 0) ? iInDn : 0;
610  maxDn = cache[maxFrom];
611  for (int i=maxFrom-1; i>=maxTo; i--)
612  if (maxDn < cache[i]) maxDn = cache[i];
613  }
614  pixels[pDn] = maxDn*sign;
615  }
616  }
617  }
618 
619  private static float nanAwareMax (int from, int to, float[] cache, float sign, float[] pixels, int p) {
620  float max = -Float.MAX_VALUE;
621  boolean anyGood = false;
622  boolean anyNaN = false;
623  for (int i=Math.max(from,0); i<=Math.min(to,cache.length-1); i++) {
624  float v = cache[i];
625  if (Float.isNaN(v)) {
626  anyNaN = true;
627  } else {
628  if (max < cache[i]) max = cache[i];
629  anyGood = true;
630  }
631  }
632  if (anyGood) pixels[p] = max*sign;
633  return anyNaN ? Float.NaN : max;
634  }
635 
636 }
Fast_Filters.setNPasses
void setNPasses(int nPasses)
Definition: Fast_Filters.java:297
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Fast_Filters
Definition: Fast_Filters.java:107
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int setup(String arg, ImagePlus imp)
Definition: Fast_Filters.java:158
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Definition: Fast_Filters.java:199
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Definition: Fast_Filters.java:165
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Definition: Fast_Filters.java:222
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  * Roberto Marabini (roberto@cnb.csic.es)
4  *
5  *
6  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
7  *
8  * This program is free software; you can redistribute it and/or modify
9  * it under the terms of the GNU General Public License as published by
10  * the Free Software Foundation; either version 2 of the License, or
11  * (at your option) any later version.
12  *
13  * This program is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  * GNU General Public License for more details.
17  *
18  * You should have received a copy of the GNU General Public License
19  * along with this program; if not, write to the Free Software
20  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
21  * 02111-1307 USA
22  *
23  * All comments concerning this program package may be sent to the
24  * e-mail address 'xmipp@cnb.csic.es'
25  ***************************************************************************/
26 package xmipp.test;
27 
28 import static org.junit.Assert.assertEquals;
29 import static org.junit.Assert.fail;
30 import org.junit.*;
31 import xmipp.jni.Filename;
32 
33 public class FilenameTest {
34 
35  // Xmipp dir
36  static String TESTS_PATH;
37 
38  String filename = "singleImage.spi";
39  String filename2 = "singleImage2.spi";
40 
41 
42  @BeforeClass
43  public static void setUpClass() throws Exception {
44  }
45 
46  @AfterClass
47  public static void tearDownClass() throws Exception {
48  }
49 
50  @Before
51  public void setUp() {
52  }
53 
54 
55  @After
56  public void tearDown() {
57  }
58 
62  @Test
63  public void testGetXmippPath() {
64  try {
65  String xmipp_home = Filename.getXmippPath();
66  String xmipp_home2 = System.getenv("XMIPP_HOME");
67  assertEquals(xmipp_home, xmipp_home2);
68  } catch (Exception ex) {
69  fail("testGetFilename");
70  }
71  }//function testGetXmippPath
72 
73 }//class FilenameTest
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Definition: FilenameTest.java:47
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Definition: FilenameTest.java:43
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class  xmipp.jni.Filename
 
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package  xmipp.jni
 
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Filename.java
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1 package xmipp.jni;
2 
3 import java.io.File;
4 
5 public class Filename {
6 
7  public final static String PROJECT_FILE = ".project.sqlite";
8  public final static String SEPARATOR = "@";
9  // image extensions
10  public final static String EXT_SPI = ".spi";
11  public final static String EXT_XMP = ".xmp";
12  public final static String EXT_VOL = ".vol";
13  public final static String EXT_STK = ".stk";
14  public final static String EXT_MRC = ".mrc";
15  public final static String EXT_MRC2 = ".map";
16  public final static String EXT_MRCS = ".mrcs";
17  public final static String EXT_MRCS2 = ".st";
18  public final static String EXT_MRCREC = ".rec";
19  public final static String EXT_MRCSALI = ".ali";
20  public final static String EXT_MRCSPREALI = ".preali";
21  public final static String EXT_IMG = ".img";
22  public final static String EXT_HED = ".hed";
23  public final static String EXT_SER = ".ser";
24  public final static String EXT_DM3 = ".dm3";
25  public final static String EXT_DM4 = ".dm4";
26  public final static String EXT_EM = ".em";
27  public final static String EXT_EMS = ".ems";
28  public final static String EXT_PIF = ".pif";
29  public final static String EXT_RAW = ".raw";
30  public final static String EXT_INF = ".inf";
31  public final static String EXT_SPE = ".spe";
32  public final static String EXT_TIF = ".tif";
33  public final static String EXT_JPG = ".jpg";//supported only in black and white
34  public final static String EXT_PNG = ".png";
35  public final static String EXT_PSD = ".psd";
36  public final static String EXT_HDF = ".hdf";
37  public final static String EXT_HDF5 = ".hdf5";
38  public final static String EXT_H5 = ".h5";
39 
40  // metadata extensions
41  public final static String EXT_XMD = ".xmd";
42  public final static String EXT_SEL = ".sel";
43  public final static String EXT_DOC = ".doc";
44  public final static String EXT_CTFPARAM = ".ctfparam";
45  public final static String EXT_CTFDAT = ".ctfdat";
46  public final static String EXT_POS = ".pos";
47  public final static String EXT_LOG = ".log";
48  public final static String EXT_OUT = ".out";
49  public final static String EXT_ERR = ".err";
50  public final static String EXT_PY = ".py";
51  public final static String EXT_TXT = ".txt";
52  public final static String EXT_BOX = ".box";
53 
54  // Initialize library.
55  static {
56  System.loadLibrary("XmippJNI");
57  // storeIds();
58  }
59 
60  public final static String[] SINGLE_IMAGES = new String[] { EXT_XMP,
61  EXT_IMG, EXT_HED, EXT_PSD, EXT_SER, EXT_DM3, EXT_EM, EXT_PIF,
62  EXT_RAW, EXT_INF, EXT_SPE, EXT_SPI, EXT_TIF, EXT_MRC, EXT_MRC2, EXT_PNG, EXT_JPG };
63 
64  public final static String[] VOLUMES = new String[] { EXT_MRC, EXT_MRC2, EXT_MRCREC,
65  EXT_VOL, EXT_EM, EXT_PIF };
66 
67  public final static String[] STACKS = new String[] { EXT_MRCS, EXT_MRCS2, EXT_MRCSALI, EXT_MRCSPREALI,
68  EXT_STK, EXT_PIF, EXT_EMS, EXT_DM4};
69 
70  public final static String[] METADATAS = new String[] { EXT_XMD, EXT_SEL,
71  EXT_DOC, EXT_CTFPARAM, EXT_CTFDAT, EXT_POS };
72 
73  public final static String[] SPIDER = new String[] { EXT_SPI, EXT_VOL };
74 
75  public final static String[] TEXT = new String[] { EXT_TXT, EXT_LOG,
76  EXT_ERR, EXT_OUT, EXT_BOX };
77 
78  public final static String[] XMIPP_SUPPORTED = new String[]{EXT_RAW, EXT_SPI, EXT_XMP, EXT_VOL, EXT_STK, EXT_MRC, EXT_MRC2, EXT_MRCS2, EXT_MRCS,
79  EXT_MRCSALI, EXT_MRCSPREALI, EXT_MRCREC,
80  EXT_HED, EXT_IMG, EXT_INF, EXT_RAW, EXT_TIF, EXT_DM3, EXT_DM4, EXT_SER, EXT_SPE, EXT_EM, EXT_EMS, EXT_PIF, EXT_HDF, EXT_HDF5, EXT_H5, EXT_PSD};
81 
82  public static boolean isPSD(String filename) {
83  return filename != null && filename.endsWith(EXT_PSD);
84  }
85 
86  public static boolean isSpiderVolume(String filename) {
87  return filename != null && isFileType(filename, SPIDER);
88  }
89 
90  public static native boolean hasStackExtension(String filename)
91  throws Exception;
92 
93  public static native boolean hasVolumeExtension(String filename)
94  throws Exception;
95 
96  private static native boolean isMetaDataFile(String filename)
97  throws Exception;
98 
99  public static native String compose(int slice, String path)
100  throws Exception;
101 
102  public static native String getXmippPath() throws Exception;
103 
104 
105  public static String getXmippPath(String relpath) {
106  try {
107  return getXmippPath() + File.separator + relpath;
108  } catch (Exception e) {
109  // TODO Auto-generated catch block
110  e.printStackTrace();
111  }
112  return null;
113  }
114 
115  public static boolean isSingleImage(String filename) throws Exception {
116  try {
117  if(isXmippSupported(filename))
118  return (new ImageGeneric(filename)).isSingleImage();
119  else
120  return isFileType(filename, SINGLE_IMAGES);
121  } catch (Exception ex) {
122  return filename != null && isFileType(filename, SINGLE_IMAGES);
123  }
124  }
125 
126  public static boolean isSingleImageExt(String filename) {
127  return filename != null && isFileType(filename, SINGLE_IMAGES);
128  }
129 
130  public static boolean isStackOrVolume(String filename) {
131  return isStack(filename) || isVolume(filename);
132  }
133 
134  public static boolean isVolume(String filename) {
135 
136  try {
137  if(isXmippSupported(filename))
138  return (new ImageGeneric(filename)).isVolume();
139  else
140  return isFileType(filename, VOLUMES);
141  } catch (Exception ex) {
142  return isFileType(filename, VOLUMES);
143  }
144  }
145 
146  public static boolean isVolumeExt(String filename) {
147  return filename != null && isFileType(filename, VOLUMES);
148  }
149 
150  public static boolean isStack(String filename){
151  try {
152  if(isXmippSupported(filename))
153  return (new ImageGeneric(filename)).isStack();
154  else
155  return isFileType(filename, STACKS);
156  } catch (Exception ex) {
157  return filename != null && isFileType(filename, STACKS);
158  }
159  }
160 
161  public static boolean isStackExt(String filename) {
162  return filename != null && isFileType(filename, STACKS);
163  }
164 
165  public static boolean isMetadata(String filename) {
166  try {
167  if (filename != null)
168  return isMetaDataFile(filename);
169  } catch (Exception e) {
170  e.printStackTrace();
171  }
172  return false;
173  }// function isMetadata
174 
175  public static boolean isMetadataExt(String filename) {
176  return filename != null && isFileType(filename, METADATAS);
177  }
178 
179  public static boolean isTextfile(String filename) {
180  return isFileType(filename, TEXT) || isFileType(filename, METADATAS)
181  || isMetadata(filename);
182  }
183 
184  private static boolean isFileType(String filename, String filetypes[]) {
185  if(filename == null)
186  return false;
187 
188  if(filename.contains(":")) {
189  // If filename contains : it means that the user want
190  // to force for specific image type, ignoring the filename
191  // extension, for example:
192  // output.ctf:mrc should be treat as a mrc image
193  String metaExt = filename.substring(filename.lastIndexOf(":")+1);
194  for (int i = 0; i < filetypes.length; i++) {
195  if (filetypes[i].endsWith(metaExt))
196  return true;
197  }
198  }
199  // At this point use the filename extension to check
200  // if it is one of the recognized image types
201  for (int i = 0; i < filetypes.length; i++) {
202  if (filename.toLowerCase().endsWith(filetypes[i])) {
203  return true;
204  }
205  }
206 
207  return false;
208  }
209 
225  public static String findImagePath(String filename, String mdFilename,
226  boolean shouldExist) {
227  if(filename == null || filename.equals(""))
228  return null;
229  String path = Filename.getFilename(filename); // Remove special chars
230  String foundPath = null;
231  File f = new File(path);
232  // 1. Check if exists from current dir
233  if (f.exists()) {
234  foundPath = path;
235  } else if (mdFilename != null) {
236  // 2. Check if exists from mdFilename
237  f = new File(mdFilename);
238  if (!f.isDirectory())
239  f = f.getParentFile();
240  f = new File(f, path);
241  if (f.exists())
242  foundPath = f.getPath();
243  else {
244  // 3. Check if it is relative to project dir
245  File projectDir = findProjectDir(mdFilename);
246  if (projectDir != null) {
247  f = new File(projectDir, path);
248  if (f.exists())
249  foundPath = f.getPath();
250  }
251  }
252  }
253 
254  if (foundPath != null && hasPrefix(filename)) {
255  foundPath = compose(getPrefix(filename), foundPath);
256  }
257  if (foundPath != null && hasSuffix(filename)) {
258  foundPath += getSuffix(filename);
259  }
260  return foundPath;
261  }
262 
266  public static boolean exists(String path) {
267  File f = new File(Filename.getFilename(path));
268  return f.exists();
269  }
270 
272  public static String findProjectPath(String filename) {
273  File dir = findProjectDir(filename);
274  if (dir != null)
275  return dir.getPath();
276  return null;
277  }
278 
283  public static File findProjectDir(String filename) {
284  filename = getFilename(filename);
285  File dir = new File(filename).getAbsoluteFile(); // Remove Xmipp special
286  // characters
287  if (!dir.isDirectory())
288  dir = dir.getParentFile();
289  while (dir != null) {
290  File f = new File(dir, PROJECT_FILE);
291  if (f.exists())
292  return dir;
293  dir = dir.getParentFile();
294  }
295 
296  return null;
297  }
298 
302  public static String getFilename(String filename) {
303 
304  if (filename.contains(SEPARATOR))
305  filename = filename.split(SEPARATOR)[1];
306 
307  if (filename.contains(":"))
308  filename = filename.split(":")[0];
309  if (filename.contains("#"))
310  filename = filename.split("#")[0];
311 
312  return filename;
313  }
314 
315  public static String getPath(String baseDir, String fileName, int slice)
316  throws Exception {
317  return compose(slice, baseDir + File.separatorChar + fileName);
318  }
319 
320  public static long getNimage(String filename) {
321  String prefix = getPrefix(filename);
322 
323  return prefix != null ? Long.valueOf(prefix).longValue()
324  : ImageGeneric.ALL_IMAGES;
325  }
326 
327  public static String compose(String prefix, String path) {
328  return prefix + SEPARATOR + path;
329  }
330 
331  public static boolean hasPrefix(String filename) {
332  return filename.contains(SEPARATOR);
333  }
334 
335  public static boolean hasSuffix(String filename) {
336  return filename.contains(":") || filename.contains("#");
337  }
338 
339  public static String getPrefix(String filename) {
340  if (hasPrefix(filename)) {
341  String prefix = "";
342  String str = filename.split(SEPARATOR)[0];
343  // if (!str.isEmpty()) {
344  // // str may have a string prefix before the number, so
345  // // grab the leftmost part
346  // int i = str.length() - 1;
347  // while (i >= 0) {
348  // if (str.charAt(i) == File.separatorChar) {
349  // break;
350  // }
351  // i--;
352  // }
353  //
354  // prefix = str.substring(i + 1, str.length());
355  // }
356  // return prefix;
357  return str;
358  }
359 
360  return null;
361  }
362 
363  public static String getSuffix(String filename) {
364  if (filename.contains(":")) {
365  return ":" + filename.split(":")[1];
366  } else if (filename.contains("#")) {
367  return "#" + filename.split("#")[1];
368  }
369 
370  return null;
371  }
372 
373  public static String removePrefix(String filename) {
374  String prefix = getPrefix(filename);
375  if (prefix == null)
376  return filename;
377  else
378  return filename.split(SEPARATOR)[1];
379  }
380 
385  public static String getClassBlockName(int ref) {
386  return String.format("class%06d_images", ref);
387  }
388 
390  public static String getCurrentDir() {
391  return System.getProperty("user.dir");
392  }
393 
394  /***********
395  * Create the relative path from one path to another Taken from: /*
396  * http://mrpmorris.blogspot.com/2007/05/convert-absolute-path
397  * -to-relative-path.html
398  *
399  * @param absolutePath
400  * @param relativeTo
401  * @return
402  */
403  public static String getRelativePath(String absolutePath, String relativeTo) {
404  StringBuilder relativePath = null;
405 
406  absolutePath = absolutePath.replaceAll("\\\\", "/");
407  relativeTo = relativeTo.replaceAll("\\\\", "/");
408 
409  if (absolutePath.equals(relativeTo) == true) {
410 
411  } else {
412  String[] absoluteDirectories = absolutePath.split("/");
413  String[] relativeDirectories = relativeTo.split("/");
414 
415  // Get the shortest of the two paths
416  int length = absoluteDirectories.length < relativeDirectories.length ? absoluteDirectories.length
417  : relativeDirectories.length;
418 
419  // Use to determine where in the loop we exited
420  int lastCommonRoot = -1;
421  int index;
422 
423  // Find common root
424  for (index = 0; index < length; index++) {
425  if (absoluteDirectories[index]
426  .equals(relativeDirectories[index])) {
427  lastCommonRoot = index;
428  } else {
429  break;
430  // If we didn't find a common prefix then throw
431  }
432  }
433  if (lastCommonRoot != -1) {
434  // Build up the relative path
435  relativePath = new StringBuilder();
436  // Add on the ..
437  for (index = lastCommonRoot + 1; index < absoluteDirectories.length; index++) {
438  if (absoluteDirectories[index].length() > 0) {
439  relativePath.append("../");
440  }
441  }
442  for (index = lastCommonRoot + 1; index < relativeDirectories.length - 1; index++) {
443  relativePath.append(relativeDirectories[index] + "/");
444  }
445  relativePath
446  .append(relativeDirectories[relativeDirectories.length - 1]);
447  }
448  }
449  return relativePath == null ? null : relativePath.toString();
450  }// function getRelativePath
451 
453  public static String getRelativePath(String path) {
454  return getRelativePath(path, getCurrentDir());
455  }
456 
458  public static String getBaseName(String path) {
459  int index = path.lastIndexOf(File.separatorChar);
460  if (index != -1)
461  path = path.substring(index + 1, path.length());
462  return path;
463  }
464 
465  public static String removeExtension(String path) {
466  int index = path.lastIndexOf(".");
467  if (index != -1)
468  path = path.substring(0, index);
469  return path;
470  }
471 
473  public static String join(String... paths) {
474  String joined = paths[0];
475  for (int i = 1; i < paths.length; ++i) {
476  if (!joined.endsWith(File.separator))
477  joined += File.separator;
478  joined += paths[i];
479  }
480  return joined;
481  }
482 
483  public static String humanReadableByteCount(long bytes) {
484  int unit = 1024;
485  if (bytes < unit)
486  return bytes + " B";
487  int exp = (int) (Math.log(bytes) / Math.log(unit));
488  String pre = "KMGTPE".charAt(exp - 1) + "i";
489  return String.format("%.1f %sB", bytes / Math.pow(unit, exp), pre);
490  }
491 
492  public static String putExtension(String file, String ext)
493  {
494  int sepindex = file.lastIndexOf(".");//-1 if separator does not exists
495  if(sepindex == -1)
496  return file + "." + ext;
497  String part1 = file.substring(0, sepindex);
498  return part1 + "." + ext;
499 
500  }
501 
502  public static boolean isXmippSupported(String filename) {
503  return isFileType(filename, XMIPP_SUPPORTED);
504  }
505 
506 
507 }
xmipp.jni.Filename.isSingleImageExt
static boolean isSingleImageExt(String filename)
Definition: Filename.java:126
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xmipp.jni.Filename.TEXT
static final String [] TEXT
Definition: Filename.java:75
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xmipp.jni.Filename.hasStackExtension
static native boolean hasStackExtension(String filename)
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xmipp.jni.Filename.findProjectPath
static String findProjectPath(String filename)
Definition: Filename.java:272
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xmipp.jni.Filename.hasVolumeExtension
static native boolean hasVolumeExtension(String filename)
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xmipp.jni.Filename.EXT_SER
static final String EXT_SER
Definition: Filename.java:23
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xmipp.jni.Filename.EXT_MRCS
static final String EXT_MRCS
Definition: Filename.java:16
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xmipp.jni.Filename.join
static String join(String... paths)
Definition: Filename.java:473
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xmipp.jni.Filename.SINGLE_IMAGES
static final String [] SINGLE_IMAGES
Definition: Filename.java:60
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xmipp.jni.Filename.hasPrefix
static boolean hasPrefix(String filename)
Definition: Filename.java:331
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xmipp.jni.Filename.EXT_IMG
static final String EXT_IMG
Definition: Filename.java:21
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xmipp.jni.Filename.PROJECT_FILE
static final String PROJECT_FILE
Definition: Filename.java:7
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xmipp.jni.Filename.EXT_JPG
static final String EXT_JPG
Definition: Filename.java:33
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xmipp.jni.Filename.EXT_SPI
static final String EXT_SPI
Definition: Filename.java:10
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xmipp.jni.Filename.SPIDER
static final String [] SPIDER
Definition: Filename.java:73
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xmipp.jni.Filename.getBaseName
static String getBaseName(String path)
Definition: Filename.java:458
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xmipp.jni.Filename.EXT_EMS
static final String EXT_EMS
Definition: Filename.java:27
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xmipp.jni.Filename.EXT_DOC
static final String EXT_DOC
Definition: Filename.java:43
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xmipp.jni.Filename.isPSD
static boolean isPSD(String filename)
Definition: Filename.java:82
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xmipp.jni.Filename.EXT_TXT
static final String EXT_TXT
Definition: Filename.java:51
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xmipp.jni.Filename.getPath
static String getPath(String baseDir, String fileName, int slice)
Definition: Filename.java:315
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xmipp.jni.Filename.EXT_POS
static final String EXT_POS
Definition: Filename.java:46
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xmipp.jni.Filename.EXT_HDF
static final String EXT_HDF
Definition: Filename.java:36
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xmipp.jni.Filename.EXT_MRCSALI
static final String EXT_MRCSALI
Definition: Filename.java:19
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xmipp.jni.Filename.getRelativePath
static String getRelativePath(String path)
Definition: Filename.java:453
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xmipp.jni.Filename.getCurrentDir
static String getCurrentDir()
Definition: Filename.java:390
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xmipp.jni.Filename.EXT_CTFPARAM
static final String EXT_CTFPARAM
Definition: Filename.java:44
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xmipp.jni.Filename.EXT_ERR
static final String EXT_ERR
Definition: Filename.java:49
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xmipp.jni.Filename.isStackExt
static boolean isStackExt(String filename)
Definition: Filename.java:161
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xmipp.jni.Filename.METADATAS
static final String [] METADATAS
Definition: Filename.java:70
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xmipp.jni.Filename.compose
static String compose(String prefix, String path)
Definition: Filename.java:327
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xmipp.jni.Filename.EXT_MRC
static final String EXT_MRC
Definition: Filename.java:14
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xmipp.jni.Filename.EXT_HED
static final String EXT_HED
Definition: Filename.java:22
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xmipp.jni.Filename.EXT_MRCS2
static final String EXT_MRCS2
Definition: Filename.java:17
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xmipp.jni.Filename.getXmippPath
static native String getXmippPath()
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xmipp.jni.Filename.removePrefix
static String removePrefix(String filename)
Definition: Filename.java:373
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xmipp.jni.Filename.isSpiderVolume
static boolean isSpiderVolume(String filename)
Definition: Filename.java:86
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xmipp.jni.Filename.EXT_MRCSPREALI
static final String EXT_MRCSPREALI
Definition: Filename.java:20
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xmipp.jni.Filename.isMetadataExt
static boolean isMetadataExt(String filename)
Definition: Filename.java:175
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xmipp.jni.Filename.isVolumeExt
static boolean isVolumeExt(String filename)
Definition: Filename.java:146
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xmipp.jni.Filename.isVolume
static boolean isVolume(String filename)
Definition: Filename.java:134
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xmipp.jni.Filename.EXT_VOL
static final String EXT_VOL
Definition: Filename.java:12
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xmipp.jni.Filename.putExtension
static String putExtension(String file, String ext)
Definition: Filename.java:492
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xmipp.jni.Filename.isStackOrVolume
static boolean isStackOrVolume(String filename)
Definition: Filename.java:130
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xmipp.jni.Filename.EXT_PIF
static final String EXT_PIF
Definition: Filename.java:28
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xmipp.jni.Filename.getXmippPath
static String getXmippPath(String relpath)
Definition: Filename.java:105
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xmipp.jni.Filename.EXT_TIF
static final String EXT_TIF
Definition: Filename.java:32
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xmipp.jni.Filename.EXT_BOX
static final String EXT_BOX
Definition: Filename.java:52
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xmipp.jni.Filename.EXT_MRC2
static final String EXT_MRC2
Definition: Filename.java:15
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xmipp.jni.Filename.EXT_H5
static final String EXT_H5
Definition: Filename.java:38
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xmipp.jni.Filename.getSuffix
static String getSuffix(String filename)
Definition: Filename.java:363
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xmipp.jni.Filename.hasSuffix
static boolean hasSuffix(String filename)
Definition: Filename.java:335
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xmipp.jni.Filename.EXT_STK
static final String EXT_STK
Definition: Filename.java:13
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xmipp.jni.Filename.findImagePath
static String findImagePath(String filename, String mdFilename, boolean shouldExist)
Definition: Filename.java:225
-
xmipp.jni.Filename.isMetadata
static boolean isMetadata(String filename)
Definition: Filename.java:165
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xmipp.jni.Filename.EXT_CTFDAT
static final String EXT_CTFDAT
Definition: Filename.java:45
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xmipp.jni.Filename.isTextfile
static boolean isTextfile(String filename)
Definition: Filename.java:179
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xmipp.jni.Filename.EXT_DM4
static final String EXT_DM4
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class  Fit_Polynomial
 
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1 import ij.*;
2 import ij.plugin.filter.ExtendedPlugInFilter;
3 import ij.plugin.filter.PlugInFilterRunner;
4 import ij.gui.GenericDialog;
5 import ij.gui.DialogListener;
6 import ij.process.*;
7 import ij.plugin.filter.GaussianBlur;
8 import ij.measure.Calibration;
9 import ij.gui.Roi;
10 import java.util.Vector;
11 import java.awt.*;
12 
65 public class Fit_Polynomial implements ExtendedPlugInFilter, DialogListener {
66 
68  private static int xOrder = 1;
70  private static int yOrder = 1;
72  private static int xyOrder = 0;
74  private static boolean outputFit = false;
76  private static boolean shiftToDisplay = false;
78  private final int flags = DOES_ALL|CONVERT_TO_FLOAT|FINAL_PROCESSING|KEEP_PREVIEW|PARALLELIZE_STACKS;
80  private ImagePlus imp = null;
82  private float offset = 0f;
84  private int baseSize;
86  private boolean matrixCalculated = false;
88  private double[][] matrix;
90  private int[] xPower, yPower;
95  private double[] powerOfX, powerOfY;
97  private int endPower;
99  private int nPasses = 2;
101  private int pass;
103  final static int MAKE_MATRIX_PASSES = 10;
104 
105  public int setup(String arg, ImagePlus imp) {
106  if (arg.equals("final") && !outputFit) {
107  setCalibration(); //at the very end: calibration (non-float images)
108  return DONE;
109  } else {
110  if (IJ.versionLessThan("1.38u")) // generates an error message for older versions
111  return DONE;
112  this.imp = imp;
113  return flags;
114  }
115  }
116 
119  public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
120  GenericDialog gd = new GenericDialog(command);
121  gd.addSlider("x Direction: Order", 0., 10., xOrder);
122  gd.addSlider("y Direction: Order", 0., 10., yOrder);
123  gd.addSlider("mixed xy: Order", 0., 10., xyOrder);
124  gd.addCheckbox("Output Fit (Don't Subtract)", outputFit);
125  gd.addCheckbox("Shift Values to Display Range", shiftToDisplay);
126  gd.addPreviewCheckbox(pfr);
127  gd.addDialogListener(this);
128  gd.addHelp("http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:fit_polynomial:start");
129  gd.showDialog(); //input by the user (or macro) happens here
130  if (gd.wasCanceled()) return DONE;
131  IJ.register(this.getClass()); //protect static class variables (filter parameters) from garbage collection
132  return IJ.setupDialog(imp, flags); //ask whether to process all slices of stack (if a stack)
133  }
134 
135  public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
136  Vector numericFields = gd.getNumericFields();
137  xOrder = (int)gd.getNextNumber();
138  yOrder = (int)gd.getNextNumber();
139  xyOrder = (int)gd.getNextNumber();
140  if (xOrder < 0 || yOrder < 0 || xyOrder < 0 || xOrder>50 || yOrder>50 || xyOrder>10)
141  return false;
142  outputFit = gd.getNextBoolean();
143  shiftToDisplay = gd.getNextBoolean();
144  if (e!=null && !(e.getSource() instanceof Checkbox))
145  matrixCalculated = false;
146  setOffset();
147  return true;
148  }
149 
150  private void setOffset() {
151  ImageProcessor ip = imp.getProcessor();
152  if (shiftToDisplay) {
153  offset = (float)(ip.getMin() + ip.getMax())/2;
154  } else {
155  offset = 0f;
156  if (ip instanceof ByteProcessor || ip instanceof ColorProcessor)
157  offset = 128f;
158  else if (ip instanceof ShortProcessor)
159  offset = 32768f;
160  }
161  }
162 
163  private void setCalibration() {
164  if (matrix==null) return; //fit failed
165  ImageProcessor ip = imp.getProcessor();
166  /* Calibrate the image to reflect zero level (8-bit and 16-bit only) */
167  if (!(ip instanceof FloatProcessor) && !(ip instanceof ColorProcessor)) {
168  Calibration cal = imp.getCalibration();
169  double slope = 1;
170  String valueUnit = "Gray Value";
171  if (cal != null && cal.calibrated() && cal.getFunction()== Calibration.STRAIGHT_LINE) {
172  slope = cal.getCoefficients()[1];
173  valueUnit = cal.getValueUnit();
174  }
175  double[] coefficients = new double[] {-offset*slope, slope};
176  cal.setFunction(Calibration.STRAIGHT_LINE, coefficients, valueUnit);
177  }
178  if (!shiftToDisplay && (ip instanceof ShortProcessor || ip instanceof FloatProcessor)) {
179  double range = ip.getMax() - ip.getMin();
180  ip.setMinAndMax(offset-range/2, offset+range/2);
181  }
182  }
183 
188  public void run(ImageProcessor ip) {
189  Rectangle roi = ip.getRoi();
190  int width = ip.getWidth();
191  int height = ip.getHeight();
192  float[] pixels = (float[])ip.getPixels();
193  byte[] mask = ip.getMaskArray();
194  Thread thread = Thread.currentThread();
195  synchronized(this) {
196  if (!matrixCalculated) {
197  matrixCalculated = true;
198  calculateMatrixEtc(ip);
199  if (matrix == null)
200  IJ.error("Fit failed, use lower order.");
201  }
202  }
203  if (matrix==null || thread.isInterrupted()) return;
204  double[] vector = new double[baseSize]; //calculate fit
205  long lastTime = System.currentTimeMillis();
206  for (int y=roi.y, powerY=y*endPower; y<roi.y+roi.height; y++, powerY+=endPower) {
207  long time = System.currentTimeMillis();
208  if (time-lastTime > 100) {
209  lastTime = time;
210  if (thread.isInterrupted()) return;
211  showProgress((y-roi.y)/(double)(roi.height));
212  }
213  for (int x=roi.x, p=width*y+x, m=(y-roi.y)*roi.width, powerX=x*endPower; x<roi.x+roi.width; x++, p++, m++, powerX+=endPower)
214  if (mask == null || mask[m] != 0)
215  for (int iBase=0; iBase<baseSize; iBase++)
216  vector[iBase] += pixels[p]*
217  powerOfX[powerX+xPower[iBase]]*powerOfY[powerY+yPower[iBase]];
218  //for iBase
219  //if inside mask
220  //for x
221  } //for y
222  pass++;
223  double[] coeff = new double[baseSize];
224  for (int i=0; i<baseSize; i++)
225  for (int j=0; j<baseSize; j++)
226  coeff[i] += matrix[i][j]*vector[j];
227  //IJ.log("coeff:");printVector(coeff);
228  // // apply fit
229  for (int y=0, p=0, powerY=0; y<height; y++, powerY+=endPower) {
230  long time = System.currentTimeMillis();
231  if (time-lastTime > 100) {
232  lastTime = time;
233  if (thread.isInterrupted()) return;
234  showProgress(y/(double)(height));
235  }
236  for (int x=0, powerX=0; x<width; x++, p++, powerX+=endPower) {
237  double background = 0.;
238  for (int iBase=0; iBase<baseSize; iBase++)
239  background += coeff[iBase]*powerOfX[powerX+xPower[iBase]]*powerOfY[powerY+yPower[iBase]];
240  if (outputFit)
241  pixels[p] = (float)background;
242  else
243  pixels[p] += offset - (float)background;
244  } //for x
245  } //for y
246  pass++;
247  }
248 
251  private void calculateMatrixEtc(ImageProcessor ip) {
252  Thread thread = Thread.currentThread();
253  Rectangle roi = ip.getRoi();
254  int width = ip.getWidth();
255  int height = ip.getHeight();
256  byte[] mask = ip.getMaskArray();
257  baseSize = xyOrder*(xyOrder-1)/2; // t h e b a s e
258  if (baseSize < 0) baseSize = 0;
259  baseSize += xOrder + yOrder + 1;
260  xPower = new int[baseSize];
261  yPower = new int[baseSize];
262  int iBase = 0; //get powers of x, y in the base
263  for (int ix=0; ix<=xOrder; ix++, iBase++)
264  xPower[iBase] = ix;
265  for (int iy=1; iy<=yOrder; iy++, iBase++)
266  yPower[iBase] = iy;
267  for (int ix=1; ix<xyOrder; ix++)
268  for (int iy=1; ix+iy<=xyOrder; iy++, iBase++) {
269  xPower[iBase] = ix;
270  yPower[iBase] = iy;
271  }
272  //IJ.log("xPower:");String s="";for (int i=0;i<baseSize;i++) s+=xPower[i]+","; IJ.log(s);
273  //IJ.log("yPower:");s="";for (int i=0;i<baseSize;i++) s+=yPower[i]+","; IJ.log(s);
274  endPower = xOrder > yOrder ? xOrder : yOrder;
275  if (xyOrder-1 > endPower) endPower = xyOrder-1;
276  endPower++;
277  powerOfX = new double[endPower*width];
278  powerOfY = new double[endPower*height];
279  for (int x=0,p=0; x<width; x++) { //tabulate powers of x coordinates
280  double power = 1.;
281  double xScaled = 3*(x-roi.x)/(double)roi.width-1.5; //scale to get well-conditioned matrix
282  for (int iPow = 0; iPow<endPower; iPow++,p++) {
283  powerOfX[p] = power;
284  power *= xScaled;
285  }
286  }
287  for (int y=0,p=0; y<height; y++) { //tabulate powers of y coordinates
288  double power = 1.;
289  double yScaled = 3*(y-roi.y)/(double)roi.height-1.5;
290  for (int iPow = 0; iPow<endPower; iPow++,p++) {
291  powerOfY[p] = power;
292  power *= yScaled;
293  }
294  } // t h e m a t r i x
295  matrix = new double[baseSize][baseSize];
296  long lastTime = System.currentTimeMillis();
297  for (int y=roi.y, powerY=y*endPower; y<roi.y+roi.height; y++, powerY+=endPower) {
298  long time = System.currentTimeMillis();
299  if (time-lastTime > 100) {
300  lastTime = time;
301  if (thread.isInterrupted()) return;
302  showProgress(MAKE_MATRIX_PASSES*(y-roi.y)/(double)(roi.height));
303  }
304  for (int x=roi.x, p=width*y+x, m=(y-roi.y)*roi.width, powerX=x*endPower; x<roi.x+roi.width; x++, p++, m++, powerX+=endPower)
305  if (mask == null || mask[m] != 0)
306  for (iBase=0; iBase<baseSize; iBase++) {
307  double fct = powerOfX[powerX+xPower[iBase]]*powerOfY[powerY+yPower[iBase]];
308  matrix[iBase][iBase] += fct*fct;
309  for (int iBase1=0; iBase1<iBase; iBase1++) {
310  double fct1 = powerOfX[powerX+xPower[iBase1]]*powerOfY[powerY+yPower[iBase1]];
311  matrix[iBase][iBase1] += fct*fct1;
312  matrix[iBase1][iBase] += fct*fct1;
313  }
314  }
315  //for x
316  //if inside mask
317  } //for y
318  if (!invertSymmetricMatrix(matrix)) matrix = null;
319  pass += MAKE_MATRIX_PASSES;
320  }
321 
324  public static boolean invertSymmetricMatrix(double[][] matrix) {
325  int n = matrix.length;
326  if (matrix[0].length != n) {
327  IJ.error("invertSymmetricMatrix - not a square matrix");
328  return false;
329  }
330  boolean[] processed = new boolean[n];
331  double[] qq = new double[n];
332  double[] pp = new double[n];
333  double pivot0 = 1e-50; //absolute value of the first (largest) pivot
334  //IJ.log("---invert matrix---"); printMatrix(matrix);
335  for (int i=0; i<n; i++) { //loop: process all matrix lines&columns
336  double max = pivot0 * 1e-14; //pivot must be bigger than this
337  int iPivot = -1;
338  for (int j=0; j<n; j++) //find pivot
339  if (!processed[j]) {
340  double abs = matrix[j][j];
341  abs = abs<0 ? -abs : abs;//abs = Math.abs(matrix[j][j]); but faster
342  if (abs > max) {
343  max = abs;
344  iPivot = j;
345  }
346  }
347  if (iPivot < 0)
348  return false; //no pivot large enough, looks singular
349  if (i==0)
350  pivot0 = max;
351  processed[iPivot] = true;
352  pp[iPivot] = 1.;
353  double q = 1./matrix[iPivot][iPivot];
354  qq[iPivot] = q;
355  matrix[iPivot][iPivot] = 0.;
356  for (int j=0; j<iPivot; j++) {
357  pp[j] = matrix[j][iPivot];
358  qq[j] = matrix[j][iPivot]*q*(processed[j]?1:-1);
359  matrix[j][iPivot] = 0.;
360  }
361  for (int j=iPivot+1; j<n; j++) {
362  pp[j] = matrix[iPivot][j]*(processed[j]?-1:1);
363  qq[j] = -matrix[iPivot][j]*q;
364  matrix[iPivot][j] = 0.;
365  }
366  for (int j=0; j<n; j++)
367  for (int k=j; k<n; k++)
368  matrix[j][k] += pp[j]*qq[k];
369  //printMatrix(matrix);
370  } //for i
371  //IJ.log("asymmetric:");printMatrix(matrix);
372  for (int i=1; i<n; i++) //fill bottom left to make symmetric again
373  for (int j=0; j<i; j++)
374  matrix[i][j] = matrix[j][i];
375  //IJ.log("result:");printMatrix(matrix);
376  return true;
377  }
380  public void setNPasses (int nPasses) {
381  this.nPasses = 2*nPasses; //one pass for fitting, one for subtracting
382  if (!matrixCalculated) this.nPasses += MAKE_MATRIX_PASSES; //+time for making the matrix
383  pass = 0;
384  }
385 
386  private void showProgress(double percent) {
387  percent = (pass + percent)/nPasses;
388  IJ.showProgress(percent);
389  }
390 
392  /*
393  static void printMatrix(double[][] matrix) {
394  int n = matrix.length;
395  for (int i=0; i<n; i++) {
396  StringBuffer b = new StringBuffer(n*13);
397  for (int j=0; j<n; j++)
398  addToStringBuffer(b, matrix[i][j]);
399  IJ.log(b.toString());
400  }
401  }
402  static void printVector(double[] vector) {
403  int n = vector.length;
404  StringBuffer b = new StringBuffer(n*13);
405  for (int i=0; i<n; i++)
406  addToStringBuffer(b, vector[i]);
407  IJ.log(b.toString());
408  }
409  static void addToStringBuffer(StringBuffer b, double x) {
410  String s = Float.toString((float)x);
411  b.append(" ");
412  for (int i=s.length();i<12;i++)
413  b.append(" ");
414  b.append(s);
415  }
416  */
417 }
Fit_Polynomial.run
void run(ImageProcessor ip)
Definition: Fit_Polynomial.java:188
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Fit_Polynomial.setup
int setup(String arg, ImagePlus imp)
Definition: Fit_Polynomial.java:105
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Fit_Polynomial.showDialog
int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr)
Definition: Fit_Polynomial.java:119
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Fit_Polynomial.invertSymmetricMatrix
static boolean invertSymmetricMatrix(double[][] matrix)
Definition: Fit_Polynomial.java:324
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Fit_Polynomial.dialogItemChanged
boolean dialogItemChanged(GenericDialog gd, AWTEvent e)
Definition: Fit_Polynomial.java:135
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Fit_Polynomial
Definition: Fit_Polynomial.java:65
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Fit_Polynomial.setNPasses
void setNPasses(int nPasses)
Definition: Fit_Polynomial.java:380
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1 package xmipp.viewer;
2 
3 import java.awt.Component;
4 import javax.swing.JLabel;
5 import javax.swing.JTable;
6 import javax.swing.table.DefaultTableCellRenderer;
7 
8 import xmipp.utils.DEBUG;
9 
10 public class FloatRenderer extends DefaultTableCellRenderer {
11  private static final long serialVersionUID = 1L;
12 
13  public FloatRenderer() {
14  super();
15  setOpaque(true);
16  setHorizontalAlignment(JLabel.RIGHT);
17  setHorizontalTextPosition(JLabel.CENTER);
18  setVerticalTextPosition(JLabel.BOTTOM);
19  }
20 
21  @Override
22  public Component getTableCellRendererComponent(JTable table, Object object, boolean isSelected, boolean hasFocus, int row, int column) {
23  Object item = object;
24  // Calls super class so foreground, background, borders and rest of stuff is set.
25  super.getTableCellRendererComponent(table, null,
26  item != null && isSelected,
27  item != null && hasFocus, row, column);
28 
29  if (item != null) {
30  //DEBUG.printMessage("*** 2. Rendering: " + item.getLabel());
31  //AbstractXmippTableModel tableModel = (AbstractXmippTableModel) table.getModel();
32  String v = item.toString();
33  try {
34  // float f = Float.parseFloat(v);
35  v = String.format("%10.4f ", (Double)item);
36  } catch (Exception e) {
37  // TODO: handle exception
38  }
39  setText(v);
40  }
41  return this;
42  }
43 }
xmipp.viewer.FloatRenderer.getTableCellRendererComponent
Component getTableCellRendererComponent(JTable table, Object object, boolean isSelected, boolean hasFocus, int row, int column)
Definition: FloatRenderer.java:22
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class  Floyd_Steinberg_Dithering
 
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Floyd_Steinberg_Dithering.java
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1 import ij.*;
2 import ij.process.*;
3 import ij.plugin.*;
4 
9 public class Floyd_Steinberg_Dithering implements PlugIn {
10 
11  public void run(String arg) {
12  ImagePlus imp = IJ.getImage();
13  Undo.setup(Undo.TRANSFORM, imp);
14  ImageProcessor ip = imp.getProcessor();
15  int width = imp.getWidth();
16  int height = imp.getHeight();
17  ip = ip.convertToByte(true);
18  int[][] pixel = ip.getIntArray();
19  int oldpixel, newpixel, error;
20  boolean nbottom, nleft, nright;
21  for (int y=0; y<height; y++) {
22  nbottom=y<height-1;
23  for (int x=0; x<width; x++) {
24  nleft=x>0; nright=x<width-1;
25  oldpixel = pixel[x][y];
26  newpixel = oldpixel<128?0:255;
27  pixel[x][y] = newpixel;
28  error = oldpixel-newpixel;
29  if (nright) pixel[x+1][y] += 7*error/16;
30  if (nleft&nbottom) pixel[x-1][y+1] += 3*error/16;
31  if (nbottom) pixel[x][y+1] += 5*error/16;
32  if (nright&&nbottom) pixel[x+1][y+1] += error/16;
33  }
34  }
35  ip.setIntArray(pixel);
36  imp.setProcessor(null, ip);
37  }
38 
39 }
Floyd_Steinberg_Dithering
Definition: Floyd_Steinberg_Dithering.java:9
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Floyd_Steinberg_Dithering.run
void run(String arg)
Definition: Floyd_Steinberg_Dithering.java:11
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enum  xmipp.viewer.particlepicker.Format
 
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package  xmipp.viewer.particlepicker
 
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1 package xmipp.viewer.particlepicker;
2 
3 public enum Format
4 {
5  Auto, Xmipp24, Xmipp30, Xmipp301, Eman, None, Relion, Xmipp
6 }
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class  xmipp.viewer.models.GalleryColumnModel
 
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package  xmipp.viewer.models
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.models;
27 
28 import javax.swing.JTable;
29 import javax.swing.table.DefaultTableColumnModel;
30 import javax.swing.table.TableColumn;
31 
32 public class GalleryColumnModel extends DefaultTableColumnModel {
33  private static final long serialVersionUID = 1L;
34 
35  protected int width;
36 
37  public GalleryColumnModel(int w){
38  super();
39 
40  width = w;
41  }
42 
44  @Override
45  public void addColumn(TableColumn tc) {
46  tc.setPreferredWidth(width);
47  super.addColumn(tc);
48  }
49 
50 // // @TODO this method causes problems. It's overrided to check it out.
51 // @Override
52 // public TableColumn getColumn(int columnIndex) {
53 // try {
54 // return super.getColumn(columnIndex);
55 // } catch (Exception ex) {
56 // return super.getColumn(0);
57 // }
58 // }
59 
61  public void setWidth(int width) {
62  this.width = width;
63  //adjustColumnsWidth();
64  }
65 
67  public void adjustColumnsWidth(JTable table) {
68  for (int i = 0; i < getColumnCount(); i++) {
69  getColumn(i).setPreferredWidth(width);
70  }
71  }
72 }
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class  xmipp.viewer.models.GalleryData
 
enum  xmipp.viewer.models.GalleryData.Mode
 
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1 
26 package xmipp.viewer.models;
27 
28 import ij.ImagePlus;
29 
30 import java.awt.Color;
31 import java.io.File;
32 import java.util.ArrayList;
33 import java.util.Arrays;
34 import java.util.Date;
35 import java.util.HashMap;
36 import java.util.Hashtable;
37 import java.util.List;
38 import java.util.logging.Level;
39 import java.util.logging.Logger;
40 
41 import xmipp.ij.commons.Geometry;
42 import xmipp.ij.commons.Tool;
43 import xmipp.ij.commons.XmippImageConverter;
44 import xmipp.ij.commons.XmippUtil;
45 import xmipp.jni.EllipseCTF;
46 import xmipp.jni.Filename;
47 import xmipp.jni.ImageGeneric;
48 import xmipp.jni.MDLabel;
49 import xmipp.jni.MDRow;
50 import xmipp.jni.MetaData;
51 import xmipp.utils.DEBUG;
52 import xmipp.utils.Params;
53 import xmipp.utils.XmippDialog;
54 import xmipp.utils.XmippMessage;
55 import xmipp.utils.XmippStringUtils;
56 import xmipp.viewer.ctf.CTFAnalyzerJFrame;
57 import xmipp.viewer.ctf.CTFRecalculateImageWindow;
58 import xmipp.viewer.ctf.EstimateFromCTFTask;
59 import xmipp.viewer.ctf.TasksEngine;
60 import xmipp.viewer.scipion.ScipionGalleryData;
61 import xmipp.viewer.scipion.ScipionMetaData;
62 import xmipp.viewer.windows.AddObjectJDialog;
63 import xmipp.viewer.windows.GalleryJFrame;
64 import xmipp.viewer.windows.SaveJDialog;
65 
69 public class GalleryData {
70 
71 
72  protected HashMap<String, ColumnInfo> displaycis;
73  protected MetaData md;
74  protected long[] ids;
75  protected String[] mdBlocks = null;
76  protected String selectedBlock;
77  // The following is only used in VolumeGallery mode
78  protected String selectedVolFn = "";
79  //protected String commonVolPrefix = "";
80 
81  protected List<ColumnInfo> labels = null;
82  // First label that can be rendered
83  protected ColumnInfo ciFirstRender = null;
84  protected Integer zoom;
85  protected String filename;
86  protected int resliceView;
87  protected Mode mode;
88  protected boolean showLabel = false;
89  protected boolean renderImages;
90  public final Params parameters;
91 
92 
93  // flag to perform global normalization
94  protected boolean normalize = false;
95  // flag to use geometry info
96  protected boolean useGeo;
97  // flag to wrapping
98  protected boolean wrap;
99  // flag to check if is 2d classification
100  protected boolean isClassification = false;
101  protected int refLabel;
102  // Store the selection state for each item
103 
104 
105  // Array with all ClassInfo
106  protected ArrayList<ClassInfo> classesArray;
107  // ClassInfo reference for each element
108  protected ClassInfo[] classes;
109  // Flags to check if md or classes has changed
110  protected boolean hasMdChanges, hasClassesChanges;
111  protected GalleryJFrame window;
112 
113  protected String[] displayLabels;
114  protected String[] sortby;
115 
116  protected boolean isVolumeMd;
117  protected Integer rows, columns;
118 
119 
120 
121  protected String[] renderLabels;
122  protected String renderLabel = "first";
123  protected String[] visibleLabels;
124  protected String[] orderLabels;
125  protected boolean inverty;
126 
127  public boolean isObjectCmd(String cmd) {
128  for(String objCmd: parameters.objectCommands)
129  if(objCmd.equals(cmd))
130  return true;
131  return false;
132  }
133 
134  public boolean isVolumeMd()
135  {
136  return isVolumeMd;
137  }
138 
139  public Integer getModelRows()
140  {
141  return rows;
142  }
143 
144  public Integer getModelColumns()
145  {
146  return columns;
147  }
148 
149  public void runObjectCommand(int index, String objectCommand) {
150  try {
151  String[] cmd = new String[]{objectCommand};
152  System.out.println(Arrays.toString(cmd));
153  } catch (Exception ex) {
154  Logger.getLogger(GalleryData.class.getName()).log(Level.SEVERE, null, ex);
155  }
156  }
157 
158  public String getTmpFile(String suffix) {
159  String ext = XmippStringUtils.getFileExtension(filename);
160  String ext2 = suffix + ext;
161  String tmpfile = filename;
162  if(!filename.endsWith(ext2))
163  tmpfile = filename.replace(ext, ext2);
164  return tmpfile;
165  }
166 
167  public void selectVolumeAt(int selectedIndex) {
168  String vol = getVolumeAt(selectedIndex);
169  String file = vol;
170  if (vol.contains(":"))
171  file = vol.substring(0, vol.lastIndexOf(":"));
172  if (vol.contains("@"))
173  file = file.substring(file.lastIndexOf("@") + 1);
174  if(new File(file).exists())
175  {
176  selectedVolFn = vol;
177  }
178  else
179  throw new IllegalArgumentException(XmippMessage.getPathNotExistsMsg(file));
180  }
181 
182  public boolean isAutoAdjust()
183  {
184  return rows == null && columns == null;
185  }
186 
187  public void setModelDim(Integer rows, Integer cols) {
188  if(cols != null && cols == 0)
189  throw new IllegalArgumentException(XmippMessage.getIllegalValueMsg("columns", 0));
190  this.rows = rows;
191  this.columns = cols;
192  }
193 
194  public boolean isScipionInstance() {
195  return this instanceof ScipionGalleryData;
196  }
197 
198  public boolean isInvertY() {
199  return inverty;
200  }
201 
202  public String getChimeraProjectionCmd(int row) {
203  String rot = getValueFromLabel(row, MDLabel.MDL_ANGLE_ROT);
204  String tilt = getValueFromLabel(row, MDLabel.MDL_ANGLE_TILT);
205  String psi = getValueFromLabel(row, MDLabel.MDL_ANGLE_PSI);
206  String command = String.format("rotate %s %s %s", rot, tilt, psi);
207  return command;
208  }
209 
210 
211  public enum Mode {
212 
213  GALLERY_MD, GALLERY_VOL, TABLE_MD
214  };
215 
216  // define min and max render dimensions
217  public static int MIN_SIZE = 16;
218  public static int MAX_SIZE = 256;
219 
220  public GalleryData(GalleryJFrame window, String fn, Params parameters)
221  {
222  this(window, parameters, new MetaData(fn));
223  }
224  // max dimension allowed to render images
231  public GalleryData(GalleryJFrame window, Params parameters, MetaData md) {
232  this.window = window;
233  this.parameters = parameters;
234 
235  try {
236  selectedBlock = "";
237  this.md = md;
238  setFileName(md.getPath());
239  zoom = parameters.zoom;
240  resliceView = parameters.resliceView;
241  if(parameters.rows > 0)
242  rows = parameters.rows;
243  if(parameters.columns > 0)
244  columns = parameters.columns;
245  loadMd();
246 
247  } catch (Exception e) {
248  e.printStackTrace();
249  md = null;
250  }
251 
252  }// constructor GalleryData
253 
254  protected void readMdParameters()
255  {
256  renderLabels = null;
257  renderLabel = "first";
258  visibleLabels = null;
259  orderLabels = null;
260  sortby = null;
261 
262  useGeo = wrap = false;
263  displayLabels = null;
264 
265  if (mode == null)
266  mode = Mode.GALLERY_MD;
267  this.renderImages = true;
268  displaycis = new HashMap<String, ColumnInfo>();
269  this.inverty = parameters.inverty;
270 
271  if(parameters.getBlock() == null)
272  parameters.setBlock(selectedBlock);//Identifies parameters with first block loaded
273 
274  if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_METADATA))
275  mode = Mode.TABLE_MD;
276  else if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_GALLERY))
277  mode = Mode.GALLERY_MD;
278 
279  if(parameters.getBlock().equals(selectedBlock))
280  {
281  setRenderLabels(parameters.renderLabels);
282  setRenderLabel(parameters.getRenderLabel());
283  setVisibleLabels(parameters.visibleLabels);
284  setOrderLabels(parameters.orderLabels);
285  useGeo = parameters.useGeo;
286  wrap = parameters.wrap;
287  displayLabels = parameters.getDisplayLabels();
288  this.renderImages = parameters.renderImages;
289 
290  }
291  }
292 
293  public List<ColumnInfo> getColumns() {
294  return labels;
295  }
296 
297  public void setRenderColumn(String key) {
298  if(key.equalsIgnoreCase("none"))
299  ciFirstRender = null;
300  for(ColumnInfo ci: labels)
301  if(ci.labelName.equals(key))
302  ciFirstRender = ci;
303  renderLabel = ciFirstRender.labelName;
304  }
305 
306  public ColumnInfo getRenderColumn() {
307  return ciFirstRender;
308  }
309 
313  public String getMdFilename() {
314  if (selectedBlock.isEmpty()) {
315  return filename;
316  }
317  return String.format("%s@%s", selectedBlock, filename);
318  }// function getMdFilename
319 
320  public String getMdSaveFileName() {
321  if (filename == null) {
322  return null;
323  }
324 
325  String savefn;
326  if (selectedBlock.isEmpty()) {
327  savefn = filename;
328  } else {
329  savefn = String.format("%s@%s", selectedBlock, filename);
330  }
331  String ext;
332  if (savefn.contains(".")) {
333  ext = savefn.substring(savefn.lastIndexOf("."));
334  if (ext.equals(".stk")) {
335  return savefn.replace(ext, ".xmd");
336  }
337  } else {
338  savefn = savefn + ".xmd";
339  }
340  return savefn;
341  }
342 
343  public void setFileName(String file) {
344  filename = file;
345  if (file != null) {
346  if (Filename.hasPrefix(file)) {
347  if (Filename.isMetadata(file)) {
348  selectedBlock = Filename.getPrefix(file);
349  filename = Filename.getFilename(file);
350  }
351  }
352  if (Filename.exists(filename)) {
353  mdBlocks = MetaData.getBlocksInMetaDataFile(filename);
354  if (mdBlocks.length >= 1 && selectedBlock.isEmpty()) {
355  selectedBlock = mdBlocks[0];
356  }
357  }
358  }
359  }
360 
361  public void setDisplayLabel(String key, boolean selected) {
362  if(!selected)
363  {
364  displaycis.remove(key);
365  return;
366  }
367 
368  for(ColumnInfo ci: labels)
369  if(ci.labelName.equals(key))
370  {
371  displaycis.put(key, ci);
372  break;
373  }
374  }
375 
379  public void loadMd() throws Exception {
380  readMdParameters();
381  ids = md.findObjects();
382  loadLabels();
383 
384  if (!containsGeometryInfo()) {
385  useGeo = false;
386  wrap = false;
387  }
388 
389  isClassification = checkifIsClassificationMd();
390 
391  if (isClassification) {
392  classes = new ClassInfo[ids.length];
393  classesArray = new ArrayList<ClassInfo>();
394  loadClassesInfo();
395  }
396 
397 
398  if (!md.isColumnFormat() ) {
399  mode = Mode.TABLE_MD;
400  renderImages = false;
401  }
402 
403  if (isGalleryMode()) {
404  mode = Mode.GALLERY_MD;
405  }
406  isVolumeMd = false;
407  if (hasRenderLabel()) {
408  int renderLabel = ciFirstRender.label;
409  ImageGeneric image = null;
410  String imageFn = null;
411 
412 
413  // Try to find at least one image to render
414  // and take dimensions from that
415  for (int i = 0; i < ids.length && image == null; ++i) {
416  if(i == 100)//after 100 items if there is no image available break
417  break;
418  imageFn = md.getValueString(renderLabel, ids[i]);
419  if(imageFn != null)
420  imageFn = Filename.findImagePath(imageFn , filename, true);
421  if (imageFn != null) {
422  try {
423  image = new ImageGeneric(imageFn);
424  } catch (Exception e) {
425  image = null;
426  }
427  break;
428  }
429 
430  }
431  if (image != null) { // Image file was found to render
432  if (zoom == null) { // if default value, calculate zoom
433  // If in micrograph mode, reduce the
434  // MAX_SIZE constant
435  if (md.containsMicrographsInfo()) {
436  MAX_SIZE /= 2;
437  }
438  zoom = getDefaultZoom(image.getXDim());
439 
440  }
441  if (image.isVolume()) { // We are assuming all are volumes
442  // or images, don't mix it
443  if (isGalleryMode())
444  mode = Mode.GALLERY_VOL;
445 
446  isVolumeMd = true;
447  if (selectedVolFn.isEmpty()) {
448  selectedVolFn = imageFn;
449  }
450 
451  }
452  image.destroy();
453  }
454  } else {
455  // force this mode when there aren't render label
456  mode = Mode.TABLE_MD;
457  }
458  if(parameters.sortby != null && parameters.getBlock().equals(selectedBlock))
459  {
460  ColumnInfo sortci = getColumnInfo(parameters.sortby[0]);
461  boolean asc = parameters.sortby.length == 1 || parameters.sortby[1].equalsIgnoreCase("asc");
462  if(sortci != null)
463  sortMd(sortci, asc);
464  }
465 
466  }// function loadMd
467 
468 
469  public static int getDefaultZoom(int xdim)
470  {
471  int x = Math.min(Math.max(xdim, MIN_SIZE), MAX_SIZE);
472  float scale = (float) x / xdim;
473  int zoom = (int) Math.ceil(scale * 100);
474  return zoom;
475  }
476 
477  public ColumnInfo getColumnInfo(String labelName) {
478  for (ColumnInfo ci : labels) {
479  if (ci.labelName.equals(labelName)) {
480  return ci;
481  }
482  }
483  return null;
484  }
485 
486 
487  public boolean isDisplayLabel()
488  {
489  return displaycis != null;
490  }
491 
492 
493 
494  public String getDisplayLabel(long id)
495  {
496  String label = "";
497 
498  for(ColumnInfo ci: displaycis.values())
499  label += ci.labelName + "=" + md.getValueString(ci.label, id) + ", ";
500  if(!label.isEmpty())
501  label = label.substring(0, label.length() - 2);
502  return label;
503  }
504 
509  public void loadLabels() {
510 
511  ColumnInfo ci;
512  try {
513  int[] labelids = md.getActiveLabels();
514  ArrayList<ColumnInfo> newLabels = new ArrayList<ColumnInfo>(
515  labelids.length);
516  ciFirstRender = null;
517  ColumnInfo ciFirstRenderVisible = null;
518  String inputRenderLabel = "";
519 
520  if (!renderLabel.equalsIgnoreCase("first")) {
521  inputRenderLabel = renderLabel;
522  }
523  String sampleImage;
524  ColumnInfo auxRender = null;
525  for (int i = 0; i < labelids.length; ++i) {
526  ci = initColumnInfo(labelids[i]);
527 
528  ci.render = isRenderLabel(ci);
529  if(ci.render)
530  auxRender = ci;
531  ci.visible = isVisibleLabel(ci);
532  newLabels.add(ci);
533  if (inputRenderLabel.equals(ci.labelName) && ci.render) {//render label specified and included on renders
534  ciFirstRender = ci;
535  if (ci.visible) {
536  ciFirstRenderVisible = ci;
537  }
538  }
539 
540 
541  if (ciFirstRender == null && ci.allowRender)
542  {
543  sampleImage = getSampleImage(ci);
544  if(sampleImage != null)
545  {
546  ciFirstRender = ci;
547  if (ciFirstRenderVisible == null && ci.visible)
548  ciFirstRenderVisible = ci;
549  }
550  }
551  }
552  if(ciFirstRender == null)
553  ciFirstRender = ciFirstRenderVisible = auxRender;//if there are no images found render none image on gallery mode
554  if (ciFirstRenderVisible != null) {
555  ciFirstRender = ciFirstRenderVisible;
556  }
557 
558  // Add MDL_ENABLED if not present
559  if (!md.containsLabel(MDLabel.MDL_ENABLED) && (md.containsLabel(MDLabel.MDL_IMAGE) || md.containsLabel(MDLabel.MDL_MICROGRAPH))) {
560  newLabels.add(0, new ColumnInfo(MDLabel.MDL_ENABLED));
561  md.addLabel(MDLabel.MDL_ENABLED);
562  for (long id : ids) {
563  md.setEnabled(true, id);
564  }
565  // hasMdChanges = true;
566  }
567 
568 
569  labels = newLabels;
570  orderLabels();
571  if(displayLabels != null)
572  for(String label: displayLabels)
573  setDisplayLabel(label, true);
575  } catch (Exception e) {
576  e.printStackTrace();
577  }
578  }// function loadLabels
579 
580  public String getSampleImage(ColumnInfo ci)
581  {
582  String imageFn, mddir = md.getBaseDir();
583  for (int i = 0; i < ids.length; ++i)
584  {
585  if( i == 100)
586  break;
587  imageFn = getValueFromLabel(i, ci.label);
588  if(imageFn != null)
589  {
590  imageFn = Filename.findImagePath(imageFn, mddir, true);
591  if (imageFn != null && Filename.exists(imageFn))
592  return imageFn;
593  }
594  }
595  return null;
596  }
597 
598  public ColumnInfo initColumnInfo(int label)
599  {
600  return new ColumnInfo(label);
601  }
602 
606  private void readMetadata(String fn) {
607  try {
608  hasMdChanges = false;
609  hasClassesChanges = false;
610  md.read(fn);
611 
612  } catch (Exception e) {
613  // TODO Auto-generated catch block
614  e.printStackTrace();
615  md = null;
616  ids = null;
617  }
618  }
619 
624  public void sortMd(ColumnInfo sortci, boolean asc) {
625  try {
626  if(sortby == null)
627  sortby = new String[2];
628  sortby[0] = sortci.labelName;
629  sortby[1] = (asc)? "ASC": "DESC";
630  md.sort(sortci.label, asc);
631  hasMdChanges = true;
632  ids = md.findObjects();
633  } catch (Exception e) {
634  e.printStackTrace();
635  }
636  }
637 
638 
639 
640 
641 
645  public void readMd() {
646  if (filename != null) {
647  readMetadata(getMdFilename());
648  }
649  }
650 
654  public void selectBlock(String block) {
655  selectedBlock = block;
656  selectedVolFn = ""; // Set to empty string to get the first vol
657  readMd();
658  }
659 
665  public ImageGalleryTableModel createModel(boolean[] selection) {
666  try {
667  switch (mode) {
668  case GALLERY_VOL:
669  return new VolumeGalleryTableModel(this);
670  case GALLERY_MD:
671  if (md.size() > 0 && hasRenderLabel()) {
672 
673  return new MetadataGalleryTableModel(this, selection);
674  }
675  // else fall in the next case
676  case TABLE_MD:
677  mode = Mode.TABLE_MD; // this is necessary when coming from
678  // previous case
679  if (!md.isColumnFormat()) {
680  return new MetadataRowTableModel(this);
681  }
682 
683  return new MetadataTableModel(this, selection);
684 
685  }
686  } catch (Exception e) {
687  e.printStackTrace();
688  }
689  return null;
690  }
691 
692  public int getNumberOfBlocks() {
693  return mdBlocks != null ? mdBlocks.length : 0;
694  }
695 
696 
697 
701  public Mode getMode() {
702  return mode;
703  }
704 
708  public boolean hasRenderLabel() {
709  return ciFirstRender != null;
710  }
711 
715  public int getRenderLabel() {
716  return ciFirstRender.label;
717  }
718 
722  public boolean allowGallery() {
723  return hasRenderLabel();
724  }
725 
726  // some mode shortcuts
727  public boolean isGalleryMode() {
728  return mode == Mode.GALLERY_MD || mode == Mode.GALLERY_VOL;
729 
730  }
731 
732  public boolean isVolumeMode() {
733  return mode == Mode.GALLERY_VOL;
734  }
735 
736  public boolean isTableMode() {
737  return mode == Mode.TABLE_MD;
738  }
739 
743  public boolean isColumnFormat() {
744  return md.isColumnFormat();
745  }
746 
747 
748  public boolean isMicrographsMode() {
749  return md.containsMicrographsInfo();
750  }
751 
752  // utility function to change of mode
753  public void changeMode() {
754  if (isGalleryMode()) {
755  mode = Mode.TABLE_MD;
756 
757  }
758  else if ( isVolumeMd)
759  mode = Mode.GALLERY_VOL;
760  else
761  mode = Mode.GALLERY_MD;
762  }
763 
767  public String getVolumeAt(int index) {
768  return md.getValueString(ciFirstRender.label, ids[index]);
769  }
770 
771  public boolean containsGeometryInfo()
772  {
773  return containsGeometryInfo("2D");
774  }
775 
776  // Check if the underlying data has geometrical information
777  public boolean containsGeometryInfo(String type)
778  {
779  try {
780  return md.containsGeometryInfo(type);
781  } catch (Exception e) {
782  e.printStackTrace();
783  return false;
784  }
785  }
786 
790  public boolean isEnabled(int index) {
791  try {
792  if (isVolumeMode()) {
793  return true;
794  }
795  return md.getEnabled(ids[index]);
796  } catch (Exception e) {
797  e.printStackTrace();
798  }
799  return true;
800  }
801 
805  public void setEnabled(int index, boolean value) {
806  try {
807  if (!isVolumeMode()) { // slices in a volume are always enabled
808  md.setEnabled(value, ids[index]);
809  hasMdChanges = true;
810  }
811  } catch (Exception e) {
812  e.printStackTrace();
813  }
814  }
815 
819  public void setRow(MDRow mdRow, long objId) {
820  md.setRow(mdRow, objId);
821  setMdChanges(true);
822  }
823 
827  public boolean isFile(ColumnInfo ci) {
828  try {
829  return MetaData.isPathField(ci.label);
830  } catch (Exception e) {
831  e.printStackTrace();
832  }
833  return false;
834  }
835 
836  public boolean isFile(int col) {
837  return isFile(labels.get(col));
838  }
839 
840  public boolean isImageFile(int col) {
841  return isImageFile(labels.get(col));
842  }
843 
844  public boolean isImageFile(ColumnInfo ci) {
845  try {
846 
847  return ci.render;
848  } catch (Exception e) {
849  e.printStackTrace();
850  }
851  return false;
852  }
853 
854  public boolean isClassificationMd() {
855  return isClassification;
856  }
857 
861  public boolean checkifIsClassificationMd() {
862  try {
863  boolean valid = selectedBlock.startsWith("classes")
864  && (md.containsLabel(MDLabel.MDL_REF) || md.containsLabel(MDLabel.MDL_REF3D))
865  && md.containsLabel(MDLabel.MDL_CLASS_COUNT);
866 
867  if (!valid) {
868  return false;
869  }
870 
871  refLabel = md.containsLabel(MDLabel.MDL_REF) ? MDLabel.MDL_REF : MDLabel.MDL_REF3D;
872 
873  for (long id : ids) {
874  int ref = md.getValueInt(refLabel, id);
875  long count = md.getValueLong(MDLabel.MDL_CLASS_COUNT, id);
876  String s = Filename.getClassBlockName(ref);
877  if (count > 0 && !containsBlock(s)) {
878  DEBUG.printFormat("2Dclass: for ref: %d, no block '%s'\n", ref, s);
879  return false;
880  }
881  }
882  } catch (Exception e) {
883  // TODO Auto-generated catch block
884  e.printStackTrace();
885  }
886  return true;
887  }
888 
892  public ClassInfo getItemClassInfo(int index) {
893  if (isClassification && index < classes.length) {
894  return classes[index];
895  }
896  return null;
897  }
898 
902  private void setItemClassInfo(long id, ClassInfo cli) {
903  String comment = "None";
904  int ref2 = -1;
905  int color = -1;
906  try {
907  if (cli != null) {
908  ref2 = cli.index + 1;
909  color = cli.getColor().getRGB();
910  comment = cli.getComment();
911  }
912  md.setValueInt(MDLabel.MDL_REF2, ref2, id);
913  md.setValueString(MDLabel.MDL_KEYWORDS, comment, id);
914  md.setValueInt(MDLabel.MDL_COLOR, color, id);
915  } catch (Exception ex) {
916  ex.printStackTrace();
917  }
918  }
919 
923  public void setItemClass(int index, ClassInfo cli) {
924  hasClassesChanges = true;
925  classes[index] = cli;
926  long id = ids[index];
927  setItemClassInfo(id, cli);
928  }
929 
930  public ClassInfo getClassInfo(int classNumber) {
931  return classesArray.get(classNumber);
932  }
933 
938  public void updateClassesInfo() {
939  try {
940  int i = 0;
941  for (ClassInfo cli : classesArray) {
942  cli.numberOfClasses = 0;
943  cli.numberOfImages = 0;
944  cli.index = i++;
945  }
946  i = 0;
947  for (long id : ids) { // iterate over all references
948  long count = md.getValueLong(MDLabel.MDL_CLASS_COUNT, id);
949 
950  ClassInfo cli = getItemClassInfo(i);
951  if (cli != null) {
952  cli.numberOfClasses += 1;
953  cli.numberOfImages += count;
954  hasMdChanges = true;
955  }
956  setItemClassInfo(id, cli);
957  ++i;
958  }
959  } catch (Exception e) {
960  // TODO Auto-generated catch block
961  e.printStackTrace();
962  }
963  }// function upateClassesInfo
964 
968  public void loadClassesInfo() {
969  try {
970  if (md.containsLabel(MDLabel.MDL_REF2)) {
971  long id;
972  int ref2;
973  ClassInfo cli;
974 
975  for (int i = 0; i < ids.length; ++i) {
976  id = ids[i];
977  ref2 = md.getValueInt(MDLabel.MDL_REF2, id);
978 
979  if (ref2 > 0) {
980  cli = null;
981 
982  for (ClassInfo cli2 : classesArray) {
983  if (cli2.index == ref2) {
984  cli = cli2;
985  break;
986  }
987  }
988 
989  if (cli == null) {
990  String comment = md.getValueString(
991  MDLabel.MDL_KEYWORDS, id);
992  int color = md.getValueInt(MDLabel.MDL_COLOR, id);
993  cli = new ClassInfo(comment, new Color(color));
994  cli.index = ref2;
995  classesArray.add(cli);
996  }
997  classes[i] = cli;
998  }
999  }
1000  }
1001  } catch (Exception e) {
1002  e.printStackTrace();
1003  }
1004  }// function loadClassesInfo
1005 
1006 
1007 
1011  public MetaData getSelectionMd(boolean[] selection) {
1012  MetaData selectionMd = null;
1013  if (!isVolumeMode()) {
1014  long[] selectedIds = new long[selection.length];
1015  int count = 0;
1016  for (int i = 0; i < selection.length; i++) {
1017  if (selection[i]) {
1018  selectedIds[count++] = ids[i];
1019  }
1020  }
1021  try {
1022  selectionMd = new MetaData();
1023  selectionMd.importObjects(md, selectedIds);
1024  } catch (Exception e) {
1025  e.printStackTrace();
1026  }
1027  }
1028  return selectionMd;
1029  }
1030 
1034  public MetaData[] getClassesMd() {
1035  try {
1036  if (!classesArray.isEmpty()) {
1037  updateClassesInfo();
1038  // Count the number of non-empty classes
1039  MetaData[] mds = new MetaData[classesArray.size() + 1];
1040  mds[0] = new MetaData();
1041  MetaData mdAux = mds[0];
1042  int i = 0;
1043  long id;
1044  // Md for classes block
1045  for (ClassInfo cli : classesArray) {
1046  id = mdAux.addObject();
1047  mdAux.setValueInt(MDLabel.MDL_REF, ++i, id);
1048  mdAux.setValueLong(MDLabel.MDL_CLASS_COUNT,
1049  cli.numberOfImages, id);
1050  mdAux.setValueString(MDLabel.MDL_KEYWORDS,
1051  cli.getComment(), id);
1052  mds[i] = new MetaData();
1053  }
1054  i = 0;
1055  // Fill the classX_images blocks
1056  for (i = 0; i < ids.length; ++i) {
1057  ClassInfo cli = getItemClassInfo(i);
1058  if (cli != null) {
1059  id = ids[i];
1060  md.setValueInt(MDLabel.MDL_REF2, cli.index + 1, id);
1061  md.setValueString(MDLabel.MDL_KEYWORDS,
1062  cli.getComment(), id);
1063  mdAux = getClassImages(i);
1064  if (mdAux != null) {
1065  mds[cli.index + 1].unionAll(mdAux);
1066  }
1067  }
1068  }
1069  return mds;
1070  }
1071  } catch (Exception e) {
1072  // TODO Auto-generated catch block
1073  e.printStackTrace();
1074  }
1075  return null;
1076  }
1077 
1081  public MetaData getClassImages(int index) {
1082  try {
1083  long id = ids[index];
1084  int ref = md.getValueInt(refLabel, id);
1085  String blockName = Filename.getClassBlockName(ref);
1086  if (containsBlock(blockName)) {
1087  return new MetaData(blockName + Filename.SEPARATOR + filename);
1088  }
1089  } catch (Exception e) {
1090  e.printStackTrace();
1091  }
1092  return null;
1093  }
1094 
1098  public MetaData getClassesImages(boolean[] selection) {
1099  MetaData mdImages = new MetaData();
1100  MetaData md;
1101  for (int i = 0; i < selection.length; i++) {
1102  if (selection[i]) {
1103  md = getClassImages(i);
1104  if (md != null) {
1105  mdImages.unionAll(md);
1106  md.destroy();
1107  }
1108  }
1109  }
1110  return mdImages;
1111  }
1112 
1113  public MetaData getEnabledClassesImages() {
1114  MetaData mdImages = new MetaData();
1115  MetaData md;
1116  for (int i = 0; i < ids.length; ++i) {
1117  if (isEnabled(i)) {
1118  md = getClassImages(i);
1119  if (md != null) {
1120  mdImages.unionAll(md);
1121  md.destroy();
1122  }
1123  }
1124  }
1125  return mdImages;
1126  }
1127 
1128 
1132  public boolean containsBlock(String block) {
1133  if (mdBlocks != null) {
1134  for (String b : mdBlocks) {
1135  if (b.equalsIgnoreCase(block)) {
1136  return true;
1137  }
1138  }
1139  }
1140  return false;
1141  }
1142 
1150  public int getVisibleColumnIndex(int col) {
1151  int visibleIndex = 0;
1152  for (int i = 0; i < labels.size(); i++) {
1153  if (labels.get(i).visible) {
1154  if (col == visibleIndex) {
1155  return i;
1156  }
1157  visibleIndex++;
1158  }
1159  }
1160  return -1;
1161  }
1162 
1163  public int getLabelFromCol(int col) {
1164  return labels.get(col).label;
1165  }
1166 
1167  public ColumnInfo getColumnInfo(int col) {
1168  return labels.get(col);
1169  }
1170 
1171 
1172 
1173  public String getValueFromCol(int index, int col) {
1174  if (!isColumnFormat()) {
1175  col = index;
1176  index = 0;
1177  }
1178  return getValueFromCol(index, labels.get(col));
1179  }
1180 
1181  public String getValueFromCol(int index, ColumnInfo ci) {
1182  try {
1183  return md.getValueString(ci.label, ids[index]);
1184  } catch (Exception e) {
1185  e.printStackTrace();
1186  }
1187  return null;
1188  }
1189 
1190  public String getValueFromLabel(int index, int label) {
1191  try {
1192  return md.getValueString(label, ids[index]);
1193  } catch (Exception e) {
1194  e.printStackTrace();
1195  }
1196  return null;
1197  }
1198 
1199  public void setValueToCol(int index, ColumnInfo ci, String value) {
1200  try {
1201  md.setValueString(ci.label, value, ids[index]);
1202  setMdChanges(true);
1203  } catch (Exception e) {
1204  e.printStackTrace();
1205  }
1206  }
1207 
1211  public void removeSelection(boolean[] selection) throws Exception {
1212  for (int i = 0; i < selection.length; i++) {
1213  if (selection[i]) {
1214  md.removeObject(ids[i]);
1215  hasMdChanges = true;
1216  }
1217  }
1218  }
1219 
1223  public void addClass(ClassInfo ci) {
1224  classesArray.add(ci);
1225  hasClassesChanges = true;
1226  }
1227 
1231  public void removeClass(int classNumber) {
1232  ClassInfo cli = getClassInfo(classNumber);
1233  for (int i = 0; i < ids.length; ++i) {
1234  if (getItemClassInfo(i) == cli) {
1235  setItemClass(i, null);
1236  }
1237  }
1238  classesArray.remove(classNumber);
1239  hasClassesChanges = true;
1240  }
1241 
1242  public boolean hasMdChanges() {
1243  return hasMdChanges;
1244  }
1245 
1246  public void setMdChanges(boolean value) {
1247  hasMdChanges = value;
1248  }
1249 
1250  public boolean hasClassesChanges() {
1251  return hasClassesChanges;
1252  }
1253 
1254  public boolean hasMicrographParticles() {
1255  return md.containsMicrographParticles();
1256  }
1257 
1258  public String getFileName() {
1259  return filename;
1260 
1261  }
1262 
1263  public String getBlock(int index) {
1264  int size = getNumberOfBlocks();
1265  if (size > 0 && index >= 0 && index < size) {
1266  return mdBlocks[index];
1267  }
1268  return null;
1269  }
1270 
1271 
1272 
1273  public MDRow[] getImages(MetaData md) {
1274  int idlabel = getRenderLabel();
1275  if (md == null) {
1276  return null;
1277  }
1278  if (!md.containsLabel(idlabel)) {
1279  return null;
1280  }
1281 
1282  MDRow mdRow = null;
1283  ArrayList<MDRow> imagesmd = new ArrayList<MDRow>();
1284  int index = 0;
1285  String imagepath;
1286 
1287  for (long id : md.findObjects()) {
1288  if (isEnabled(index)) {
1289 
1290  imagepath = md.getValueString(idlabel, id, true);
1291  if (imagepath != null && ImageGeneric.exists(imagepath)) {
1292  mdRow = new MDRow();
1293 
1294  if (useGeo) {
1295 
1296  md.getRow(mdRow, id);
1297  mdRow.setValueString(idlabel, imagepath);
1298 
1299  } else {
1300  mdRow.setValueString(MDLabel.MDL_IMAGE, imagepath);
1301  }
1302 
1303  imagesmd.add(mdRow);
1304  }
1305  }
1306  index++;
1307  }
1308 
1309  return imagesmd.toArray(new MDRow[]{});
1310  }
1311 
1312  public String getFileInfo() {
1313  File file = new File(getFileName());
1314 
1315  String fileInfo = "Path: " + file.getAbsolutePath() + "\n";
1316 
1317  fileInfo += "Last Modified: "
1318  + new Date(file.lastModified()) + "\n"
1319  + "Size: " + Filename.humanReadableByteCount(file.length());
1320  return fileInfo;
1321  }
1322 
1323  public void saveClassSelection(boolean[]selection, String path) {
1324  try {
1325  saveSelection(selection, "classes" + Filename.SEPARATOR + path, true);
1326  MetaData imagesmd;
1327  // Fill the classX_images blocks
1328  for (int i = 0; i < selection.length; i++) {
1329  if (selection[i]) {
1330  long id = ids[i];
1331  int ref = md.getValueInt(MDLabel.MDL_REF, id);
1332  String blockName = Filename.getClassBlockName(ref);
1333  if (containsBlock(blockName)) {
1334  imagesmd = new MetaData(blockName + Filename.SEPARATOR + filename);
1335  imagesmd.writeBlock(blockName + Filename.SEPARATOR + path);
1336  imagesmd.destroy();
1337  }
1338  }
1339  }
1340 
1341  } catch (Exception ex) {
1342  Logger.getLogger(GalleryJFrame.class.getName()).log(Level.SEVERE, null, ex);
1343  }
1344  }
1345 
1346  public boolean isCTFMd() {
1347  return md.isCTFMd();
1348  }
1349 
1353  public void saveSelection(boolean[] selection) throws Exception {
1354 
1355  SaveJDialog dlg = new SaveJDialog(window, "selection" + getFileExtension(), true);
1356  boolean save = dlg.showDialog();
1357  if (save) {
1358  boolean overwrite = dlg.isOverwrite();
1359  String path = dlg.getMdFilename();
1360  saveSelection(selection, path, overwrite);
1361  }
1362 
1363  }
1364 
1368  public void saveSelection(boolean[] selection, String path, boolean overwrite) throws Exception {
1369  MetaData md = getSelectionMd(selection);
1370 
1371  String file = path.substring(path.lastIndexOf("@") + 1, path.length());
1372  if (!new File(file).exists())// overwrite or append, save selection
1373  {
1374  md.write(path);
1375  } else {
1376  if (overwrite) {
1377  md.write(path);// overwrite with active block only, other
1378  } // blocks were dismissed
1379  else {
1380  md.writeBlock(path);// append selection
1381  }
1382  }
1383 
1384  md.destroy();
1385  }
1386 
1387  public int size() {
1388  return ids.length;
1389  }
1390 
1391  public Integer getZoom() {
1392  return zoom;
1393  }
1394 
1395  public boolean useGeo() {
1396  return useGeo;
1397  }
1398 
1399  public void fillConstant(int label, String value) {
1400  md.fillConstant(label, value);
1401  }
1402 
1403  public void fillLinear(int label, Double start, Double step) {
1404  md.fillLinear(label, start, step);
1405  }
1406 
1407  public void fillRandom(int label, String mode, double op1, double op2) {
1408  md.fillRandom(label, mode, op1, op2);
1409  }
1410 
1411  public void removeDisabled() {
1412  md.removeDisabled();
1413  }
1414 
1415  public void removeLabel(int label) {
1416  md.removeLabel(label);
1417  }
1418 
1419  public long[] getIds() {
1420  return ids;
1421  }
1422 
1423  public int[] getLabels() {
1424  return md.getActiveLabels();
1425  }
1426 
1427  public String getValueString(int label, long id) {
1428  return md.getValueString(label, id);
1429  }
1430 
1431  public boolean setValueString(int label, String newValue, long l) {
1432  return md.setValueString(label, newValue, l);
1433  }
1434 
1435  public Object getSelectedBlock() {
1436  return selectedBlock;
1437  }
1438 
1439 
1440 
1441  public String getSelVolumeFile() {
1442  return selectedVolFn;
1443  }
1444 
1445  public void setResliceView(int view) {
1446  resliceView = view;
1447  }
1448 
1449  public boolean isWrap() {
1450  return wrap;
1451  }
1452 
1453  public boolean renderImages() {
1454  return renderImages;
1455  }
1456 
1457  public int getResliceView() {
1458  return resliceView;
1459  }
1460 
1461  public boolean addObject() {
1462  AddObjectJDialog dlg = new AddObjectJDialog(window);
1463  if (dlg.showDialog()) {
1464  md.unionAll(dlg.md);
1465  return true;
1466  }
1467  return false;
1468  }
1469 
1470  public String[] getBlocks() {
1471  return mdBlocks;
1472  }
1473 
1474  public long getId(int i) {
1475  return ids[i];
1476  }
1477 
1478  public String createSortFile(String psdFile, int row) {
1479 
1480  MetaData mdRow = new MetaData();
1481  MDRow row2 = new MDRow();
1482  md.getRow(row2, getId(row));
1483  mdRow.setRow(row2, mdRow.addObject());
1484  String sortFn = psdFile.replace(".psd", ".xmd");
1485  mdRow.write(sortFn);
1486  mdRow.destroy();
1487  return sortFn;
1488 
1489  }
1490 
1491  public ArrayList<ClassInfo> getClasses() {
1492  return classesArray;
1493  }
1494 
1495  public List<ColumnInfo> getLabelsInfo() {
1496  return labels;
1497  }
1498 
1499  public MetaData getMetaDataRow() {
1500  return md.getMetaDataRow();
1501  }
1502 
1503  public String getLabel(long objId, int label) {
1504  try {
1505  if (isClassification) {
1506  int ref = md.getValueInt(MDLabel.MDL_REF, objId);
1507  long count = md.getValueLong(MDLabel.MDL_CLASS_COUNT, objId);
1508  return String.format("class %d (%d images)", ref, count);
1509  } else {
1510  return md.getValueString(label, objId);
1511  }
1512  } catch (Exception e) {
1513  e.printStackTrace();
1514  }
1515  return null;
1516  }
1517 
1518  public String getFileExtension() {
1519  if (getFileName() == null) {
1520  return "";
1521  }
1522  return XmippStringUtils.getFileExtension(filename);
1523  }
1524 
1525  public void saveAll(String path, boolean overwrite) throws Exception {
1526  String from = getFileName();
1527  String blockto = path;
1528  String to;
1529  String block;
1530  if (blockto.contains("@")) {
1531  int sep = blockto.lastIndexOf("@");
1532  block = blockto.substring(0, sep);
1533  to = blockto.substring(sep + 1, blockto.length());
1534  } else {
1535  to = blockto;
1536  blockto = selectedBlock + "@" + blockto;
1537  block = selectedBlock;
1538  }
1539 
1540  if (from != null) {
1541  MetaData md;
1542  Hashtable<String, MetaData> mds = new Hashtable<String, MetaData>();
1543  for (String blockit : getBlocks()) {
1544  mds.put(blockit, getMetaData(blockit));
1545  }
1546  File file = new File(to);
1547  if (overwrite) {
1548  file.delete();
1549  }
1550  if (!file.exists() && file.getParentFile() != null) {
1551  file.getParentFile().mkdirs();
1552  }
1553  for (String blockit : getBlocks()) {
1554  md = mds.get(blockit);
1555  if (blockit.equals(selectedBlock)) {
1556  saveMd(blockto, true, overwrite);
1557  } else {
1558  md.writeBlock(blockit + "@" + to);
1559  }
1560  md.destroy();
1561  }
1562  } else {
1563  saveMd(blockto, true, overwrite);
1564  }
1565 
1566  setMdChanges(false);
1567  setFileName(to);
1568  if (blockto.contains("@")) {
1569  selectBlock(block);
1570  }
1571  }
1572 
1573  public void saveMd(String path, boolean saveall, boolean isoverwrite) throws Exception {
1574  try {
1575 
1576  if (path == null) {
1577  throw new IllegalArgumentException();
1578  }
1579 
1580  boolean overwritewithblock;
1581  String file;
1582  if (path.contains("@")) {
1583  file = path.substring(path.lastIndexOf("@") + 1);
1584  } else {
1585  file = path;
1586  path = selectedBlock + "@" + file;
1587  }
1588 
1589  File iofile = new File(file);
1590  if (!iofile.exists())// overwrite or append, save active
1591  {
1592  if (iofile.getParentFile() != null) {
1593  iofile.getParentFile().mkdirs();
1594  }
1595  md.write(path);
1596  } else {
1597 
1598  overwritewithblock = isoverwrite && !saveall;
1599  if (overwritewithblock) {
1600  md.write(path);// overwrite with active block only,
1601  } // other blocks were dismissed
1602  else {
1603  md.writeBlock(path);// either if save active block or all, save active, other blocks where already managed
1604  }
1605  }
1606 
1607  } catch (Exception e) {
1608  e.printStackTrace();
1609  }
1610  }// function saveMd
1611 
1612  public MetaData getMetaData(String block) {
1613  return new MetaData(block + "@" + filename);
1614  }
1615 
1616  public boolean hasClasses() {
1617  return isClassification;
1618  }
1619 
1620  public boolean getNormalized() {
1621  return normalize;
1622  }
1623 
1624 
1625 
1626  public MetaData getMd(List<Long> ids) {
1627  MetaData selmd = null;
1628  try {
1629  long[] ids2 = new long[ids.size()];
1630  for (int i = 0; i < ids.size(); i++) {
1631  ids2[i] = ids.get(i);
1632  }
1633  selmd = new MetaData();
1634  selmd.importObjects(md, ids2);
1635  } catch (Exception e) {
1636  e.printStackTrace();
1637  }
1638  return selmd;
1639  }
1640 
1641 
1642  public void setWindow(GalleryJFrame frame) {
1643  window = frame;
1644  }
1645 
1646  public void write(String path) {
1647  md.write(path);
1648  }
1649 
1650 
1651 
1652  public MetaData getMd() {
1653  return md;
1654  }
1655 
1656  public boolean isRenderLabel(ColumnInfo ci) {
1657  if(!renderImages)
1658  return false;
1659  if (renderLabel.equals("first") )
1660  {
1661  if(md instanceof ScipionMetaData)
1662  return ci.render && ci.visible;
1663  else
1664  return MetaData.isImage(ci.label) && ci.visible;
1665  }
1666 
1667  for (String i : getRenderLabels()) {
1668  if (i.equals(ci.labelName) && ci.visible) {
1669  return true;
1670  }
1671  }
1672  return false;
1673  }
1674 
1675  public boolean isVisibleLabel(ColumnInfo ci) {
1676  if (getVisibleLabels() == null) {
1677  return true;
1678  }
1679  for (String i : getVisibleLabels()) {
1680  if (i.equals(ci.labelName)) {
1681  return true;
1682  }
1683  }
1684  return false;
1685  }
1686 
1687  public void orderLabels() {
1688  String[] orderLabels = getOrderLabels();
1689  if (orderLabels == null) {
1690  return;
1691  }
1692 
1693  ColumnInfo aux;
1694  int j, k = 0;//k index added to avoid errors if some order columns are not present. This way order index is k not i
1695  for (int i = 0; i < orderLabels.length; i++) {
1696  j = 0;
1697  for (ColumnInfo ci : labels) {
1698  if (ci.labelName.equals(orderLabels[i])) {
1699 
1700  aux = labels.get(k);
1701  labels.set(k, ci);
1702  labels.set(j, aux);
1703  k ++;
1704  }
1705  j ++;
1706  }
1707  }
1708  }
1709 
1710  public void removeCTF(int row) {
1711  md.removeCTF(ids[row]);
1712  }
1713 
1714  public boolean isRecalculateCTF(int row) {
1715  if(!isCTFMd())
1716  return false;
1717  long id = ids[row];
1718  if(md.containsCTF(id))
1719  return true;
1720  return false;
1721  }
1722 
1723  public boolean hasRecalculateCTF()
1724  {
1725  return md.hasRecalculateCTF();
1726  }
1727 
1728  public void recalculateCTF(int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)
1729  {
1730  if(isEnabled(row))
1731  {
1732  for(int i = 0; i <selection.length; i ++ )
1733  if(selection[i] && isEnabled(i))
1734  md.putCTF(ids[i], ellipseCTF);
1735  EstimateFromCTFTask estimateFromCTFTask = new EstimateFromCTFTask(
1736  ellipseCTF, 90 - ellipseCTF.getDefocusAngle(),
1737  md.getPSDFile(ids[row]), ellipseCTF.getD(), window.getTasksEngine(), row, sortFn);
1738  window.getTasksEngine().add(estimateFromCTFTask);
1739  }
1740  }
1741 
1742  public void showCTF(boolean profile, int row, boolean[] selection, TasksEngine ctfTasks) {
1743  try {
1744  long id = ids[row];
1745 
1746  String psd = md.getPSDFile(id);
1747  String psden = md.getPSDEnhanced(id);
1748 
1749  boolean noPsdEnhanced = (psden == null);
1750  // Use the same PSD image in case no PSD enhanced
1751 
1752  if (noPsdEnhanced)
1753  psden = psd;
1754 
1755  if (profile)
1756  {
1757  if (noPsdEnhanced)
1758  new CTFAnalyzerJFrame(psden, md.getCTFDescription(id), psd, md.getEllipseCTF(id).getSamplingRate());
1759  else
1760  new CTFAnalyzerJFrame(psden, md.getCTFFile(id), psd);
1761  }
1762  else
1763  {
1764  ImageGeneric img = new ImageGeneric(psden);
1765  ImagePlus imp = XmippImageConverter.readToImagePlus(img);
1766  img.destroy();
1767  EllipseCTF ctfparams = md.getEllipseCTF(id, imp.getWidth());
1768  String sortfn = createSortFile(psd, row);
1769  XmippUtil.showImageJ(Tool.VIEWER); // removed Toolbar.FREEROI
1770  CTFRecalculateImageWindow ctfiw = new CTFRecalculateImageWindow(this, selection, imp, psd, ctfparams,
1771  ctfTasks, row, sortfn);
1772  }
1773 
1774  } catch (Exception e) {
1775  XmippDialog.showError(window, e.getMessage());
1776  }
1777  }
1778 
1779  public Geometry getGeometry(long id, ColumnInfo ci)
1780  {
1781  return getGeometry(id, "2D", ci);
1782  }
1783 
1784 
1785  public Geometry getGeometry(long id, String type, ColumnInfo ci)
1786  {
1787  if(md.containsLabel(MDLabel.MDL_IMAGE) && ci.label != MDLabel.MDL_IMAGE)
1788  return null;
1789 
1790  if(md.containsLabel(MDLabel.RLN_IMAGE_NAME) && ci.label != MDLabel.RLN_IMAGE_NAME)
1791  return null;
1792 
1793 
1794  double shiftx, shifty, psiangle, scaleFactor=1;
1795  boolean flip;
1796 
1797  if(md.containsLabel(MetaData.GEOMETRY_LABELS))
1798  {
1799  shiftx = md.getValueDouble(MDLabel.MDL_SHIFT_X, id);
1800  shifty = md.getValueDouble(MDLabel.MDL_SHIFT_Y, id);
1801  psiangle = md.getValueDouble(MDLabel.MDL_ANGLE_PSI, id);
1802  flip = md.getValueBoolean(MDLabel.MDL_FLIP, id);
1803 
1804  if(md.containsLabel(MDLabel.MDL_SCALE))
1805  scaleFactor = md.getValueDouble(MDLabel.MDL_SCALE, id);
1806  }
1807  else if(md.containsLabel(MetaData.GEOMETRY_RELION_LABELS))
1808  {
1809  shiftx = md.getValueDouble(MDLabel.RLN_ORIENT_ORIGIN_X, id);
1810  shifty = md.getValueDouble(MDLabel.RLN_ORIENT_ORIGIN_Y, id);
1811  psiangle = -1 * md.getValueDouble(MDLabel.RLN_ORIENT_PSI, id);
1812  flip = md.getValueBoolean(MDLabel.MDL_FLIP, id);
1813  }
1814  else
1815  return null;
1816 
1817  return new Geometry(shiftx, shifty, psiangle, flip, scaleFactor);
1818  }
1819 
1820  public void setRenderLabels(String[] renderLabels) {
1821  this.renderLabels = renderLabels;
1822  }
1823 
1824  public void setVisibleLabels(String[] visibleLabels) {
1825  this.visibleLabels = visibleLabels;
1826  }
1827 
1828  public void setOrderLabels(String[] orderLabels) {
1829  this.orderLabels = orderLabels;
1830  }
1831 
1832  public void setRenderLabel(String renderLabel) {
1833  this.renderLabel = renderLabel;
1834  }
1835 
1836 
1837  public String[] getRenderLabels()
1838  {
1839  return renderLabels;
1840  }
1841 
1842  public String[] getVisibleLabels()
1843  {
1844  return visibleLabels;
1845  }
1846 
1847  public String[] getOrderLabels()
1848  {
1849  return orderLabels;
1850  }
1851 
1852  public Long getSelVolId()
1853  {
1854  if(selectedVolFn == null || selectedVolFn.isEmpty())
1855  return null;
1856  String vol;
1857  for(Long id: ids)
1858  {
1859  vol = md.getValueString(ciFirstRender.label, id);
1860  if(vol.equals(selectedVolFn))
1861  return id;
1862  }
1863  return null;
1864  }
1865 
1866  public MetaData getImagesMd() {
1867  return getImagesMd(null, false);
1868  }
1869 
1870  public MetaData getImagesMd(boolean[] selection, boolean selected) {
1871  int idlabel = getRenderLabel();
1872  MDRow mdRow;
1873  MetaData imagesmd = new MetaData();
1874  int index = 0;
1875  String imagepath;
1876  long imageid;
1877  for (long id : md.findObjects()) {
1878  if (isEnabled(index) && (!selected || selection[index])) {
1879  imagepath = md.getValueString(idlabel, id, true);
1880  if (imagepath != null && ImageGeneric.exists(imagepath)) {
1881  imageid = imagesmd.addObject();
1882  if (useGeo())
1883  {
1884  Geometry geo = getGeometry(id, ciFirstRender);
1885  mdRow = new MDRow();
1886  //md.getRow(mdRow, id);//copy geo info in mdRow
1887  mdRow.setValueDouble(MDLabel.MDL_SHIFT_X, geo.shiftx);
1888  mdRow.setValueDouble(MDLabel.MDL_SHIFT_Y, geo.shifty);
1889  mdRow.setValueDouble(MDLabel.MDL_ANGLE_PSI, geo.psiangle);
1890  mdRow.setValueBoolean(MDLabel.MDL_FLIP, geo.flip);
1891  imagesmd.setRow(mdRow, imageid);
1892  }
1893  imagesmd.setValueString(MDLabel.MDL_IMAGE, imagepath, imageid);
1894  }
1895  }
1896  index++;
1897  }
1898  return imagesmd;
1899  }
1900 
1901 
1902 
1903  public String[] getSortBy()
1904  {
1905  return sortby;
1906  }
1907 
1908 
1909  public boolean isChimeraClient()
1910  {
1911  return parameters.getChimeraPort() != null;
1912  }
1913 
1914  public boolean hasDisabled()
1915  {
1916  for(int i = 0; i < ids.length; i ++)
1917  if(!isEnabled(i))
1918  return true;
1919  return false;
1920  }
1921 
1922  public int getEnabledCount()
1923  {
1924  int count = 0;
1925  for(int i = 0; i < ids.length; i ++)
1926  if(isEnabled(i))
1927  count ++;
1928  return count;
1929  }
1930 
1931  public String getPreffix() {
1932  return selectedBlock;
1933  }
1934 
1935  public void setZoom(int zoom)
1936  {
1937  this.zoom = zoom;
1938  }
1939 
1940  public boolean allowsVolumeMode()
1941  {
1942  boolean allowsVolumeMode = !selectedVolFn.isEmpty();
1943  return allowsVolumeMode;
1944  }
1945 }// class GalleryData
- - -
xmipp.viewer.models.GalleryData.setDisplayLabel
void setDisplayLabel(String key, boolean selected)
Definition: GalleryData.java:361
- -
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
-
xmipp.jni.MetaData.getValueLong
native long getValueLong(int label, long objId)
- - - - -
xmipp.jni.MDRow.setValueString
native boolean setValueString(int label, String value)
-
xmipp.jni.ImageGeneric.destroy
synchronized native void destroy()
-
xmipp.jni.MDLabel.MDL_ANGLE_PSI
static final int MDL_ANGLE_PSI
Special label to be used when gathering MDs in MpiMetadataPrograms.
Definition: MDLabel.java:8
-
xmipp.viewer.models.GalleryData.getSelectionMd
MetaData getSelectionMd(boolean[] selection)
Definition: GalleryData.java:1011
-
xmipp.viewer.models.GalleryData.getGeometry
Geometry getGeometry(long id, String type, ColumnInfo ci)
Definition: GalleryData.java:1785
- -
xmipp.utils.Params.useGeo
boolean useGeo
Definition: Params.java:80
-
xmipp.viewer.models.GalleryData.selectVolumeAt
void selectVolumeAt(int selectedIndex)
Definition: GalleryData.java:167
-
xmipp.viewer.models.GalleryData.getLabel
String getLabel(long objId, int label)
Definition: GalleryData.java:1503
- - - -
xmipp.jni.MetaData.addObject
native long addObject()
-
xmipp.viewer.models.GalleryData.getImages
MDRow [] getImages(MetaData md)
Definition: GalleryData.java:1273
- -
xmipp.utils.Params.sortby
String [] sortby
Definition: Params.java:86
-
xmipp.jni.MetaData.setValueString
native boolean setValueString(int label, String value, long objId)
- - -
xmipp.viewer.models.GalleryData.getClassImages
MetaData getClassImages(int index)
Definition: GalleryData.java:1081
- - -
xmipp.viewer.models.GalleryData.isImageFile
boolean isImageFile(ColumnInfo ci)
Definition: GalleryData.java:844
-
xmipp.viewer.models.GalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: GalleryData.java:1779
-
xmipp.jni.MDLabel.MDL_CLASS_COUNT
static final int MDL_CLASS_COUNT
< Average cross-correlation for the image (double)
Definition: MDLabel.java:37
-
xmipp.jni.MDLabel.RLN_IMAGE_NAME
static final int RLN_IMAGE_NAME
< Phase-shift from a phase-plate (in degrees)
Definition: MDLabel.java:474
-
xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
- - -
xmipp.viewer.models.GalleryData.getItemClassInfo
ClassInfo getItemClassInfo(int index)
Definition: GalleryData.java:892
- - -
xmipp.jni.MetaData.containsMicrographsInfo
boolean containsMicrographsInfo()
Definition: MetaData.java:218
-
xmipp.viewer.models.GalleryData.getLabelsInfo
List< ColumnInfo > getLabelsInfo()
Definition: GalleryData.java:1495
- -
xmipp.jni.MetaData.write
native void write(String filename)
- -
xmipp.jni.MetaData.fillConstant
native void fillConstant(int label, String value)
-
xmipp.jni.MetaData.getEllipseCTF
EllipseCTF getEllipseCTF(long id)
Definition: MetaData.java:605
- - -
xmipp.viewer.models.GalleryData.setRenderLabels
void setRenderLabels(String[] renderLabels)
Definition: GalleryData.java:1820
- -
xmipp.jni.Filename.hasPrefix
static boolean hasPrefix(String filename)
Definition: Filename.java:331
- -
xmipp.jni.MetaData.getPSDFile
String getPSDFile(long id)
Definition: MetaData.java:633
-
xmipp.viewer.models.GalleryData.isRenderLabel
boolean isRenderLabel(ColumnInfo ci)
Definition: GalleryData.java:1656
- - - -
xmipp.viewer.ctf.TasksEngine.add
synchronized void add(CommandTask task)
Definition: TasksEngine.java:22
-
xmipp.viewer.models.GalleryData.isObjectCmd
boolean isObjectCmd(String cmd)
Definition: GalleryData.java:127
- -
xmipp.viewer.models.GalleryData.fillConstant
void fillConstant(int label, String value)
Definition: GalleryData.java:1399
- -
xmipp.viewer.models.GalleryData.GalleryData
GalleryData(GalleryJFrame window, String fn, Params parameters)
Definition: GalleryData.java:220
- - - -
xmipp.viewer.models.GalleryData.getClassesImages
MetaData getClassesImages(boolean[] selection)
Definition: GalleryData.java:1098
- - - - -
xmipp.viewer.models.GalleryData.displaycis
HashMap< String, ColumnInfo > displaycis
Definition: GalleryData.java:72
- -
xmipp.jni.ImageGeneric.exists
static boolean exists(String imagepath)
Definition: ImageGeneric.java:291
-
xmipp.viewer.models.GalleryData.getColumnInfo
ColumnInfo getColumnInfo(int col)
Definition: GalleryData.java:1167
- - - - -
xmipp.viewer.models.GalleryData.createModel
ImageGalleryTableModel createModel(boolean[] selection)
Definition: GalleryData.java:665
- -
xmipp.jni.MDLabel.MDL_SHIFT_Y
static final int MDL_SHIFT_Y
< difference in Shift along X axis (double)
Definition: MDLabel.java:367
- -
xmipp.jni.MetaData.writeBlock
native void writeBlock(String filename)
- -
xmipp.viewer.models.GalleryData.removeClass
void removeClass(int classNumber)
Definition: GalleryData.java:1231
- -
xmipp.jni.MetaData.read
final void read(String filename)
Definition: MetaData.java:125
- -
xmipp.viewer.models.GalleryData.setEnabled
void setEnabled(int index, boolean value)
Definition: GalleryData.java:805
-
xmipp.jni.MetaData.getBlocksInMetaDataFile
static native String [] getBlocksInMetaDataFile(String filename)
- -
xmipp.jni.MDLabel.MDL_ANGLE_ROT
static final int MDL_ANGLE_ROT
< difference between psi angles (double,degrees)
Definition: MDLabel.java:12
-
xmipp.viewer.models.GalleryData.sortMd
void sortMd(ColumnInfo sortci, boolean asc)
Definition: GalleryData.java:624
- - - - -
xmipp.jni.MetaData.getRow
native void getRow(MDRow mdRow, long objId)
- -
xmipp.jni.MetaData.sort
native void sort(int sortLabel, boolean ascending)
- -
xmipp.jni.MetaData.removeDisabled
native void removeDisabled()
- -
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static final int MDL_SCALE
< sampling rate in A/pixel (double)
Definition: MDLabel.java:336
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String getValueFromLabel(int index, int label)
Definition: GalleryData.java:1190
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String getSampleImage(ColumnInfo ci)
Definition: GalleryData.java:580
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xmipp.jni.MetaData.isCTFMd
boolean isCTFMd()
Definition: MetaData.java:591
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static final int RLN_ORIENT_ORIGIN_X
Definition: MDLabel.java:662
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void setModelDim(Integer rows, Integer cols)
Definition: GalleryData.java:187
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static XmippImageJ showImageJ(Tool tool)
Definition: XmippUtil.java:28
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xmipp.utils.Params.getDisplayLabels
String [] getDisplayLabels()
Definition: Params.java:313
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static final int RLN_ORIENT_ORIGIN_Y
Definition: MDLabel.java:664
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xmipp.jni.MetaData.GEOMETRY_RELION_LABELS
static final int GEOMETRY_RELION_LABELS[]
Definition: MetaData.java:80
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xmipp.viewer.models.GalleryData.fillLinear
void fillLinear(int label, Double start, Double step)
Definition: GalleryData.java:1403
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native long [] findObjects()
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native void unionAll(MetaData mdIn)
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synchronized native void destroy()
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void saveMd(String path, boolean saveall, boolean isoverwrite)
Definition: GalleryData.java:1573
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xmipp.viewer.models.GalleryData.recalculateCTF
void recalculateCTF(int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)
Definition: GalleryData.java:1728
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native void addLabel(int label)
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String getBlock()
Definition: Params.java:323
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native int [] getActiveLabels()
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static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
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double getDefocusAngle()
Definition: EllipseCTF.java:32
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static String findImagePath(String filename, String mdFilename, boolean shouldExist)
Definition: Filename.java:225
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.jni.Filename.isMetadata
static boolean isMetadata(String filename)
Definition: Filename.java:165
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xmipp.utils.Params.orderLabels
String [] orderLabels
Definition: Params.java:85
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boolean renderImages
Definition: Params.java:92
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ColumnInfo getColumnInfo(String labelName)
Definition: GalleryData.java:477
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static final int MDL_REF2
< Class to which the image belongs (int)
Definition: MDLabel.java:313
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xmipp.viewer.models.GalleryData.setRow
void setRow(MDRow mdRow, long objId)
Definition: GalleryData.java:819
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xmipp.utils.DEBUG.printFormat
static void printFormat(String format, Object...objects)
Definition: DEBUG.java:24
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native int getValueInt(int label, long objId)
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void setWindow(GalleryJFrame frame)
Definition: GalleryData.java:1642
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void showCTF(boolean profile, int row, boolean[] selection, TasksEngine ctfTasks)
Definition: GalleryData.java:1742
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xmipp.jni.MetaData.getPSDEnhanced
String getPSDEnhanced(long id)
Definition: MetaData.java:637
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xmipp.jni.MetaData.GEOMETRY_LABELS
static final int GEOMETRY_LABELS[]
Definition: MetaData.java:77
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xmipp.viewer.models.GalleryData.setValueString
boolean setValueString(int label, String newValue, long l)
Definition: GalleryData.java:1431
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xmipp.utils.Params.getChimeraPort
Integer getChimeraPort()
Definition: Params.java:339
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xmipp.viewer.models.GalleryData.selectBlock
void selectBlock(String block)
Definition: GalleryData.java:654
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native String getValueString(int label, long objId)
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String getChimeraProjectionCmd(int row)
Definition: GalleryData.java:202
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GalleryData(GalleryJFrame window, Params parameters, MetaData md)
Definition: GalleryData.java:231
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xmipp.viewer.models.GalleryData.getClassInfo
ClassInfo getClassInfo(int classNumber)
Definition: GalleryData.java:930
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xmipp.jni.Filename.exists
static boolean exists(String path)
Definition: Filename.java:266
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boolean isFile(ColumnInfo ci)
Definition: GalleryData.java:827
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xmipp.viewer.models.GalleryData.setOrderLabels
void setOrderLabels(String[] orderLabels)
Definition: GalleryData.java:1828
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xmipp.jni.MDLabel.MDL_SHIFT_X
static final int MDL_SHIFT_X
< A collection of micrographs, e.g. a tilt serie (std::string)
Definition: MDLabel.java:363
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xmipp.jni.MetaData.putCTF
void putCTF(long id, EllipseCTF ellipseCTF)
Definition: MetaData.java:694
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xmipp.viewer.models.GalleryData.saveClassSelection
void saveClassSelection(boolean[]selection, String path)
Definition: GalleryData.java:1323
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xmipp.jni.MetaData.getCTFFile
String getCTFFile(long id)
Definition: MetaData.java:600
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xmipp.jni.Filename.getClassBlockName
static String getClassBlockName(int ref)
Definition: Filename.java:385
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xmipp.viewer.models.GalleryData.fillRandom
void fillRandom(int label, String mode, double op1, double op2)
Definition: GalleryData.java:1407
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xmipp.jni.MetaData.setEnabled
boolean setEnabled(boolean value, long objId)
Definition: MetaData.java:442
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xmipp.jni.MDLabel.MDL_IMAGE
static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
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xmipp.utils.Params.OPENING_MODE_GALLERY
static final String OPENING_MODE_GALLERY
Definition: Params.java:29
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xmipp.viewer.models.GalleryData.getValueFromCol
String getValueFromCol(int index, int col)
Definition: GalleryData.java:1173
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xmipp.viewer.models.GalleryData.isVisibleLabel
boolean isVisibleLabel(ColumnInfo ci)
Definition: GalleryData.java:1675
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xmipp.utils.Params.objectCommands
String [] objectCommands
Definition: Params.java:88
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xmipp.utils.XmippStringUtils.getFileExtension
static String getFileExtension(String filename)
Definition: XmippStringUtils.java:70
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xmipp.viewer.models.GalleryData.containsBlock
boolean containsBlock(String block)
Definition: GalleryData.java:1132
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xmipp.utils.Params.OPENING_MODE_METADATA
static final String OPENING_MODE_METADATA
Definition: Params.java:30
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xmipp.viewer.models.GalleryData.getClasses
ArrayList< ClassInfo > getClasses()
Definition: GalleryData.java:1491
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xmipp.viewer.models.GalleryData.getMetaData
MetaData getMetaData(String block)
Definition: GalleryData.java:1612
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xmipp.viewer.models.GalleryData.getValueString
String getValueString(int label, long id)
Definition: GalleryData.java:1427
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xmipp.jni.MetaData.getEnabled
boolean getEnabled(long objId)
Definition: MetaData.java:448
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xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
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xmipp.utils.XmippMessage.getPathNotExistsMsg
static String getPathNotExistsMsg(String path)
Definition: XmippMessage.java:71
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xmipp.jni.MetaData.hasRecalculateCTF
boolean hasRecalculateCTF()
Definition: MetaData.java:682
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xmipp.jni.MetaData.removeObject
native boolean removeObject(long objId)
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xmipp.viewer.models.GalleryData.getDefaultZoom
static int getDefaultZoom(int xdim)
Definition: GalleryData.java:469
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xmipp.jni.Filename.getFilename
static String getFilename(String filename)
Definition: Filename.java:302
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xmipp.jni.MDLabel.MDL_FLIP
static final int MDL_FLIP
Definition: MDLabel.java:180
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xmipp.viewer.models.GalleryData.removeSelection
void removeSelection(boolean[] selection)
Definition: GalleryData.java:1211
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xmipp.jni.MetaData.setValueLong
native boolean setValueLong(int label, long value, long objId)
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xmipp.jni.MDLabel.MDL_COLOR
static final int MDL_COLOR
Definition: MDLabel.java:282
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xmipp.viewer.models.GalleryData.saveSelection
void saveSelection(boolean[] selection, String path, boolean overwrite)
Definition: GalleryData.java:1368
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.jni.MDLabel.MDL_REF
static final int MDL_REF
< 3D Class to which the image belongs (int)
Definition: MDLabel.java:312
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xmipp.jni.MDLabel.RLN_ORIENT_PSI
static final int RLN_ORIENT_PSI
Definition: MDLabel.java:672
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xmipp.utils.XmippMessage.getIllegalValueMsg
static String getIllegalValueMsg(String field, Object value)
Definition: XmippMessage.java:66
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xmipp.viewer.models.GalleryData.saveSelection
void saveSelection(boolean[] selection)
Definition: GalleryData.java:1353
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xmipp.jni.MetaData.isImage
static native boolean isImage(int label)
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xmipp.viewer.models.GalleryData.getValueFromCol
String getValueFromCol(int index, ColumnInfo ci)
Definition: GalleryData.java:1181
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xmipp.jni.MetaData.removeCTF
void removeCTF(long id)
Definition: MetaData.java:686
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xmipp.viewer.models.GalleryData.getColumns
List< ColumnInfo > getColumns()
Definition: GalleryData.java:293
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xmipp.jni.MetaData.containsCTF
boolean containsCTF(long id)
Definition: MetaData.java:690
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xmipp.utils.Params.getRenderLabel
String getRenderLabel()
Definition: Params.java:308
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xmipp.jni.MDLabel.MDL_ANGLE_TILT
static final int MDL_ANGLE_TILT
< difference between rot angles (double,degrees)
Definition: MDLabel.java:16
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xmipp.jni.MetaData.importObjects
native void importObjects(MetaData from, long ids[])
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xmipp.jni.Filename.getPrefix
static String getPrefix(String filename)
Definition: Filename.java:339
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xmipp.viewer.models.GalleryData.initColumnInfo
ColumnInfo initColumnInfo(int label)
Definition: GalleryData.java:598
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xmipp.viewer.models.GalleryData.saveAll
void saveAll(String path, boolean overwrite)
Definition: GalleryData.java:1525
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xmipp.viewer.models.GalleryData.setVisibleLabels
void setVisibleLabels(String[] visibleLabels)
Definition: GalleryData.java:1824
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xmipp.viewer.models.GalleryData.setValueToCol
void setValueToCol(int index, ColumnInfo ci, String value)
Definition: GalleryData.java:1199
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xmipp.viewer.models.GalleryData.getTmpFile
String getTmpFile(String suffix)
Definition: GalleryData.java:158
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xmipp.viewer.models.GalleryData.setRenderLabel
void setRenderLabel(String renderLabel)
Definition: GalleryData.java:1832
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xmipp.viewer.models.GalleryData.getImagesMd
MetaData getImagesMd(boolean[] selection, boolean selected)
Definition: GalleryData.java:1870
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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xmipp.jni.MetaData.getBaseDir
String getBaseDir()
Definition: MetaData.java:430
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xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.viewer.models.GalleryData.setItemClass
void setItemClass(int index, ClassInfo cli)
Definition: GalleryData.java:923
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xmipp.jni.MDLabel.MDL_KEYWORDS
static final int MDL_KEYWORDS
< Sigma value (double)
Definition: MDLabel.java:210
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xmipp.viewer.models.GalleryData.getMd
MetaData getMd(List< Long > ids)
Definition: GalleryData.java:1626
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xmipp.jni.MDLabel.MDL_REF3D
static final int MDL_REF3D
< Seed for random number generator
Definition: MDLabel.java:311
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xmipp.jni.MetaData.getValueBoolean
native boolean getValueBoolean(int label, long objId)
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xmipp.jni.Filename.SEPARATOR
static final String SEPARATOR
Definition: Filename.java:8
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xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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xmipp.viewer.models.GalleryData.runObjectCommand
void runObjectCommand(int index, String objectCommand)
Definition: GalleryData.java:149
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xmipp.utils.Params.setBlock
void setBlock(String block)
Definition: Params.java:318
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xmipp.jni.MetaData.getMetaDataRow
MetaData getMetaDataRow()
Definition: MetaData.java:384
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xmipp.viewer.models.GalleryData.createSortFile
String createSortFile(String psdFile, int row)
Definition: GalleryData.java:1478
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xmipp.jni.Filename.humanReadableByteCount
static String humanReadableByteCount(long bytes)
Definition: Filename.java:483
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xmipp.viewer.models.GalleryData.containsGeometryInfo
boolean containsGeometryInfo(String type)
Definition: GalleryData.java:777
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xmipp.jni.MetaData.containsGeometryInfo
boolean containsGeometryInfo(String type)
Definition: MetaData.java:147
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xmipp.utils.Params.renderLabels
String [] renderLabels
Definition: Params.java:64
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xmipp.utils.Params.inverty
boolean inverty
Definition: Params.java:91
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xmipp.jni.MetaData.containsMicrographParticles
boolean containsMicrographParticles()
Definition: MetaData.java:206
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xmipp.jni.MetaData.getCTFDescription
CTFDescription getCTFDescription(long id)
Definition: MetaData.java:641
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xmipp.jni.MetaData.isPathField
static boolean isPathField(int label)
Definition: MetaData.java:399
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xmipp.jni.MetaData.fillRandom
native void fillRandom(int label, String mode, double op1, double op2)
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native boolean setValueDouble(int label, double value)
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String [] visibleLabels
Definition: Params.java:84
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-Classes

class  xmipp.viewer.windows.GalleryJFrame
 
class  xmipp.viewer.windows.GalleryJFrame.GalleryScroll
 
class  xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel
 
class  xmipp.viewer.windows.GalleryJFrame.GalleryMenu
 
class  xmipp.viewer.windows.GalleryJFrame.GalleryMenu.DisplayLabelActionListener
 
class  xmipp.viewer.windows.GalleryJFrame.GalleryMenu.RenderColumnActionListener
 
class  xmipp.viewer.windows.GalleryJFrame.GalleryPopupMenu
 
class  xmipp.viewer.windows.GalleryJFrame.ResliceActionListener
 
- - - -

-Packages

package  xmipp.viewer.windows
 
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- - diff --git a/html/GalleryJFrame_8java_source.html b/html/GalleryJFrame_8java_source.html deleted file mode 100644 index 59bac707..00000000 --- a/html/GalleryJFrame_8java_source.html +++ /dev/null @@ -1,417 +0,0 @@ - - - - - - - -Xmipp: xmippViz/java/src/xmipp/viewer/windows/GalleryJFrame.java Source File - - - - - - - - - -
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GalleryJFrame.java
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1 /***************************************************************************
2  * Authors: Juanjo Vega
3  * J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
4  *
5  *
6  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
7  *
8  * This program is free software; you can redistribute it and/or modify
9  * it under the terms of the GNU General Public License as published by
10  * the Free Software Foundation; either version 2 of the License, or
11  * (at your option) any later version.
12  *
13  * This program is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  * GNU General Public License for more details.
17  *
18  * You should have received a copy of the GNU General Public License
19  * along with this program; if not, write to the Free Software
20  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
21  * 02111-1307 USA
22  *
23  * All comments concerning this program package may be sent to the
24  * e-mail address 'xmipp@cnb.csic.es'
25  ***************************************************************************/
26 
27 package xmipp.viewer.windows;
28 
29 import java.awt.Component;
30 import java.awt.Container;
31 import java.awt.Dimension;
32 import java.awt.FlowLayout;
33 import java.awt.GridBagConstraints;
34 import java.awt.GridBagLayout;
35 import java.awt.Point;
36 import java.awt.Rectangle;
37 import java.awt.event.ActionEvent;
38 import java.awt.event.ActionListener;
39 import java.awt.event.KeyEvent;
40 import java.awt.event.KeyListener;
41 import java.awt.event.MouseAdapter;
42 import java.awt.event.MouseEvent;
43 import java.awt.event.MouseWheelEvent;
44 import java.awt.event.MouseWheelListener;
45 import java.awt.event.WindowAdapter;
46 import java.awt.event.WindowEvent;
47 import java.io.File;
48 import java.util.Arrays;
49 import java.util.Collections;
50 import java.util.HashMap;
51 import java.util.LinkedHashMap;
52 import java.util.List;
53 import java.util.Map;
54 import java.util.logging.Level;
55 import java.util.logging.Logger;
56 
57 import javax.swing.AbstractAction;
58 import javax.swing.AbstractButton;
59 import javax.swing.ActionMap;
60 import javax.swing.ButtonGroup;
61 import javax.swing.ComboBoxModel;
62 import javax.swing.ImageIcon;
63 import javax.swing.InputMap;
64 import javax.swing.JButton;
65 import javax.swing.JCheckBoxMenuItem;
66 import javax.swing.JComboBox;
67 import javax.swing.JComponent;
68 import javax.swing.JFrame;
69 import javax.swing.JLabel;
70 import javax.swing.JList;
71 import javax.swing.JMenuItem;
72 import javax.swing.JPanel;
73 import javax.swing.JPopupMenu;
74 import javax.swing.JRadioButtonMenuItem;
75 import javax.swing.JScrollPane;
76 import javax.swing.JSpinner;
77 import javax.swing.JTable;
78 import javax.swing.JToggleButton;
79 import javax.swing.JToolBar;
80 import javax.swing.KeyStroke;
81 import javax.swing.LookAndFeel;
82 import javax.swing.SwingUtilities;
83 import javax.swing.BoxLayout;
84 import javax.swing.Box;
85 import javax.swing.border.EmptyBorder;
86 import javax.swing.event.ListDataListener;
87 import javax.swing.event.TableModelEvent;
88 import javax.swing.event.TableModelListener;
89 import javax.swing.table.JTableHeader;
90 
91 import xmipp.ij.commons.ImagePlusLoader;
92 import xmipp.ij.commons.Tool;
93 import xmipp.ij.commons.XmippApplication;
94 import xmipp.ij.commons.XmippUtil;
95 import xmipp.jni.Filename;
96 import xmipp.jni.ImageGeneric;
97 import xmipp.jni.MetaData;
98 import xmipp.utils.DEBUG;
99 import xmipp.utils.Params;
100 import xmipp.utils.QuickHelpJDialog;
101 import xmipp.utils.XmippDialog;
102 import xmipp.utils.XmippFileChooser;
103 import xmipp.utils.XmippLabel;
104 import xmipp.utils.XmippMenuBarCreator;
105 import xmipp.utils.XmippMessage;
106 import xmipp.utils.XmippPopupMenuCreator;
107 import xmipp.utils.XmippQuestionDialog;
108 import xmipp.utils.XmippResource;
109 import xmipp.utils.XmippWindowUtil;
110 import xmipp.viewer.RowHeaderRenderer;
111 import xmipp.viewer.ctf.TasksEngine;
112 import xmipp.viewer.ctf.iCTFGUI;
113 import xmipp.viewer.models.ColumnInfo;
114 import xmipp.viewer.models.GalleryData;
115 import xmipp.viewer.models.GalleryRowHeaderModel;
116 import xmipp.viewer.models.ImageGalleryTableModel;
117 import xmipp.viewer.models.MetadataGalleryTableModel;
118 import xmipp.viewer.models.MetadataTableModel;
119 import xmipp.viewer.particlepicker.extract.ExtractParticlePicker;
120 import xmipp.viewer.particlepicker.extract.ExtractPickerJFrame;
121 
127 public class GalleryJFrame extends JFrame implements iCTFGUI
128 {
129  private static final long serialVersionUID = -8957336972082018823L;
130 
131  private final static int DELAY_TO_UPDATE = 500;
132  public static final String CHIMERA_LAUNCHER = "CHIMERA_LAUNCHER";
133  private static int update_counter = 0;
134  // The following counter will be used to keep track of how many
135  // windows are opened, the last one, should do System.exit
136  // private static short windows_counter = 0;
137  protected ImageGalleryTableModel gallery;
138  private GalleryRowHeaderModel rowHeaderModel;
139  private int previousSelectedRow, previousSelectedCol;
140  private JList rowHeader;
141  // this flag will be used to avoid firing properties change events
142  // when the change is from our code and not external user interaction
143  private boolean isUpdating;
144  private GalleryPopupMenu jpopUpMenuTable;
145  protected GalleryMenu menu;
146  protected XmippFileChooser fc;
147  private SaveJDialog dlgSave = null;
148  private boolean saved = false;
149  private ClassesJDialog dlgClasses = null;
150 
151  private JLabel jlZoom;
152  private JLabel jlGoToImage;
153  private JLabel jlRows;
154  private JLabel jlColumns;
155  private JToggleButton jcbAutoAdjustColumns;
156  private JButton btnChangeView;
157  protected JPanel jpBottom;
158  protected JSpinner jsColumns;
159  protected JSpinner jsGoToImage;
160  private JScrollPane jspContent;
161  protected JSpinner jsRows;
162  protected JSpinner jsZoom;
163  // Components for combos
164  protected JPanel cbPanel;
165  protected JComboBox jcbBlocks;
166  protected JComboBox jcbVolumes;
167  protected JLabel jlBlocks;
168  protected JLabel jlVolumes;
169  protected TasksEngine ctfTasks;
170  // private javax.swing.JToggleButton jtbNormalize;
171  // private javax.swing.JToggleButton jtbUseGeometry;
172  private JTable table;
173  private JToolBar toolBar;
174  private int width = -1;
175  private JButton reslicebt;
176  private String[] reslices = new String[] { "Z Negative (Front)", "Y Negative (Top)", "X Negative (Left)", "Y Positive (Bottom)",
177  "X Positive (Right)" };
178 
179  protected static final float MAX_HEIGHT_RATE = 2.0f / 3.0f;
180  // this rate is width/height
181  protected static final float DIM_RATE = 4.0f / 3.0f;
182  protected static final int MIN_WIDTH = 800;
183  protected static int MIN_HEIGHT;
184  protected static int MAX_HEIGHT;
185  protected static int MAX_WIDTH;
186  protected static Dimension screenSize;
187 
188 
189 
190  /* Store data about visualization */
191  protected GalleryData data;
192  private ExtractPickerJFrame extractframe;
193  private ButtonGroup reslicegroup;
194  protected JPanel buttonspn;
195  protected JButton searchbt;
196  protected JButton plotbt;
197  protected JButton chimerabt;
198 
199  /* Some static initialization for fancy default dimensions */
200  static
201  {
202  screenSize = XmippWindowUtil.getScreenRectangle().getSize();
203  float aux = (float) screenSize.height * MAX_HEIGHT_RATE;
204  MAX_HEIGHT = Math.round(aux);
205  aux = (float) MIN_WIDTH / DIM_RATE;
206  MIN_HEIGHT = Math.round(aux);
207  aux = (float) MAX_HEIGHT * DIM_RATE;
208  MAX_WIDTH = Math.round(aux);
209  }
210 
211 
212 
214  private void init(GalleryData data)
215  {
216  try
217  {
218 
219  this.data = data;
220  data.setWindow(this);
221  createModel();
222  createGUI();
223  XmippApplication.addInstance(false);
224  }
225  catch (Exception e)
226  {
227  DEBUG.printException(e);
228  setVisible(false);
229  dispose();
230 
231  throw new IllegalArgumentException(e);
232  }
233  }
234 
236  public GalleryJFrame(String filename, Params parameters)
237  {
238  super();
239  init(new GalleryData(this, filename, parameters));
240  }
241 
242  public GalleryJFrame(MetaData md, Params parameters)
243  {
244  super();
245  init(new GalleryData(this, parameters, md));
246  }
247 
248  public GalleryJFrame(GalleryData data)
249  {
250  super();
251  init(data);
252  }
253 
257  public void openMetadata(final MetaData md)
258  {
259  try
260  {
261  SwingUtilities.invokeLater(new Runnable() {
262 
263  @Override
264  public void run() {
265  new GalleryJFrame(md, new Params());
266  }
267  });
268 
269  }
270  catch(Exception e)
271  {
272  XmippDialog.showError(this, e.getMessage());
273  }
274 
275  }
276 
277  protected void createModel() throws Exception
278  {
279  createModel(null);
280  }
284  protected void createModel(boolean[] selection)
285  {
286  gallery = data.createModel(selection);
287  if (data.getModelColumns() != null)
288  gallery.setColumns(data.getModelColumns());
289  else if (data.getModelRows() != null)
290  gallery.setRows(data.getModelRows());
291  int index = gallery.getSelTo();
292  if(jsGoToImage != null)
293  jsGoToImage.setValue(index + 1);
294  }
295 
296  public GalleryData getData()
297  {
298  return data;
299  }
300 
302  public void close()
303  {
304  close(true);
305  }// function close
306 
308  public void close(boolean ask)
309  {
310  boolean isclose = true;
311  if(ask)
312  isclose = proceedWithChanges();
313  if (isclose)
314  {
315  setVisible(false);
316  dispose();
317  XmippApplication.removeInstance(false);
318 
319  }
320  }// function close
321 
323  public boolean proceedWithChanges()
324  {
325  boolean proceed = true;
326  if (data.hasMdChanges())
327  {
328  XmippQuestionDialog dlg = new XmippQuestionDialog(GalleryJFrame.this, "Do you want to save metadata changes?");
329  if (dlg.showDialog())
330  try
331  {
332  save();
333  }
334  catch (Exception e)
335  {
336  showException(e);
337  }
338  else
339  proceed = !dlg.isCanceled();
340  }
341  return proceed;
342  }
343 
345  private void setGalleryTitle()
346  {
347  setTitle(gallery.getTitle());
348  }
349 
354  protected void createGUI()
355  {
356  // Create file chooser and set current dir
357  //setIconImage(XmippResource.getIcon("xmipp_logo.png").getImage());
358  if (data.getFileName() != null)
359  fc = new XmippFileChooser(new File(data.getFileName()));
360  else
361  fc = new XmippFileChooser();
362  ctfTasks = new TasksEngine(GalleryJFrame.this);
363 
364  isUpdating = true; // avoid handling some changes events
365 
366  setGalleryTitle();
367  setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
368  setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
369  addWindowListener(new WindowAdapter()
370  {
371  @Override
372  public void windowClosing(WindowEvent arg0)
373  {
374  close();
375  }
376  });
377 
378  // Get main pane and set layout
379  Container pane = getContentPane();
380  JPanel container = new JPanel(new GridBagLayout());
381  pane.add(container);
382  // container.setLayout(new GridBagLayout());
383  GridBagConstraints c = new GridBagConstraints();
384 
385  // Create toolbar buttons
386  createToolbar();
387  container.add(toolBar, XmippWindowUtil.getConstraints(c, 0, 0, 1, 1, GridBagConstraints.HORIZONTAL));
388  setInitialValues();
389 
390  // Create combos for selection of blocks and/or volumes
391  createCombos();
392  container.add(cbPanel, XmippWindowUtil.getConstraints(c, 0, 1, 1, 1, GridBagConstraints.HORIZONTAL));
393  updateVisibleCombos();
394 
395  jspContent = new GalleryScroll();
396  // Create table
397  createTable();
398 
399  c.weightx = 1.0;
400  c.weighty = 1.0;
401  container.add(jspContent, XmippWindowUtil.getConstraints(c, 0, 2, 1, 1, GridBagConstraints.BOTH));
402  c.weightx = 0;
403  c.weighty = 0;
404 
405  buttonspn = new JPanel(new FlowLayout(FlowLayout.TRAILING));
406  container.add(buttonspn, XmippWindowUtil.getConstraints(c, 0, 3, 1, 1, GridBagConstraints.HORIZONTAL));
407 
408  // Create the menu for table
409  initGalleryMenu();
410  setJMenuBar(menu.getMenuBar());
411  jpopUpMenuTable = new GalleryPopupMenu();
412  menu.update();
413 
414  // pack();
415  isUpdating = false;
416 
417  // Zoom in with Ctrl + P
418  InputMap imap = container.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
419  ActionMap amap = container.getActionMap();
420  imap.put(KeyStroke.getKeyStroke("ctrl released P"), "zoomIn");
421  amap.put("zoomIn", new AbstractAction()
422  {
423  @Override
424  public void actionPerformed(ActionEvent e)
425  {
426  zoomChange(true);
427  }
428 
429  });
430  // Zoom in with Ctrl + O
431  imap.put(KeyStroke.getKeyStroke("ctrl released M"), "zoomOut");
432  amap.put("zoomOut", new AbstractAction()
433  {
434  @Override
435  public void actionPerformed(ActionEvent e)
436  {
437  zoomChange(false);
438  }
439 
440  });
441 
442  // Change view with Ctrl + Tab
443  imap.put(KeyStroke.getKeyStroke("ctrl released I"), "changeView");
444  amap.put("changeView", new AbstractAction()
445  {
446  @Override
447  public void actionPerformed(ActionEvent e)
448  {
449  changeView();
450  }
451  });
452  enableToolBarActions();
453  pack();
454  XmippWindowUtil.centerWindows(this);
455  setVisible(true);
456  SwingUtilities.invokeLater(new Runnable()
457  {
458  public void run()
459  {
460  addComponentListener(new java.awt.event.ComponentAdapter()
461  {
462  public void componentResized(java.awt.event.ComponentEvent evt)
463  {
464  formComponentResized(evt);
465  }
466  });
467  }
468  });
469  XmippWindowUtil.setScipionImageIcon(this);
470  }
471 
472  private void setInitialValues()
473  {
474  boolean adjust = true;
475  if (data.parameters.columns > 0 || data.parameters.rows > 0)
476  adjust = false;
477 
478 
479  if (data.isMicrographsMode())
480  {
481  // setExtendedState(JFrame.MAXIMIZED_BOTH);
482  width = screenSize.width - 50;
483  int h = screenSize.height - 100;
484  setPreferredSize(new Dimension(width, h));
485  }
486  else
487  {
488  int desiredCols = adjust ? (int) Math.ceil(Math.sqrt(gallery.getSize())) : gallery.getColumnCount();
489  width = desiredCols * gallery.cellDim.width + 50;
490  width = Math.min(Math.max(width, MIN_WIDTH), MAX_WIDTH);
491  if (adjust)
492  {
493  gallery.adjustColumn(width - 50);
494  }
495  int h = gallery.getRowCount() * gallery.cellDim.height;
496  h = Math.min(Math.max(h, MIN_HEIGHT), MAX_HEIGHT);
497  setPreferredSize(new Dimension(width, h));
498  }
499  setAutoAdjustColumns(adjust);
500  }
501 
502  public void fireTableRowsUpdated(int from, int to) {
503  gallery.fireTableRowsUpdated(from, to);
504  }
505 
506 
507 
508  protected void initGalleryMenu() {
509  menu = new GalleryMenu();
510 
511  }
512 
514  public class GalleryScroll extends JScrollPane
515  {
516  }// class GalleryTable
517 
518  private void createTable()
519  {
520  // Create row header for enumerate rows
521  try
522  {
523  rowHeaderModel = (data.isColumnFormat() || !data.isTableMode()) ? new GalleryRowHeaderModel(gallery.getRowCount(), 1)
524  : new GalleryRowHeaderModel(data);
525  }
526  catch (Exception e1)
527  {
528  // TODO Auto-generated catch block
529  e1.printStackTrace();
530  }
531  rowHeader = new JList();
532  rowHeader.setModel(rowHeaderModel);
533  LookAndFeel.installColorsAndFont(rowHeader, "TableHeader.background", "TableHeader.foreground", "TableHeader.font");
534  rowHeader.setCellRenderer(new RowHeaderRenderer());
535  jspContent.setRowHeaderView(rowHeader);
536 
537  table = new JTable()
538  {
539  protected JTableHeader createDefaultTableHeader()
540  {
541  return gallery.getTableHeaderModel();
542  }
543  };
544  // Create column model
545  table.setColumnModel(gallery.getColumnModel());
546  table.setModel(gallery);
547  // int h = 25;
548  // table.setRowHeight(h);
549  // rowHeader.setFixedCellHeight(h);
550  jspContent.setViewportView(table);
551 
552  gallery.setupTable(table);
553  table.setRowSelectionAllowed(true);
554  // DEBUG.printMessage("WIDTH: " + jspContent.getVisibleRect().width);
555  // DEBUG.printMessage("preferred: " + getPreferredSize().toString());
556  gallery.addTableModelListener(new TableModelListener()
557  {
558 
559  @Override
560  public void tableChanged(TableModelEvent e)
561  {
562  updateTable();
563  }
564  });
565 
566  table.addMouseListener(new java.awt.event.MouseAdapter()
567  {
568  public void mouseReleased(java.awt.event.MouseEvent evt)
569  {
570  tableMouseClicked(evt);
571  }
572  });
573 
574  // Zoom with Shift + MouseWeel
575  table.addMouseWheelListener(new MouseWheelListener()
576  {
577  @Override
578  public void mouseWheelMoved(MouseWheelEvent evt)
579  {
580  if (evt.isShiftDown())
581  zoomChange(evt.getWheelRotation() < 0);
582  else
583  table.getParent().dispatchEvent(evt);
584  }
585  });
586 
587  // Add listener to recognize UP and DOWN keys
588  table.addKeyListener(new KeyListener()
589  {
590  @Override
591  public void keyTyped(KeyEvent arg0)
592  {
593  }
594 
595  @Override
596  public void keyReleased(KeyEvent arg0)
597  {
598  }
599 
600  @Override
601  public void keyPressed(KeyEvent arg0)
602  {
603  if(table.getSelectedRow() == -1)
604  return;
605  int vdir = 0, hdir = 0;
606 
607  switch (arg0.getKeyCode())
608  {
609  case KeyEvent.VK_DELETE:
610  removeObjects(true);
611  break;
612  case KeyEvent.VK_UP:
613  vdir = -1;
614  break;
615  case KeyEvent.VK_DOWN:
616  vdir = 1;
617  break;
618  case KeyEvent.VK_LEFT:
619  hdir = -1;
620  break;
621  case KeyEvent.VK_RIGHT:
622  hdir = 1;
623  break;
624 
625  case KeyEvent.VK_SPACE:
626  int from = gallery.getSelFrom(), to = gallery.getSelTo();
627  for (int i = from; i <= to; ++i)
628  if (gallery.isSelected(i))
629  data.setEnabled(i, !data.isEnabled(i));
630  if(from != -1)
631  gallery.fireTableRowsUpdated(from, to);
632  }
633  if (vdir != 0 || hdir != 0)
634  {
635 
636  int newRow = table.getSelectedRow() + vdir;
637  int col = (table.getSelectedColumn() == -1)? 0 : table.getSelectedColumn() + hdir;//col is -1 in metadata mode
638  //System.out.printf("newRow: %d, col: %d\n", newRow, col);
639  selectItem(newRow, col);
640 
641  }
642  }// function keyPressed
643  });
644 
645  updateViewState();
646 
647  if (!adjustColumns())
648  updateTable(); // update table if columns have not changed
649  }// function createTable
650 
651  private void zoomChange(boolean increase)
652  {
653 
654  int deltha = increase ? 10 : -10;
655  jsZoom.setValue((Integer) jsZoom.getValue() + deltha);
656  }
657 
658  private void updateTable()
659  {
660  // if (table.isShowing()) {
661  boolean updatingState = isUpdating;
662  isUpdating = true;
663  update_counter++;
664  //DEBUG.printMessage(" *** Updating table: " + update_counter); // );
665  //DEBUG.printStackTrace();
666 
667  // FIXME:gallery.updateSort();
668 
669  if (gallery.getSize() > 0)
670  {
671  // DEBUG.printMessage(String.format("updateTable: Table Model:\nsize: %d, cols: %d rows: %d",
672  // gallery.getSize(), gallery.getColumnCount(),
673  // gallery.getRowCount()));
674  Dimension dimension = gallery.getCellSize();
675  // renderer.setPreferredSize(dimension);
676 
677  // Adjusts rows size.
678  table.setRowHeight(dimension.height);
679  rowHeader.setFixedCellHeight(dimension.height);
680  rowHeaderModel.setSize(gallery.getRowCount());
681  }
682  // Adjusts columns width
683  if (gallery.adjustWidth)
684  gallery.getColumnModel().adjustColumnsWidth(table);
685  else
686  gallery.adjustWidth = true;
687  // columnModel.setWidth(dimension.width);
688 
689  // If auto adjust columns is enabled, refresh!
690  jsRows.setValue(gallery.getRowCount());
691  jsColumns.setValue(gallery.getColumnCount());
692 
693  rowHeader.revalidate();
694  rowHeader.repaint();
695  // table.revalidate();
696  // repaint();
697  // }
698 
699  jsZoom.setValue(data.getZoom());
700  isUpdating = updatingState;
701  SwingUtilities.invokeLater(new Runnable()
702  {
703  public void run()
704  {
705  gallery.updateTableSelection(table);
706  }
707  });
708 
709  // }
710  }// function updateTable
711 
712 
714  private boolean adjustColumns()
715  {
716  if (data.isAutoAdjust()){
717  //DEBUG.printStackTrace();
718  return gallery.adjustColumn(width - 50);
719  }
720  return false;
721  // DEBUG.printMessage(String.format(
722  // "==>> JFrameGallery.autoAdjust: width: %d", width));
723  // int rw = rowHeader.getWidth();
724  // FIXME
725  // gallery.autoAdjustColumns(
726  // // jsPanel.getVisibleRect().width - rowHeader.getWidth(),
727  // // jsPanel.getViewportBorderBounds().width -
728  // // rowHeader.getWidth(),
729  // // jspContent.getViewport().getWidth() - rowHeader.getWidth()
730  // w - rw, table.getIntercellSpacing().width);
731  // updateColumnsRowsValues();
732  }
733 
734  public void setAutoAdjustColumns(boolean autoAdjustColumns)
735  {
736  jcbAutoAdjustColumns.setSelected(autoAdjustColumns);
737  jcbAutoAdjustColumns.setEnabled(!data.isTableMode());
738  jsColumns.setEnabled(!autoAdjustColumns);
739  jsRows.setEnabled(!autoAdjustColumns);
740  }
741 
742  private void makeVisible(int row, int col)
743  {
744  //System.out.println(String.format("gotoImage, row: %d, col:%d", row, col));
745 
746  // Gets current selected cell bounds.
747  Rectangle rect = table.getCellRect(row, col, true);
748  // Ensures item is visible
749  Point pos = jspContent.getViewport().getViewPosition();
750  rect.translate(-pos.x, -pos.y);
751  jspContent.getViewport().scrollRectToVisible(rect);
752 
753  repaint();
754  }
755 
756  private void goToImage(int index)
757  {
758  gallery.gotoItem(index);
759  Point coords = gallery.getCoords(index);
760  makeVisible(coords.y, coords.x);
761  }
762 
763 
764 
766  public void runInBackground(int operation)
767  {
768 
769  boolean selected = false;
770  if(gallery.hasSelection())
771  {
772  int result = XmippDialog.showQuestionYesNoCancel(this, "This operation processes all images by default. Would you like to use selection instead?");
773 
774  if(result == XmippQuestionDialog.YES_OPTION)
775  selected = true;
776  else if(result == XmippQuestionDialog.CANCEL_OPTION)
777 
778  return;
779  }
780 
781 
782 
783  Worker w = new Worker(operation, selected, this);
784  XmippWindowUtil.blockGUI(this, w.getMessage());
785  Thread thr = new Thread(w);
786  thr.start();
787  }
788 
789 
790 
791  private boolean openClassesDialog()
792  {
793  if (dlgClasses == null)
794  {
795  dlgClasses = new ClassesJDialog(GalleryJFrame.this);
796  }
797  boolean result = dlgClasses.showDialog();
798  dlgClasses.resetClasses();
799  return result;
800  }
801 
802  static String forceExtension(String filename, String ext)
803  {
804  int dot = filename.lastIndexOf(".");
805  return filename.substring(0, dot) + ext;
806  }
807 
808 
809 
810  /***
811  * Helper function to create toolbar toggle buttons
812  */
813  protected void setupButton(AbstractButton btn, String icon, String text, ActionListener listener)
814  {
815  // Add toggle button to set/unset global normalization
816  // JToggleButton btn = new javax.swing.JToggleButton();
817  btn.setFocusable(false);
818  btn.setIcon(XmippResource.getIcon(icon));
819  btn.setToolTipText(text);
820  btn.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
821  btn.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
822  btn.addActionListener(listener);
823  // return btn;
824  }
825 
826  private void updateViewState()
827  {
828  ImageIcon icon;
829  String text;
830  if (!data.isGalleryMode())
831  {
832  icon = XmippResource.VIEW_GALLERY_ICON;
833  text = XmippLabel.LABEL_VIEW_GALLERY;
834  }
835  else
836  {
837  icon = XmippResource.VIEW_MD_ICON;
838  text = XmippLabel.LABEL_VIEW_MD;
839  }
840  btnChangeView.setIcon(icon);
841  btnChangeView.setToolTipText(text);
842  if (data.isTableMode())
843  { // if we are in table mode only allow change
844  // if exist render label
845  enableToolBarActions();
846  autoAdjustColumns(true);
847  }
848  else
849  autoAdjustColumns(data.isAutoAdjust());
850  }
851  public void reloadTableData()
852  {
853  reloadTableData(true, null);
854  }
855 
856  public void reloadTableData(boolean[] selection)
857  {
858  reloadTableData(true, selection);
859  }
860 
862  public void reloadTableData(boolean changed, boolean[] selection)
863  {
864  try
865  {
866  //DEBUG.printMessage("reloadTableData...");
867  if (table != null)
868  table.removeAll();
869  createModel(selection);
870  // gallery.setShowLabels(menu.getShowLabel());
871  createTable();
872 
873  menu.update();
874  updateVisibleCombos();
875  searchbt.setEnabled(data.isTableMode());
876  plotbt.setEnabled(data.isTableMode());
877  if (dlgSave != null && changed)
878  dlgSave.setInitialValues();
879 
880  this.saved = !changed;
881  setGalleryTitle();
882  Integer rows = data.getModelRows();
883  Integer cols = data.getModelColumns();
884  if (rows != null)
885  gallery.setRows(rows);
886  if (cols != null)
887  gallery.setColumns(cols);
888 
889 
890  }
891  catch (Exception e)
892  {
893  e.printStackTrace();
894  }
895  }
896 
897  private void reloadMd() throws Exception
898  {
899  reloadMd(true);
900  }
901 
908  private void reloadMd(boolean changed) throws Exception
909  {
910  data.loadMd();
911  reloadTableData(changed, gallery.getSelection());
912  data.setMdChanges(changed);
913 
914  }// function reloadMd
915 
920  public void fillLabel(int label, String mode, String... values) throws Exception
921  {
922  if (mode.equalsIgnoreCase(MetaData.FILL_CONSTANT))
923  data.fillConstant(label, values[0]);
924  else
925  {
926  double v1 = Double.parseDouble(values[0]);
927  double v2 = Double.parseDouble(values[1]);
928  if (mode.equalsIgnoreCase(MetaData.FILL_LINEAR))
929  data.fillLinear(label, v1, v2);
930  else if (mode.equalsIgnoreCase(MetaData.FILL_RAND_UNIFORM))
931  data.fillRandom(label, "uniform", v1, v2);
932  else if (mode.equalsIgnoreCase(MetaData.FILL_RAND_GAUSSIAN))
933  data.fillRandom(label, "gaussian", v1, v2);
934  else
935  throw new Exception("Unknown label fill mode: " + mode);
936  }
937  reloadMd();
938  }
939 
944  public void removeObjects(boolean selected)
945  {
946  try
947  {
948  String type = selected ? "selected" : "disabled";
949  if (XmippDialog.showWarning(this, String.format("Are you sure to delete %s items?", type)))
950  {
951  if (selected)
952  data.removeSelection(gallery.getSelection());
953  else
954  data.removeDisabled();
955  gallery.clearSelection();
956  reloadMd();
957  }
958  }
959  catch (Exception ex)
960  {
961  showException(ex);
962  }
963  }
964 
965 
966 
968  public void findReplace()
969  {
970  MDSearchJDialog dlg = new MDSearchJDialog(this, table, data);
971  dlg.setVisible(true);
972  }
973 
975  public void removeLabel(int label) throws Exception
976  {
977  data.removeLabel(label);
978  reloadMd();
979  }
980 
981  /***
982  * Function to create the main toolbar
983  */
984 
985  protected void changeView()
986  {
987  data.changeMode();
988  boolean[] selection = null;
989  if(!data.isVolumeMd())
990  selection = gallery.getSelection();
991  reloadTableData(selection);
992  if(gallery.getSelTo() != -1)
993  {
994  Point coords = gallery.getCoords(gallery.getSelTo());
995  makeVisible(coords.y, coords.x);
996  }
997 
998  }
999 
1000  protected void createToolbar() {
1001  // Create Main TOOLBAR
1002  toolBar = new JToolBar();
1003  toolBar.setFloatable(false);
1004  toolBar.setRollover(true);
1005  toolBar.setLayout(new FlowLayout(FlowLayout.LEFT));
1006 
1007  btnChangeView = new JButton();
1008  // updateViewState();
1009  btnChangeView.addActionListener(new ActionListener() {
1010  @Override
1011  public void actionPerformed(ActionEvent e) {
1012  changeView();
1013  }
1014  });
1015 
1016  toolBar.add(btnChangeView);
1017  toolBar.addSeparator();
1018 
1019  jlZoom = new javax.swing.JLabel();
1020  jsZoom = new javax.swing.JSpinner();
1021  jlZoom.setIcon(XmippResource.getIcon(XmippResource.ZOOM));
1022  jlZoom.setToolTipText(XmippLabel.LABEL_ZOOM);
1023  toolBar.add(jlZoom);
1024 
1025  jsZoom.setModel(new javax.swing.SpinnerNumberModel(Integer.valueOf(1), Integer.valueOf(1), null, Integer.valueOf(1)));
1026  jsZoom.addChangeListener(new javax.swing.event.ChangeListener() {
1027  public void stateChanged(javax.swing.event.ChangeEvent evt) {
1028  Integer zoom = (Integer) jsZoom.getValue();
1029  if (gallery.getCellSize().getHeight() < 30 && zoom < gallery.data.getZoom()) {
1030  jsZoom.setValue(gallery.data.getZoom());//keep previous zoom
1031  return;
1032  }
1033  gallery.setZoom(zoom);
1034  makeVisible(gallery.getFirstSelectedIndex(), 0);
1035  // gallery.updateTableSelection(table);
1036  }
1037  });
1038 
1039  toolBar.add(jsZoom);
1040  toolBar.addSeparator();
1041 
1042  jlGoToImage = new javax.swing.JLabel();
1043  jsGoToImage = new javax.swing.JSpinner();
1044  jlGoToImage.setIcon(XmippResource.getIcon(XmippResource.GOTO));
1045  jlGoToImage.setToolTipText(XmippLabel.LABEL_GOTO_ITEM);
1046  toolBar.add(jlGoToImage);
1047 
1048  if (gallery.getSize() > 0)
1049  jsGoToImage.setValue(1);
1050 
1051  jsGoToImage.addChangeListener(new javax.swing.event.ChangeListener() {
1052  public void stateChanged(javax.swing.event.ChangeEvent evt) {
1053  jsGoToImageStateChanged(evt);
1054  }
1055  });
1056  toolBar.add(jsGoToImage);
1057 
1058  toolBar.addSeparator();
1059 
1060  jcbAutoAdjustColumns = new JToggleButton();
1061  setupButton(jcbAutoAdjustColumns, XmippResource.ADJUST_COLS, XmippLabel.MSG_ADJUST_COLS, new java.awt.event.ActionListener() {
1062  public void actionPerformed(java.awt.event.ActionEvent evt) {
1063  autoAdjustColumns(jcbAutoAdjustColumns.isSelected());
1064  }
1065  });
1066  jcbAutoAdjustColumns.setSelected(data.isAutoAdjust());
1067  jlRows = new javax.swing.JLabel();
1068  jsRows = new javax.swing.JSpinner();
1069  jlColumns = new javax.swing.JLabel();
1070  jsColumns = new javax.swing.JSpinner();
1071  toolBar.add(jcbAutoAdjustColumns);
1072 
1073  jlColumns.setText(XmippLabel.LABEL_COLUMNS);
1074  toolBar.add(jlColumns);
1075 
1076  jsColumns.addChangeListener(new javax.swing.event.ChangeListener() {
1077  public void stateChanged(javax.swing.event.ChangeEvent evt) {
1078  jsColumnsStateChanged(evt);
1079  }
1080  });
1081  toolBar.add(jsColumns);
1082 
1083  jlRows.setText(XmippLabel.LABEL_ROWS);
1084  toolBar.add(jlRows);
1085 
1086  jsRows.addChangeListener(new javax.swing.event.ChangeListener() {
1087  public void stateChanged(javax.swing.event.ChangeEvent evt) {
1088  jsRowsStateChanged(evt);
1089  }
1090  });
1091  toolBar.add(jsRows);
1092 
1093  // Some settings of the spinners
1094 
1095 // if (gallery.getSize() > 0)
1096 // {
1097 //
1098 // jsRows.setModel(new SpinnerNumberModel(1, 1, gallery.getSize(), 1));
1099 // jsColumns.setModel(new SpinnerNumberModel(1, 1, gallery.getSize(), 1));
1100 // jsGoToImage.setModel(new SpinnerNumberModel(1, 1, gallery.getSize(), 1));
1101 // }
1102 
1103  int TEXTWIDTH = 4;
1104  ((JSpinner.NumberEditor) jsZoom.getEditor()).getTextField().setColumns(TEXTWIDTH);
1105  ((JSpinner.NumberEditor) jsGoToImage.getEditor()).getTextField().setColumns(TEXTWIDTH);
1106  ((JSpinner.NumberEditor) jsRows.getEditor()).getTextField().setColumns(TEXTWIDTH);
1107  ((JSpinner.NumberEditor) jsColumns.getEditor()).getTextField().setColumns(TEXTWIDTH);
1108 
1109  initResliceButtonMenu();
1110  toolBar.add(reslicebt);
1111  searchbt = new JButton(XmippResource.getIcon("binocular.png"));
1112  searchbt.setEnabled(data.isTableMode());
1113  searchbt.addActionListener(new ActionListener() {
1114 
1115  @Override
1116  public void actionPerformed(ActionEvent ae) {
1117  try {
1118  findReplace();
1119  } catch (Exception ex) {
1120  Logger.getLogger(GalleryJFrame.class.getName()).log(Level.SEVERE, null, ex);
1121  }
1122  }
1123  });
1124  toolBar.add(searchbt);
1125  plotbt = new JButton(XmippResource.getIcon("plot.png"));
1126  plotbt.setEnabled(data.isTableMode());
1127  plotbt.addActionListener(new ActionListener() {
1128 
1129  @Override
1130  public void actionPerformed(ActionEvent ae) {
1131  try {
1132  plotColumns();
1133  } catch (Exception ex) {
1134  Logger.getLogger(GalleryJFrame.class.getName()).log(Level.SEVERE, null, ex);
1135  }
1136  }
1137  });
1138 
1139  toolBar.add(plotbt);
1140  chimerabt = new JButton(XmippResource.getIcon("chimera.png"));
1141  chimerabt.setEnabled(data.isVolumeMode());
1142 
1143  if ( getChimera() == null){
1144  chimerabt.setEnabled(false);
1145  chimerabt.setToolTipText("ChimeraX not available, looking at " + CHIMERA_LAUNCHER);
1146  }
1147 
1148  chimerabt.addActionListener(new ActionListener() {
1149 
1150  @Override
1151  public void actionPerformed(ActionEvent ae) {
1152  openWithChimera();
1153  }
1154  });
1155  toolBar.add(chimerabt);
1156 
1157  }// function createToolbar
1158 
1160  protected void createCombos()
1161  {
1162  cbPanel = new JPanel();
1163  // add some padding
1164  cbPanel.setBorder(new EmptyBorder(5, 5, 5, 5));
1165  cbPanel.setLayout(new BoxLayout(cbPanel,BoxLayout.LINE_AXIS));
1166 
1167  // Add blocks selector combo
1168  jlBlocks = new JLabel(XmippLabel.LABEL_BLOCK);
1169  jcbBlocks = new JComboBox();
1170  DEBUG.printFormat("data.getNumberOfBlocks: %d\n", data.getNumberOfBlocks());
1171 
1172  if (data.getNumberOfBlocks() > 0)
1173  {
1174  cbPanel.add(jlBlocks);
1175  jcbBlocks.setModel(new ComboBoxModel()
1176  {
1177 
1178  @Override
1179  public int getSize()
1180  {
1181  return data.getNumberOfBlocks();
1182  }
1183 
1184  @Override
1185  public Object getElementAt(int index)
1186  {
1187  return data.getBlock(index);
1188  }
1189 
1190  @Override
1191  public void setSelectedItem(Object item)
1192  {
1193  if (proceedWithChanges())
1194  selectBlock((String)item);
1195  }
1196 
1197  @Override
1198  public Object getSelectedItem()
1199  {
1200  return data.getSelectedBlock();
1201  }
1202 
1203  @Override
1204  public void removeListDataListener(ListDataListener arg0)
1205  {
1206  }
1207 
1208  @Override
1209  public void addListDataListener(ListDataListener arg0)
1210  {
1211  // TODO Auto-generated method stub
1212  }
1213  });
1214 
1215  cbPanel.add(jcbBlocks);
1216  }
1217  // Add volumes selector combo
1218  cbPanel.add(Box.createRigidArea(new Dimension(5,0)));
1219  jlVolumes = new JLabel(XmippLabel.LABEL_VOLUME);
1220  cbPanel.add(jlVolumes);
1221  jcbVolumes = new JComboBox();
1222  jcbVolumes.setModel(new VolumesComboBoxModel());
1223  cbPanel.add(jcbVolumes);
1224  }
1225 
1226  public void selectBlock(String block)
1227  {
1228  data.selectBlock(block);
1229  jcbVolumes.invalidate();
1230  try
1231  {
1232  data.loadMd();
1233  reloadTableData();
1234  autoAdjustColumns(data.isAutoAdjust());
1235  enableToolBarActions();
1236  }
1237  catch (Exception e)
1238  {
1239  // TODO Auto-generated catch block
1240  e.printStackTrace();
1241  }
1242  }
1243 
1244  protected void enableToolBarActions()
1245  {
1246  boolean hasRender = data.allowGallery();
1247  boolean isCol = data.isColumnFormat();
1248 
1249  btnChangeView.setEnabled(hasRender && isCol && data.renderImages());
1250  jsZoom.setEnabled(hasRender);
1251  jlZoom.setEnabled(hasRender);
1252 
1253  jsGoToImage.setEnabled(isCol && gallery.getSize() > 0);
1254  jlGoToImage.setEnabled(isCol);
1255 
1256  }
1257 
1258  public class VolumesComboBoxModel implements ComboBoxModel
1259  {
1260  private HashMap<Integer, String> indexToVolume;
1261  private HashMap<String, Integer> volumeToIndex;
1262  private int size;
1263 
1264  public VolumesComboBoxModel()
1265  {
1266  String volume;
1267  size = data.allowsVolumeMode()? data.size(): 0;
1268  indexToVolume = new HashMap(size);
1269  volumeToIndex = new HashMap(size);
1270  for(int i = 0; i < size; i ++)
1271  {
1272  volume = data.getVolumeAt(i);
1273  volume = getVolumeName(volume);
1274  indexToVolume.put(i, volume);
1275  volumeToIndex.put(volume, i);
1276  }
1277  }
1278 
1279 
1280 
1281  @Override
1282  public int getSize()
1283  {
1284 
1285  return size;
1286  }
1287 
1288  @Override
1289  public Object getElementAt(int index)
1290  {
1291  return indexToVolume.get(index);
1292  }
1293 
1294  @Override
1295  public void setSelectedItem(Object anItem)
1296  {
1297  try
1298  {
1299  int index = volumeToIndex.get(anItem);
1300  data.selectVolumeAt(index);
1301  reloadTableData();
1302  }
1303  catch(Exception e)
1304  {
1305  XmippDialog.showError(GalleryJFrame.this, e.getMessage());
1306  }
1307 
1308  }
1309 
1310  public String getVolumeName(String volume)
1311  {
1312 
1313  if(Filename.hasPrefix(volume))//is stack
1314  return volume;
1315  String base = Filename.getBaseName(volume);
1316  int count = 0;
1317  for(int i = 0; i < getSize(); i ++)
1318  if(base.equals(Filename.getBaseName(data.getVolumeAt(i))))
1319  {
1320  count ++;
1321  if (count > 1)// if volumes use same name you need to keep preffix
1322  break;
1323  }
1324  if(count == 1)
1325  return base;
1326 
1327  return volume;//needs full path to differentiate volumes
1328  }
1329 
1330  @Override
1331  public Object getSelectedItem()
1332  {
1333  return getVolumeName(data.getSelVolumeFile());
1334  }
1335 
1336  @Override
1337  public void addListDataListener(ListDataListener arg0)
1338  {
1339  // TODO Auto-generated method stub
1340 
1341  }
1342 
1343  @Override
1344  public void removeListDataListener(ListDataListener arg0)
1345  {
1346  // TODO Auto-generated method stub
1347 
1348  }
1349  }
1350 
1351  protected void updateVisibleCombos()
1352  {
1353 
1354  boolean showBlocks = data.getNumberOfBlocks() > 0;
1355  boolean showVols = data.size() > 1 && data.isVolumeMode();
1356  jcbBlocks.setVisible(showBlocks);
1357  jcbVolumes.setVisible(showVols);
1358  jlBlocks.setVisible(showBlocks);
1359  jlVolumes.setVisible(showVols);
1360  cbPanel.setVisible(showBlocks || showVols);
1361  //pack();
1362  }
1363 
1364  private void jsRowsStateChanged(javax.swing.event.ChangeEvent evt)
1365  {// GEN-FIRST:event_jsRowsStateChanged
1366  if (!isUpdating)
1367  {
1368  Integer rows = (Integer) jsRows.getValue();
1369  if (rows <= 0)
1370  rows = 1;
1371  else if (rows >= gallery.getSize())
1372  rows = gallery.getSize();
1373  if (jsRows.getValue() != rows)
1374  jsRows.setValue(rows);
1375  data.setModelDim(rows, null);
1376  gallery.setRows(rows);
1377  }
1378  }
1379 
1380  private void jsColumnsStateChanged(javax.swing.event.ChangeEvent evt)
1381  {// GEN-FIRST:event_jsColumnsStateChanged
1382  if (!isUpdating)
1383  {
1384  Integer columns = (Integer) jsColumns.getValue();
1385  if (columns <= 0)
1386  columns = 1;
1387  else if (columns >= gallery.getSize())
1388  columns = gallery.getSize();
1389  if (jsColumns.getValue() != columns)
1390  jsColumns.setValue(columns);
1391  data.setModelDim(null, columns);
1392  gallery.setColumns(columns);
1393 
1394  }
1395  }
1396 
1397 
1398 
1399  private void jsGoToImageStateChanged(javax.swing.event.ChangeEvent evt)
1400  {
1401  if (!isUpdating)
1402  {
1403  Integer oValue = ((Integer) jsGoToImage.getValue());
1404  Integer value = oValue;
1405  if (oValue <= 0)
1406  {
1407  value = 1;
1408  isUpdating = true;
1409  }
1410  else if (oValue >= gallery.getSize())
1411  {
1412  value = gallery.getSize();
1413  isUpdating = true;
1414  }
1415  if (oValue != value)
1416  jsGoToImage.setValue(value);
1417  if(oValue != 0 && oValue != gallery.getSelTo() + 1)//not me and not already selected
1418  goToImage(value - 1);
1419  }
1420  else
1421  isUpdating = false;
1422  }
1423 
1424  private void formComponentResized(java.awt.event.ComponentEvent evt)
1425  {
1426  width = getSize().width;
1427  if (!isUpdating && data.isAutoAdjust())
1428  {
1429  adjustColumns();
1430  }
1431  }
1432 
1433  public void selectItem(int row, int col)
1434  {
1435  if (row < 0 || row > table.getRowCount() - 1 || col < 0 || col > table.getColumnCount())
1436  return;
1437 
1438  if (gallery.data.isGalleryMode() && row * table.getColumnCount() + col + 1 > gallery.getSize())
1439  {
1440  Point coords = gallery.getCoords(gallery.getSize() - 1);
1441  row = coords.y;
1442  col = coords.x;
1443  }
1444  gallery.clearSelection();
1445  gallery.touchItem(row, col);
1446  makeVisible(row, col);
1447 
1448  }
1449 
1450  protected void tableMouseClicked(MouseEvent evt)
1451  {
1452  final Point p = evt.getPoint();
1453  int row = table.rowAtPoint(p);
1454  int col = table.columnAtPoint(p);
1455  col = table.convertColumnIndexToModel(col);
1456  int index = gallery.getIndex(row, col);
1457  if (!gallery.isValidIndex(index))
1458  return;
1459  if (evt.getButton() == MouseEvent.BUTTON1 && evt.getClickCount() > 1)
1460  {
1461  try
1462  {
1463  gallery.handleDoubleClick(row, col);
1464  }
1465  catch (Exception e)
1466  {
1467  XmippDialog.showError(this, e.getMessage());
1468  }
1469  }
1470  else
1471  {
1472  isUpdating = true;
1473  jsGoToImage.setValue(index + 1);
1474  isUpdating = false;
1475  // Ctrl adds items to selection, otherwise previous ones are removed.
1476  if (!evt.isControlDown() && !evt.isShiftDown())
1477  {
1478  if(evt.getButton() == MouseEvent.BUTTON1)
1479  {
1480  gallery.clearSelection();
1481  gallery.touchItem(row, col);
1482 
1483  }
1484  else
1485  {
1486  if(!gallery.isSelected(row, col))
1487  gallery.clearSelection();
1488  gallery.touchItem(row, col, true);
1489  }
1490 
1491  }
1492  else
1493  {
1494  if (evt.isShiftDown())
1495  gallery.selectRange(previousSelectedRow, previousSelectedCol, row, col);
1496  else if (evt.isControlDown())
1497  {
1498  gallery.touchItem(row, col);
1499  jsGoToImage.setValue(gallery.getSelTo() + 1);
1500  }
1501  }
1502 
1503  if (!evt.isShiftDown())
1504  {
1505  previousSelectedRow = row;
1506  previousSelectedCol = col;
1507  }
1508 
1509  final MouseEvent me = evt;
1510  if (evt.getButton() == MouseEvent.BUTTON3 && gallery.handleRightClick(row, col, jpopUpMenuTable))
1511  {
1512  SwingUtilities.invokeLater(new Runnable()
1513  {
1514  public void run()
1515  {
1516  jpopUpMenuTable.show(me.getComponent(), p);
1517  }
1518  });
1519  }
1520  }
1521  table.invalidate();
1522  table.repaint();
1523  refreshExtractFrame();
1524  }// function tableMouseClicked
1525 
1526  private void autoAdjustColumns(boolean autoadjust)
1527  {
1528  setAutoAdjustColumns(autoadjust);
1529  if(autoadjust)
1530  data.setModelDim(null, null);
1531  else
1532  {
1533  int rows = (Integer)jsRows.getValue();
1534  int cols = (Integer)jsColumns.getValue();
1535  if(rows > 0 && cols > 0)
1536  data.setModelDim(rows, cols);
1537  }
1538  adjustColumns();
1539  }
1540 
1541  private void setResliceView(int view)
1542  {
1543  data.setResliceView(view);
1544  reloadTableData();
1545  }
1546 
1547  protected void plotColumns() {
1548  PlotJDialog dlg = new PlotJDialog(GalleryJFrame.this);
1549  dlg.showDialog();
1550  }
1551 
1552  protected class GalleryMenu extends XmippMenuBarCreator
1553  {
1554 
1555  protected QuickHelpJDialog quickhelpdlg;
1556 
1557  @Override
1558  protected void createItems() throws Exception
1559  {
1560  // File
1561  addItem(FILE, "File");
1562  addItem(FILE_OPEN, "Open ...", null, "control released O");
1563  addItem(FILE_OPENWITH_IJ, "Open with ImageJ", "ij.gif", "control released J");
1564  addItem(FILE_OPENWITH_CHIMERA, "Open with ChimeraX", "chimera.png", "control released H");
1565  addItem(FILE_OPENMICROGRAPHS, "Open colored particles");
1566  addItem(FILE_INFO, "File info ...");
1567  addExtraMenuItems();
1568 
1569  addSeparator(FILE);
1570  addItem(FILE_SAVE, "Save", "save.gif", "control released S");
1571  addItem(FILE_SAVEAS, "Save as", "save_as.gif");
1572 
1573  addItem(FILE_EXPORTIMAGES, "Export images ...", "export_wiz.gif");
1574  addItem(FILE_REFRESH, "Refresh", "refresh.gif", "released F5");
1575  addSeparator(FILE);
1576  addItem(FILE_EXIT, "Exit", null, "control released Q");
1577  // Display
1578 
1579 
1580  addItem(DISPLAY, "Display");
1581  addItem(DISPLAY_APPLYGEO, "Apply geometry", null, "control released G");
1582  addItem(DISPLAY_WRAP, "Wrap", null, "control released W");
1583  addItem(DISPLAY_NORMALIZE, "Normalize", null, "control released N");
1584  addItem(DISPLAY_INVERTY, "Render positive Y up");
1585  addSeparator(DISPLAY);
1586  addItem(DISPLAY_RENDERIMAGES, "Render images", null, "control released R");
1587 
1588  addRenderImageColumnItems();
1589  addDisplayLabelItems();
1590 
1591  addItem(DISPLAY_RESLICE, "Reslice");
1592  for (int i = 0; i < ImageGeneric.VIEWS.length; ++i)
1593  addItem(DISPLAY_RESLICE_VIEWS[i], reslices[i]);
1594  addItem(DISPLAY_COLUMNS, "Columns ...", "columns.gif");
1595 
1596 
1597  addItem(TOOLS, "Tools");
1598  addItem(TOOLS_AVGSTD, "Avg & Std images");
1599  addItem(TOOLS_PCA, "PCA");
1600  addItem(TOOLS_FSC, "FSC");
1601  addItem(TOOLS_PLOT, "Plot", "plot.png");
1602  addItem(MD_FIND_REPLACE, "Find & Replace", "binocular.png", "control released F");
1603 
1604  // Metadata operations
1605  addItem(METADATA, "Metadata");
1606 
1607 
1608  addItem(MD_CLASSES, "Classes");
1609  addItem(MD_EDIT_COLS, "Edit labels", "edit.gif");
1610  addItem(MD_ADD_OBJECT, "Add new object", "new_object.gif");
1611  addItem(MD_REMOVE_DISABLED, "Remove disabled", "delete.gif");
1612  addItem(MD_REMOVE_SELECTION, "Remove selection");
1613  addItem(MD_SAVE_SELECTION, "Save state", "save.gif");
1614  addSeparator(METADATA);
1615  // Help
1616  addItem(HELP, "Help");
1617  addItem(HELP_ONLINE, "Online help", "online_help.gif");
1618  addItem(KEY_ASSIST, "Tips...", "bulb.png");
1619  }// function createItems
1620 
1621  //To insert extra items inside file menu
1622  public void addExtraMenuItems()
1623  {}
1624 
1625  public void update()
1626  {
1627 
1628  boolean isscipion = data.isScipionInstance();
1629  boolean galMode = data.isGalleryMode();
1630  boolean volMode = !data.getSelVolumeFile().isEmpty();
1631  setItemEnabled(FILE_OPENWITH_CHIMERA, volMode || data.containsGeometryInfo("3D")|| data.containsGeometryInfo("Projection"));
1632  setItemEnabled(FILE_OPENMICROGRAPHS, data.hasMicrographParticles());
1633  setItemEnabled(FILE_EXPORTIMAGES, data.hasRenderLabel() && !volMode);
1634  setItemEnabled(FILE_SAVE, !volMode && !isscipion);
1635  setItemEnabled(FILE_SAVEAS, !volMode && !isscipion);
1636 
1637  setItemEnabled(DISPLAY_APPLYGEO, data.containsGeometryInfo());
1638  setItemEnabled(DISPLAY_WRAP, data.containsGeometryInfo() && data.useGeo());
1639  setItemSelected(DISPLAY_WRAP, data.containsGeometryInfo() && data.isWrap());
1640  setItemSelected(DISPLAY_APPLYGEO, data.useGeo());
1641  setItemSelected(DISPLAY_INVERTY, data.isInvertY());
1642  setItemEnabled(DISPLAY_RENDERIMAGES, data.isTableMode() && data.isColumnFormat());
1643  setItemSelected(DISPLAY_RENDERIMAGES, data.renderImages());
1644  setItemEnabled(DISPLAY_SHOWLABELS, gallery.showLabels());
1645  setItemEnabled(DISPLAY_RENDERIMAGE, galMode);
1646  for (int i = 0; i < ImageGeneric.VIEWS.length; ++i)
1647  setItemSelected(DISPLAY_RESLICE_VIEWS[i], (data.getResliceView() == ImageGeneric.VIEWS[i]));
1648  setItemEnabled(DISPLAY_COLUMNS, !galMode);
1649  setItemEnabled(DISPLAY_RESLICE, data.isVolumeMode());
1650  setItemSelected(DISPLAY_NORMALIZE, data.getNormalized());
1651  setItemEnabled(MD_CLASSES, data.isClassificationMd());
1652  setItemEnabled(TOOLS_PLOT, data.isTableMode());
1653  boolean isCol = data.isColumnFormat();
1654  boolean doStats = isCol && !volMode;
1655  setItemEnabled(TOOLS_AVGSTD, doStats);
1656  setItemEnabled(TOOLS_FSC, doStats);
1657  setItemEnabled(TOOLS_PCA, doStats);
1658  setItemEnabled(MD_ADD_OBJECT, isCol);
1659  setItemEnabled(MD_REMOVE_DISABLED, isCol);
1660  setItemEnabled(MD_REMOVE_SELECTION, isCol);
1661  setItemEnabled(MD_SAVE_SELECTION, isCol);
1662  setItemEnabled(MD_FIND_REPLACE, isCol && !galMode);
1663  reslicebt.setEnabled(data.isVolumeMode());
1664  chimerabt.setEnabled(volMode && getChimera() != null);
1665  setItemVisible(METADATA, !isscipion);
1666  addDisplayLabelItems();
1667  addRenderImageColumnItems();
1668  }// function update
1669 
1670  @Override
1671  protected void handleActionPerformed(ActionEvent evt)
1672  {
1673  String cmd = evt.getActionCommand();
1674  try
1675  {
1676  if (cmd.equals(DISPLAY_INVERTY))
1677  {
1678  gallery.setInvertY(getItemSelected(DISPLAY_INVERTY));
1679  }
1680  else if (cmd.equals(DISPLAY_NORMALIZE))
1681  {
1682  gallery.setNormalized(getItemSelected(DISPLAY_NORMALIZE));
1683  }
1684  else if (cmd.equals(DISPLAY_APPLYGEO) || cmd.equals(DISPLAY_WRAP))
1685  {
1686  if (data.containsGeometryInfo())
1687  {
1688  ((MetadataGalleryTableModel) gallery).setUseGeometry(getItemSelected(DISPLAY_APPLYGEO), getItemSelected(DISPLAY_WRAP));
1689  setItemEnabled(DISPLAY_WRAP, data.containsGeometryInfo() && data.useGeo());
1690 
1691  }
1692  }
1693 
1694  else if (cmd.equals(DISPLAY_RENDERIMAGES))
1695  {
1696  if(gallery instanceof MetadataTableModel)
1697  {
1698  ((MetadataTableModel) gallery).setRenderImages(getItemSelected(DISPLAY_RENDERIMAGES));
1699  setItemEnabled(DISPLAY_SHOWLABELS, gallery.showLabels());
1700  btnChangeView.setEnabled(data.hasRenderLabel() && data.renderImages());
1701  }
1702  makeVisible(gallery.getFirstSelectedIndex(), 0);
1703  }
1704 
1705  else if (cmd.equals(DISPLAY_COLUMNS))
1706  {
1707  ColumnsJDialog dialog = new ColumnsJDialog(GalleryJFrame.this);
1708  boolean result = dialog.showDialog();
1709  if (result)
1710  {
1711  List<ColumnInfo> columns = dialog.getColumnsResult();
1712  isUpdating = true;
1713  ((MetadataGalleryTableModel) gallery).updateColumnInfo(columns);
1714  gallery.fireTableDataChanged();
1715  //setItemEnabled(DISPLAY_RENDERIMAGES, data.renderImages());
1716  // menu.enableRenderImages(data.globalRender);
1717  isUpdating = false;
1718  }
1719  }
1720  else if (cmd.equals(TOOLS_AVGSTD))
1721  runInBackground(Worker.STATS);
1722  else if (cmd.equals(TOOLS_PCA))
1723  runInBackground(Worker.PCA);
1724  else if (cmd.equals(TOOLS_FSC))
1725  runInBackground(Worker.FSC);
1726  else if (cmd.equals(FILE_OPEN))
1727  {
1728  fc.setDialogTitle("Open");
1729  fc.setApproveButtonToolTipText("File to open");
1730  fc.setApproveButtonText("Open");
1731  if (fc.showOpenDialog(GalleryJFrame.this) != XmippFileChooser.CANCEL_OPTION)
1732  {
1733  if (Filename.exists(fc.getSelectedFile().getPath()))
1734  ImagesWindowFactory.openFileAsDefault(fc.getSelectedPath());
1735  else
1736  XmippDialog.showError(GalleryJFrame.this, String.format("File: '%s' doesn't exist.", fc.getSelectedPath()));
1737  }
1738  }
1739  else if (cmd.equals(FILE_SAVE))
1740  {
1741  save();
1742  }
1743  else if (cmd.equals(FILE_SAVEAS))
1744  {
1745  saveAs();
1746  }
1747  else if (cmd.equals(FILE_EXPORTIMAGES))
1748  {
1749  exportImages();
1750  }
1751  else if (cmd.equals(FILE_EXIT))
1752  {
1753  close();
1754  }
1755  else if (cmd.equals(FILE_OPENWITH_CHIMERA))
1756  {
1757  openWithChimera();
1758  }
1759  else if (cmd.equals(FILE_OPENMICROGRAPHS))
1760  {
1761  openMicrographs();
1762  }
1763 
1764  else if (cmd.equals(FILE_INFO))
1765  {
1766  XmippDialog.showInfo(GalleryJFrame.this, data.getFileInfo());
1767  }
1768 
1769  else if (cmd.equals(FILE_OPENWITH_IJ))
1770  {
1771  try
1772  {
1773  XmippUtil.showImageJ(Tool.VIEWER);
1774  ImagePlusLoader loader = gallery.getImageLoader();
1775  ImagesWindowFactory.openXmippImageWindow(loader, data.parameters);
1776  }
1777  catch (Exception e1)
1778  {
1779  e1.printStackTrace();
1780  }
1781  }
1782  else if (cmd.equals(FILE_REFRESH))
1783  {
1784  data.readMd();
1785  reloadTableData();
1786 
1787  }
1788  else if (cmd.contains(DISPLAY_RESLICE))
1789  {
1790  for (int i = 0; i < ImageGeneric.VIEWS.length; ++i)
1791  if (cmd.equals(DISPLAY_RESLICE_VIEWS[i]))
1792  {
1793  setResliceView(ImageGeneric.VIEWS[i]);
1794  break;
1795  }
1796  }
1797  else if (cmd.equals(TOOLS_PLOT))
1798  {
1799  plotColumns();
1800  }
1801  else if (cmd.equals(MD_CLASSES))
1802  {
1803  openClassesDialog();
1804  }
1805  else if (cmd.equals(MD_EDIT_COLS))
1806  {
1807  EditLabelsJDialog dlg = new EditLabelsJDialog(GalleryJFrame.this);
1808  dlg.showDialog();
1809  }
1810  else if (cmd.equals(MD_REMOVE_SELECTION))
1811  {
1812  if (gallery.getSelectionCount() > 0)
1813  removeObjects(true);
1814  }
1815  else if (cmd.equals(MD_REMOVE_DISABLED))
1816  {
1817  removeObjects(false);
1818  }
1819  else if (cmd.equals(MD_SAVE_SELECTION))
1820  {
1821  if(gallery.hasSelection())
1822  data.saveSelection(gallery.getSelection());
1823  }
1824  else if (cmd.equals(MD_FIND_REPLACE))
1825  {
1826  findReplace();
1827  }
1828  else if (cmd.equals(MD_ADD_OBJECT))
1829  {
1830  boolean added = data.addObject();
1831  if(added)
1832  reloadMd();
1833  }
1834  else if (cmd.equals(HELP_ONLINE))
1835  {
1836  XmippWindowUtil.openURI("http://github.com/I2PC/scipion/wiki/ShowJ");
1837  }
1838  else if (cmd.equals(KEY_ASSIST))
1839  {
1840  if (quickhelpdlg == null)
1841  quickhelpdlg = new QuickHelpJDialog(GalleryJFrame.this, false, "Tips", getKeyAssist());
1842  quickhelpdlg.setVisible(true);
1843 
1844  }
1845 
1846  }
1847  catch (Exception e)
1848  {
1849  showException(e);
1850  }
1851  }// function handleActionPerformed
1852 
1853 
1854  protected void addRenderImageColumnItems()
1855  {
1856  JMenuItem mi = getItem(DISPLAY_RENDERIMAGE);
1857  if(mi == null)
1858  mi = addItem(DISPLAY_RENDERIMAGE, "Render label");
1859  else
1860  mi.removeAll();
1861  boolean rendercolumn = false;
1862 
1863  // Create the popup menu.
1864  String id, column;
1865  for(ColumnInfo ci: data.getColumns())
1866  {
1867  if(ci.render)
1868  {
1869  column = ci.labelName;
1870  id = String.format("Display.RenderImage.%s_rb", column.replace(".", ""));
1871  mi = addItem(id, column);
1872  mi.addActionListener(new RenderColumnActionListener());
1873  if(data.getRenderColumn().toString().equals(column))
1874  setItemSelected(id, true);
1875  rendercolumn = true;
1876  }
1877  }
1878  setItemEnabled(DISPLAY_RENDERIMAGE, rendercolumn);
1879 
1880  }
1881 
1882  protected void addDisplayLabelItems()
1883  {
1884  JMenuItem mi = getItem(DISPLAY_SHOWLABELS);
1885  if(mi == null)
1886  mi = addItem(DISPLAY_SHOWLABELS, "Display label");
1887  else
1888  mi.removeAll();
1889 
1890  // Create the popup menu.
1891  String id, column;
1892  List<String> displayLabels = null;
1893  if(data.parameters.getDisplayLabels() != null)
1894  displayLabels = Arrays.asList(data.parameters.getDisplayLabels());
1895  for(ColumnInfo ci: data.getColumns())
1896  {
1897  if(ci.visible)
1898  {
1899  column = ci.labelName;
1900  id = String.format("Display.ShowLabel.%s_cb", column.replace(".", ""));
1901  mi = addItem(id, column);
1902  mi.addActionListener(new DisplayLabelActionListener());
1903 
1904  if(displayLabels!= null && displayLabels.contains(column))
1905  setItemSelected(id, true);
1906  }
1907  }
1908 
1909  }
1910 
1911 
1912 
1913  class DisplayLabelActionListener implements ActionListener
1914  {
1915 
1916  @Override
1917  public void actionPerformed(ActionEvent e)
1918  {
1919  JCheckBoxMenuItem mi = (JCheckBoxMenuItem)e.getSource();
1920  String key = mi.getText();
1921 
1922  data.setDisplayLabel(key, mi.isSelected());
1923  gallery.setShowLabels();
1924  }
1925 
1926  }
1927 
1928 
1929  class RenderColumnActionListener implements ActionListener
1930  {
1931 
1932  @Override
1933  public void actionPerformed(ActionEvent e)
1934  {
1935  JRadioButtonMenuItem mi = (JRadioButtonMenuItem)e.getSource();
1936  String key = mi.getText();
1937  data.setRenderColumn(key);
1938 
1939  reloadTableData();
1940  }
1941 
1942  }
1943 
1944  }// class GalleryMenu //////////////////////////////////////////////////////////
1945 
1946  class GalleryPopupMenu extends XmippPopupMenuCreator
1947  {
1948  protected int row;
1949  protected int col;
1950 
1951  @Override
1952  protected void createItems()
1953  {
1954  addItem(ENABLED, "Enable", "enable.gif");
1955  addItem(DISABLED, "Disable", "disable.gif");
1956  addItem(REFRESH, "Refresh", "refresh.gif");
1957  // addSeparator();
1958  addItem(OPEN, "Open");
1959  addItem(OPEN_ASTEXT, "Open as text");
1960  addItem(CTF_PROFILE, "Show CTF profile");
1961  if(data.parameters.recalculateCTF) {
1962  addItem(CTF_RECALCULATE, "Recalculate CTF");
1963  setItemSelected(CTF_RECALCULATE, data.isRecalculateCTF(gallery.getIndex(row, col)));
1964  }
1965  addSeparator();
1966  addItem(OPEN_IMAGES, "Open images");
1967  addItem(SAVE_IMAGES, "Save images", "save.gif");
1968  addItem(SET_CLASS, "Set class");
1969  addItem(SELECT, "Select");
1970  addItem(SELECT_ALL, "All", null, "control released A");
1971  addItem(SELECT_TOHERE, "To here");
1972  addItem(SELECT_FROMHERE, "From here");
1973  addItem(INVERT_SELECT, "Invert selection");
1974  if(data.parameters.objectCommands != null)
1975  for(String cmd: data.parameters.objectCommands)
1976  addItem(cmd + "_mi", cmd);
1977  initItems();
1978  }// function createItems
1979 
1980  public void show(Component cmpnt, Point location)
1981  {
1982  row = table.rowAtPoint(location);
1983  col = table.columnAtPoint(location);
1984  col = table.convertColumnIndexToModel(col);
1985  boolean isscipion = data.isScipionInstance();
1986  setItemVisible(SET_CLASS, data.isClassificationMd() && !isscipion);
1987  // This item visibility depends on current selection
1988  setItemVisible(SAVE_IMAGES, data.isClassificationMd() && gallery.getSelectionCount() > 0 && !isscipion);
1989  setItemVisible(OPEN_IMAGES, data.hasClasses() && gallery.getSelectionCount() == 1);
1990  if(data.parameters.recalculateCTF){
1991  setItemSelected(CTF_RECALCULATE, data.isRecalculateCTF(gallery.getIndex(row, col)));
1992  }
1993  // Update menu items status depending on item.
1994  getPopupMenu().show(cmpnt, location.x, location.y);
1995 
1996  }// function show
1997 
1998  private void selectRange(int first, int last)
1999  {
2000  gallery.selectRange(first, last, true);
2001  jsGoToImage.setValue(gallery.getSelTo() + 1);
2002  }
2003 
2004 
2005 
2007  @Override
2008  public void initItems()
2009  {
2010  setItemVisible(OPEN, false);
2011  setItemVisible(OPEN_ASTEXT, false);
2012  setItemVisible(CTF_PROFILE, data.isCTFMd());
2013  if(data.parameters.recalculateCTF) setItemVisible(CTF_RECALCULATE, data.isCTFMd());
2014  }
2015 
2016  @Override
2017  protected void handleActionPerformed(ActionEvent evt)
2018  {
2019  String cmd = evt.getActionCommand();
2020  switch (cmd) {
2021  case SELECT_ALL:
2022  selectRange(0, gallery.getSize() - 1);
2023  break;
2024  case SELECT_TOHERE:
2025  selectRange(0, gallery.getIndex(row, col));
2026  break;
2027  case SELECT_FROMHERE:
2028  selectRange(gallery.getIndex(row, col), gallery.getSize() - 1);
2029  break;
2030  case INVERT_SELECT:
2031  for (int i = 0; i < data.size(); i++)
2032  gallery.setSelected(i, !gallery.isSelected(i));
2033  gallery.fireTableDataChanged();
2034  jsGoToImage.setValue(gallery.getSelTo() + 1);
2035  break;
2036  case ENABLED:
2037  gallery.setSelectionEnabled(true);
2038  // gallery.clearSelection();
2039  refreshExtractFrame();
2040 
2041  break;
2042  case DISABLED:
2043  gallery.setSelectionEnabled(false);
2044  // gallery.clearSelection();
2045  refreshExtractFrame();
2046 
2047  break;
2048  case REFRESH:
2049  gallery.refreshAt(row, col);
2050  break;
2051  case OPEN:
2052 
2053  ColumnInfo ci = gallery.getColumn(row, col);
2054  if (ci.allowRender)
2055  gallery.handleDoubleClick(row, col);
2056  else {
2057  int index = gallery.getIndex(row, col);
2058  String file = data.getValueFromCol(index, ci);
2059  ImagesWindowFactory.openFileAsDefault(file);
2060  }
2061  break;
2062  case OPEN_ASTEXT:
2063  String file = gallery.getValueAt(row, col).toString();
2064  ImagesWindowFactory.openFileAsText(file, null);
2065  break;
2066  case CTF_PROFILE: {
2067  int index = gallery.getIndex(row, col);
2068  data.showCTF(true, index, gallery.getSelection(), ctfTasks);
2069  break;
2070  }
2071  case CTF_RECALCULATE: {
2072  boolean isrecalculate = getItemSelected(CTF_RECALCULATE);
2073  int index = gallery.getIndex(row, col);
2074  if (isrecalculate && !data.isEnabled(index))
2075  XmippDialog.showInfo(GalleryJFrame.this, "You must enable micrograph to recalculate its CTF");
2076  else {
2077  if (isrecalculate)
2078  data.showCTF(false, index, gallery.getSelection(), ctfTasks);
2079  else
2080  data.removeCTF(row);
2081  }
2082 
2083  break;
2084  }
2085  case SET_CLASS:
2086  if (openClassesDialog()) {
2087  int classNumber = dlgClasses.getSelectedClass();
2088  // DEBUG.printMessage(String.format("class: %d",
2089  // classNumber));
2090  gallery.setSelectionClass(classNumber);
2091  }
2092  break;
2093  case OPEN_IMAGES: {
2094  int index = gallery.getIndex(row, col);
2095  MetaData md = data.getClassImages(index);
2096  if (md != null)
2097  openMetadata(md);
2098  else
2099  XmippDialog.showWarning(GalleryJFrame.this, "This class has no images");
2100  break;
2101  }
2102  case SAVE_IMAGES:
2103  if (gallery.hasSelection()) {
2104  File f = new File(data.getFileName());
2105  SaveImagesJDialog dialog = new SaveImagesJDialog(GalleryJFrame.this, f.getParent() + "/images_selection.xmd");
2106  dialog.showDialog();
2107  }
2108  break;
2109  default:
2110  String objectCommand = cmd.replace("_mi", "");
2111  if (data.isObjectCmd(objectCommand)) {
2112  int index = gallery.getIndex(row, col);
2113  data.runObjectCommand(index, objectCommand);
2114  }
2115  break;
2116  }
2117  initItems();
2118 
2119  }
2120 
2121  }// class JPopUpMenuGallery
2122 
2123  public void showException(Exception e)
2124  {
2125  XmippDialog.showException(this, e);
2126  }
2127 
2128  @Override
2129  public void setRunning(boolean running)
2130  {
2131  // XmippDialog.showInfo(this, String.format("Calculating ctf"));
2132  // XmippWindowUtil.blockGUI(getRootPane(), "Calculating CTF");
2133  }
2134 
2135  @Override
2136  public void setRowBusy(int row)
2137  {
2138 
2139  gallery.setRowBusy(row);
2140  }
2141 
2142  @Override
2143  public void setRowIdle(int row)
2144  {
2145  gallery.setRowIdle(row);
2146 
2147  }
2148 
2149 
2150 
2151  @Override
2152  public void done()
2153  {
2154  XmippDialog.showInfo(this, "Calculating ctf: DONE");
2155  }
2156 
2157  protected void saveMd() throws Exception
2158  {
2159  saveMd(dlgSave.getMdFilename(), false, dlgSave.isOverwrite(), true );
2160  }
2161 
2162 
2163 
2164  protected void saveMd(String path, boolean saveall, boolean isoverwrite, boolean reload)
2165  {
2166  try
2167  {
2168  data.saveMd(path, saveall, isoverwrite);
2169  String file;
2170  if (path.contains("@"))
2171  file = path.substring(path.lastIndexOf("@") + 1);
2172  else
2173  {
2174  file = path;
2175  path = getBlock() + "@" + file;
2176  }
2177  if(reload)
2178  {
2179  gallery.data.setFileName(file);
2180  if (path.contains("@"))
2181  gallery.data.selectBlock(path.substring(0, path.lastIndexOf("@")));
2182  reloadFile(file, false);
2183  setGalleryTitle();
2184  }
2185  }
2186  catch (Exception e)
2187  {
2188  e.printStackTrace();
2189  }
2190  }// function saveMd
2191 
2192 
2193 
2194  public String getFilename()
2195  {
2196  return data.getFileName();
2197  }
2198 
2199 
2200  private void saveAll() throws Exception
2201  {
2202  data.saveAll(dlgSave.getMdFilename(), dlgSave.isOverwrite());
2203  this.saved = true;
2204 // reloadFile(to, false);
2205  reloadCombos();
2206  setGalleryTitle();
2207  }
2208 
2209  private void save() throws Exception
2210  {
2211  if (!saved)
2212  saveAs();
2213  else
2214  {
2215  if (dlgSave.saveActiveMetadataOnly())
2216  saveMd();
2217  else
2218  saveAll();
2219  }
2220  }// function save
2221 
2222  private void saveAs() throws Exception
2223  {
2224  if (dlgSave == null)
2225  dlgSave = new SaveJDialog(this, data.getMdSaveFileName(), false);
2226  else
2227  dlgSave.setMdFilename(data.getMdFilename());
2228  boolean save = dlgSave.showDialog(); // displays dialog and waits until
2229  // save or cancel clicked
2230  if (save)
2231  {
2232  if (dlgSave.saveActiveMetadataOnly())
2233  saveMd();
2234  else
2235  saveAll();
2236 
2237 
2238  }
2239 
2240  }
2241 
2242  private void exportImages()
2243  {
2244  SwingUtilities.invokeLater(new Runnable() {
2245 
2246  @Override
2247  public void run() {
2248  ExportImagesJDialog d = new ExportImagesJDialog(GalleryJFrame.this);
2249  }
2250  });
2251  }
2252 
2253  public void openMicrographs()
2254  {
2255  if (extractframe == null || !extractframe.isVisible())
2256  extractframe = ExtractParticlePicker.open(getBlock(), data.getFileName(), gallery.getImageWidth(), this);
2257  refreshExtractFrame();
2258  }
2259 
2260  private void refreshExtractFrame()
2261  {
2262 
2263  if (extractframe == null || !extractframe.isVisible())
2264  return;
2265  for (int i = 0; i < data.size(); i++)
2266  if (gallery.isSelected(i))
2267  extractframe.refreshActive(data.getId(i), data.isEnabled(i));
2268 
2269  }
2270 
2271  public void refreshActive(long id, boolean enabled)
2272  {
2273  for (int i = 0; i < data.size(); i++)
2274  if (id == data.getId(i))
2275  {
2276  goToImage(i);
2277  gallery.setSelectionEnabled(enabled);
2278  }
2279 
2280  }
2281 
2282  public String getBlock()
2283  {
2284  return (String) jcbBlocks.getSelectedItem();
2285  }
2286 
2287  public void reloadFile(String file, boolean changed) throws Exception
2288  {
2289  createModel(gallery.getSelection());
2290  reloadMd(changed);
2291  reloadCombos();
2292  }
2293 
2294  private void reloadCombos(){
2295  createCombos();
2296  updateVisibleCombos();
2297  jcbBlocks.setSelectedItem(gallery.data.getSelectedBlock());
2298 
2299  }
2300 
2301  protected void initResliceButtonMenu()
2302  {
2303  // Create the popup menu.
2304  String reslice;
2305  final JPopupMenu popup = new JPopupMenu();
2306  JRadioButtonMenuItem mi;
2307  reslicegroup = new ButtonGroup();
2308  for (int i = 0; i < reslices.length; i++)
2309  {
2310  reslice = reslices[i];
2311  mi = new JRadioButtonMenuItem(reslice);
2312  reslicegroup.add(mi);
2313  if (i == 0)
2314  reslicegroup.setSelected(mi.getModel(), true);
2315  mi.setActionCommand(String.valueOf(ImageGeneric.VIEWS[i]));
2316  popup.add(mi);
2317  mi.addActionListener(new ResliceActionListener());
2318 
2319  }
2320  reslicebt = new JButton(XmippResource.getIcon("topview.png"));
2321  reslicebt.setToolTipText("Reslice");
2322  reslicebt.setContentAreaFilled(false);
2323  reslicebt.setFocusPainted(false);
2324  reslicebt.setOpaque(false);
2325 
2326  reslicebt.addMouseListener(new MouseAdapter()
2327  {
2328  public void mousePressed(MouseEvent e)
2329  {
2330  popup.show(e.getComponent(), e.getX(), e.getY());
2331  }
2332  });
2333 
2334  }
2335 
2336 
2337  class ResliceActionListener implements ActionListener
2338  {
2339 
2340  @Override
2341  public void actionPerformed(ActionEvent e)
2342  {
2343  JRadioButtonMenuItem mi = (JRadioButtonMenuItem) e.getSource();
2344  int view = Integer.parseInt(mi.getActionCommand());
2345  setResliceView(view);
2346  reslicegroup.setSelected(mi.getModel(), true);
2347  }
2348 
2349  }
2350 
2351  public Map<Object, Object> getKeyAssist()
2352  {
2353  Map<Object, Object> map = Collections.synchronizedMap(new LinkedHashMap<>());
2354  map.put("Shift + scroll up/ctrl + P", "Zoom in if images displayed");
2355  map.put("Shift + scroll down/ctrl + M", "Zoom out if images displayed");
2356  map.put("Left click", "Selects a cell in gallery mode and a row in table mode");
2357  map.put("Right click", "Selects a row in table mode and displays row menu");
2358  map.put("Supr", "Delete selected cell in gallery mode and row in table mode");
2359  map.put("Up", "Select previous row in table mode and cell in previous row in gallery mode");
2360  map.put("Down", "Select next row in table mode and cell in next row in gallery mode");
2361  map.put("Left", "Select previous cell in gallery mode");
2362  map.put("Right", "Select next cell in gallery mode");
2363  map.put("Ctrl + O", "Open file");
2364  map.put("Ctrl + J", "Open with ImageJ");
2365  map.put("Ctrl + S", "Save");
2366  map.put("F5", "Refresh");
2367  map.put("Ctrl + Q", "Exit");
2368  map.put("Ctrl + N", "Display global normalization");
2369  map.put("Ctrl + L", "Display labels");
2370  map.put("Ctrl + R", "Render images");
2371  map.put("Ctrl + G", "Apply geometry");
2372  map.put("Ctrl + W", "Wrap");
2373  map.put("Space Bar", "Enable/Disable selection");
2374 
2375  return map;
2376  }
2377 
2378  public TasksEngine getTasksEngine()
2379  {
2380  return ctfTasks;
2381  }
2382 
2383 
2384 
2385  protected void openChimera(String file, boolean link)
2386  {
2387  try
2388  {
2389  // CHIMERA_LAUNCHER will be any String ready to place a file name having %1 in it
2390  String chimera_launcher = getChimera();
2391  if(chimera_launcher == null)
2392  {
2393  XmippDialog.showError(GalleryJFrame.this, "ChimeraX is not available");
2394  return;
2395  }
2396 
2397  // There must be a better way to "clean" :mrc annotations
2398  if(file.endsWith(":mrc"))
2399  file = file.replace(":mrc", "");
2400 
2401  // make file absolute
2402  // Create a file object
2403  File f = new File(file);
2404 
2405  String run = String.format(chimera_launcher, f.getAbsolutePath());
2406  HashMap<String, String> chimeraEnv = new HashMap<String, String>() {
2407  {
2408  put("LD_LIBRARY_PATH", "");
2409  }
2410  };
2411  String output = XmippWindowUtil.executeCommand(run, false, chimeraEnv);
2412 
2413  }
2414  catch (Exception ex)
2415  {
2416  ex.printStackTrace();
2417  }
2418  }
2419 
2420  private String getChimera() {
2421  return System.getenv().get(CHIMERA_LAUNCHER);
2422  }
2423 
2424  protected void openWithChimera()
2425  {
2426  if(data.containsGeometryInfo("3D") || data.containsGeometryInfo("Projection") )
2427  {
2428  fc.setApproveButtonText("Open");
2429  fc.setDialogTitle("Open with ChimeraX");
2430  fc.setApproveButtonToolTipText("Choose a chimera compatible file.");
2431  int result = fc.showOpenDialog(GalleryJFrame.this);
2432  if(result != XmippFileChooser.CANCEL_OPTION)
2433  {
2434  String path = fc.getSelectedPath();
2435  if(!Filename.isVolumeExt(path))
2436  {
2437  XmippDialog.showError(GalleryJFrame.this, XmippMessage.getFileTypeNotSupportedMsg(path));
2438  return;
2439  }
2440  openChimera(path, true);
2441  }
2442  }
2443  else
2444  openChimera(data.getSelVolumeFile(), false);
2445  }
2446 
2447 
2448 
2449 }// class JFrameGallery
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xmipp.viewer.models.GalleryData.setDisplayLabel
void setDisplayLabel(String key, boolean selected)
Definition: GalleryData.java:361
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xmipp.viewer.models.ImageGalleryTableModel.selectRange
void selectRange(int first_index, int last_index, boolean value)
Definition: ImageGalleryTableModel.java:421
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xmipp.viewer.windows.GalleryJFrame.setAutoAdjustColumns
void setAutoAdjustColumns(boolean autoAdjustColumns)
Definition: GalleryJFrame.java:734
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xmipp.utils.XmippWindowUtil.blockGUI
static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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xmipp.viewer.windows.GalleryJFrame.getKeyAssist
Map< Object, Object > getKeyAssist()
Definition: GalleryJFrame.java:2351
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xmipp.viewer.models.GalleryData.selectVolumeAt
void selectVolumeAt(int selectedIndex)
Definition: GalleryData.java:167
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xmipp.viewer.windows.Worker.FSC
static final int FSC
Definition: Worker.java:29
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xmipp.viewer.windows.ImagesWindowFactory.openFileAsDefault
static void openFileAsDefault(String filename)
Definition: ImagesWindowFactory.java:53
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xmipp.viewer.windows.GalleryJFrame.tableMouseClicked
void tableMouseClicked(MouseEvent evt)
Definition: GalleryJFrame.java:1450
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xmipp.viewer.windows.GalleryJFrame.reloadTableData
void reloadTableData(boolean changed, boolean[] selection)
Definition: GalleryJFrame.java:862
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xmipp.viewer.models.GalleryData.getClassImages
MetaData getClassImages(int index)
Definition: GalleryData.java:1081
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xmipp.utils.XmippLabel.MSG_ADJUST_COLS
static final String MSG_ADJUST_COLS
Definition: XmippLabel.java:269
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xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
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xmipp.jni.Filename.hasPrefix
static boolean hasPrefix(String filename)
Definition: Filename.java:331
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xmipp.utils.XmippLabel.LABEL_VIEW_GALLERY
static final String LABEL_VIEW_GALLERY
Definition: XmippLabel.java:209
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xmipp.viewer.windows.GalleryJFrame.fireTableRowsUpdated
void fireTableRowsUpdated(int from, int to)
Definition: GalleryJFrame.java:502
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xmipp.viewer.models.GalleryData.isObjectCmd
boolean isObjectCmd(String cmd)
Definition: GalleryData.java:127
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xmipp.viewer.models.GalleryData.fillConstant
void fillConstant(int label, String value)
Definition: GalleryData.java:1399
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xmipp.jni.Filename.getBaseName
static String getBaseName(String path)
Definition: Filename.java:458
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xmipp.viewer.models.ImageGalleryTableModel.handleRightClick
abstract boolean handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)
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xmipp.viewer.windows.GalleryJFrame.reloadFile
void reloadFile(String file, boolean changed)
Definition: GalleryJFrame.java:2287
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xmipp.viewer.models.GalleryData.createModel
ImageGalleryTableModel createModel(boolean[] selection)
Definition: GalleryData.java:665
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xmipp.viewer.models.GalleryData.setEnabled
void setEnabled(int index, boolean value)
Definition: GalleryData.java:805
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xmipp.utils.XmippMessage.getFileTypeNotSupportedMsg
static String getFileTypeNotSupportedMsg(String path)
Definition: XmippMessage.java:93
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xmipp.viewer.windows.GalleryJFrame.removeObjects
void removeObjects(boolean selected)
Definition: GalleryJFrame.java:944
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xmipp.utils.XmippDialog.showException
boolean showException(Exception e)
Definition: XmippDialog.java:217
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xmipp.utils.XmippLabel.LABEL_BLOCK
static final String LABEL_BLOCK
Definition: XmippLabel.java:231
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xmipp.jni.Filename.isVolumeExt
static boolean isVolumeExt(String filename)
Definition: Filename.java:146
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xmipp.viewer.windows.Worker.STATS
static final int STATS
Definition: Worker.java:27
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xmipp.utils.XmippLabel.LABEL_ZOOM
static final String LABEL_ZOOM
Definition: XmippLabel.java:228
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xmipp.viewer.windows.GalleryJFrame.refreshActive
void refreshActive(long id, boolean enabled)
Definition: GalleryJFrame.java:2271
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xmipp.viewer.models.GalleryData.setModelDim
void setModelDim(Integer rows, Integer cols)
Definition: GalleryData.java:187
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xmipp.utils.XmippWindowUtil.centerWindows
static void centerWindows(Window w)
Definition: XmippWindowUtil.java:94
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xmipp.ij.commons.XmippUtil.showImageJ
static XmippImageJ showImageJ(Tool tool)
Definition: XmippUtil.java:28
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xmipp.viewer.windows.Worker.PCA
static final int PCA
Definition: Worker.java:28
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Definition: Params.java:313
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void fillLinear(int label, Double start, Double step)
Definition: GalleryData.java:1403
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xmipp.viewer.windows.ImagesWindowFactory.openFileAsText
static void openFileAsText(String filename, Component parent)
Definition: ImagesWindowFactory.java:281
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void saveMd(String path, boolean saveall, boolean isoverwrite)
Definition: GalleryData.java:1573
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xmipp.viewer.windows.GalleryJFrame.fillLabel
void fillLabel(int label, String mode, String... values)
Definition: GalleryJFrame.java:920
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xmipp.viewer.windows.GalleryJFrame.openChimera
void openChimera(String file, boolean link)
Definition: GalleryJFrame.java:2385
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void setSelected(int index, boolean isselected)
Definition: ImageGalleryTableModel.java:770
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xmipp.viewer.particlepicker.extract.ExtractParticlePicker.open
static ExtractPickerJFrame open(String block, String filename, int size, GalleryJFrame galleryfr)
Definition: ExtractParticlePicker.java:220
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xmipp.utils.XmippWindowUtil.executeCommand
static String executeCommand(String[] command, boolean wait)
Definition: XmippWindowUtil.java:276
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xmipp.utils.DEBUG.printFormat
static void printFormat(String format, Object...objects)
Definition: DEBUG.java:24
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abstract ImagePlusLoader getImageLoader()
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void setWindow(GalleryJFrame frame)
Definition: GalleryData.java:1642
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.jni.MetaData.FILL_LINEAR
static final String FILL_LINEAR
Definition: MetaData.java:54
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xmipp.viewer.windows.GalleryJFrame.createModel
void createModel(boolean[] selection)
Definition: GalleryJFrame.java:284
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xmipp.viewer.models.GalleryData.showCTF
void showCTF(boolean profile, int row, boolean[] selection, TasksEngine ctfTasks)
Definition: GalleryData.java:1742
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xmipp.viewer.models.ImageGalleryTableModel.handleDoubleClick
abstract boolean handleDoubleClick(int row, int col)
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xmipp.viewer.models.GalleryData.selectBlock
void selectBlock(String block)
Definition: GalleryData.java:654
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xmipp.jni.Filename.exists
static boolean exists(String path)
Definition: Filename.java:266
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xmipp.utils.XmippLabel.LABEL_VIEW_MD
static final String LABEL_VIEW_MD
Definition: XmippLabel.java:208
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xmipp.utils.XmippResource.VIEW_GALLERY_ICON
static ImageIcon VIEW_GALLERY_ICON
Definition: XmippResource.java:49
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xmipp.utils.XmippResource.VIEW_MD_ICON
static ImageIcon VIEW_MD_ICON
Definition: XmippResource.java:48
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xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(MetaData md, Params parameters)
Definition: GalleryJFrame.java:242
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xmipp.utils.XmippWindowUtil.setScipionImageIcon
static void setScipionImageIcon(Window w)
Definition: XmippWindowUtil.java:389
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xmipp.utils.XmippResource.getIcon
static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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xmipp.utils.Params.recalculateCTF
boolean recalculateCTF
Definition: Params.java:93
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xmipp.utils.XmippLabel.LABEL_COLUMNS
static final String LABEL_COLUMNS
Definition: XmippLabel.java:230
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xmipp.viewer.windows.GalleryJFrame.reloadTableData
void reloadTableData(boolean[] selection)
Definition: GalleryJFrame.java:856
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xmipp.utils.XmippLabel.LABEL_ROWS
static final String LABEL_ROWS
Definition: XmippLabel.java:229
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xmipp.viewer.models.GalleryData.fillRandom
void fillRandom(int label, String mode, double op1, double op2)
Definition: GalleryData.java:1407
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xmipp.utils.DEBUG.printException
static void printException(Exception ex)
Definition: DEBUG.java:30
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xmipp.viewer.models.GalleryData.getValueFromCol
String getValueFromCol(int index, int col)
Definition: GalleryData.java:1173
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xmipp.utils.Params.objectCommands
String [] objectCommands
Definition: Params.java:88
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xmipp.utils.XmippResource.ADJUST_COLS
static final String ADJUST_COLS
Definition: XmippResource.java:37
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xmipp.viewer.windows.ImagesWindowFactory.openXmippImageWindow
static XmippIJWindow openXmippImageWindow(ImagePlus imp, Params params)
Definition: ImagesWindowFactory.java:134
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xmipp.jni.MetaData.FILL_RAND_GAUSSIAN
static final String FILL_RAND_GAUSSIAN
Definition: MetaData.java:56
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xmipp.utils.XmippDialog.showWarning
boolean showWarning(String message)
Definition: XmippDialog.java:205
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xmipp.viewer.models.GalleryData.removeSelection
void removeSelection(boolean[] selection)
Definition: GalleryData.java:1211
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xmipp.utils.XmippDialog.showQuestionYesNoCancel
static int showQuestionYesNoCancel(JFrame parent, String message)
Definition: XmippDialog.java:274
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.utils.XmippWindowUtil.getScreenRectangle
static Rectangle getScreenRectangle()
Definition: XmippWindowUtil.java:82
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xmipp.utils.XmippLabel.LABEL_GOTO_ITEM
static final String LABEL_GOTO_ITEM
Definition: XmippLabel.java:233
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xmipp.viewer.models.GalleryData.saveSelection
void saveSelection(boolean[] selection)
Definition: GalleryData.java:1353
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xmipp.viewer.windows.GalleryJFrame.openMetadata
void openMetadata(final MetaData md)
Definition: GalleryJFrame.java:257
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xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
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xmipp.viewer.models.GalleryData.getColumns
List< ColumnInfo > getColumns()
Definition: GalleryData.java:293
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xmipp.viewer.models.GalleryData.saveAll
void saveAll(String path, boolean overwrite)
Definition: GalleryData.java:1525
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xmipp.utils.XmippResource.ZOOM
static final String ZOOM
Definition: XmippResource.java:39
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xmipp.viewer.windows.GalleryJFrame.setupButton
void setupButton(AbstractButton btn, String icon, String text, ActionListener listener)
Definition: GalleryJFrame.java:813
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xmipp.viewer.windows.GalleryJFrame.saveMd
void saveMd(String path, boolean saveall, boolean isoverwrite, boolean reload)
Definition: GalleryJFrame.java:2164
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xmipp.jni.ImageGeneric.VIEWS
static final int VIEWS[]
Definition: ImageGeneric.java:42
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xmipp.utils.XmippWindowUtil.openURI
static void openURI(String uri)
Definition: XmippWindowUtil.java:190
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xmipp.ij.commons.XmippApplication.removeInstance
static void removeInstance(boolean isijwindow)
Definition: XmippApplication.java:28
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xmipp.utils.XmippLabel.LABEL_VOLUME
static final String LABEL_VOLUME
Definition: XmippLabel.java:232
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xmipp.ij.commons.XmippApplication.addInstance
static void addInstance(boolean isijwindow)
Definition: XmippApplication.java:18
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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xmipp.viewer.models.GalleryData.runObjectCommand
void runObjectCommand(int index, String objectCommand)
Definition: GalleryData.java:149
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xmipp.utils.XmippResource.GOTO
static final String GOTO
Definition: XmippResource.java:38
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xmipp.jni.MetaData.FILL_CONSTANT
static final String FILL_CONSTANT
Definition: MetaData.java:53
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xmipp.jni.MetaData.FILL_RAND_UNIFORM
static final String FILL_RAND_UNIFORM
Definition: MetaData.java:55
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- - diff --git a/html/GalleryRowHeaderModel_8java.html b/html/GalleryRowHeaderModel_8java.html deleted file mode 100644 index c912688f..00000000 --- a/html/GalleryRowHeaderModel_8java.html +++ /dev/null @@ -1,95 +0,0 @@ - - - - - - - -Xmipp: xmippViz/java/src/xmipp/viewer/models/GalleryRowHeaderModel.java File Reference - - - - - - - - - -
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class  xmipp.viewer.models.GalleryRowHeaderModel
 
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package  xmipp.viewer.models
 
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1 /***************************************************************************
2  * Authors: Juanjo Vega
3  * J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
4  *
5  *
6  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
7  *
8  * This program is free software; you can redistribute it and/or modify
9  * it under the terms of the GNU General Public License as published by
10  * the Free Software Foundation; either version 2 of the License, or
11  * (at your option) any later version.
12  *
13  * This program is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  * GNU General Public License for more details.
17  *
18  * You should have received a copy of the GNU General Public License
19  * along with this program; if not, write to the Free Software
20  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
21  * 02111-1307 USA
22  *
23  * All comments concerning this program package may be sent to the
24  * e-mail address 'xmipp@cnb.csic.es'
25  ***************************************************************************/
26 package xmipp.viewer.models;
27 
28 import javax.swing.ListModel;
29 import javax.swing.event.ListDataListener;
30 
31 public class GalleryRowHeaderModel implements ListModel {
32  private int first_index = 0;
33  private int n = 0;
34  private GalleryData data = null;
35 
36  public GalleryRowHeaderModel(int n, int first_index) {
37 
38  this.first_index = first_index;
39  this.n = n;
40  }
41 
42  public GalleryRowHeaderModel(int n) {
43  this.n = n;
44  }
45 
46  public GalleryRowHeaderModel(GalleryData data){
47  this.data = data;
48  }
49 
50  public int getSize() {
51  if (data != null)
52  return data.labels.size();
53  return n;
54  }
55 
56  public void setSize(int n){
57  this.n = n;
58  }
59 
60  public Object getElementAt(int i) {
61  if (data != null)
62  return data.labels.get(i).labelName;
63  return new Integer(first_index + i);
64  }
65 
66  public void addListDataListener(ListDataListener ll) {
67  }
68 
69  public void removeListDataListener(ListDataListener ll) {
70  }
71 }
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 import java.io.File;
4 import java.io.FileInputStream;
5 import java.io.FileNotFoundException;
6 import java.io.FileOutputStream;
7 import java.io.IOException;
8 import java.util.ArrayList;
9 import java.util.HashMap;
10 import java.util.Properties;
11 
12 import javax.swing.JFrame;
13 
14 import xmipp.jni.Classifier;
15 import xmipp.jni.MetaData;
16 import xmipp.jni.Particle;
17 import xmipp.utils.XmippDialog;
18 import xmipp.utils.XmippWindowUtil;
19 import xmipp.utils.DEBUG;
20 
21 
22 public class GenericClassifier extends Classifier
23 {
24 
25  protected String classifierProperties;
26  protected Properties properties;
27 
28 
29  public GenericClassifier(String classifierProperties)
30  {
31  try
32  {
33  this.classifierProperties = classifierProperties;
34  // create and load properties
35  properties = new Properties();
36  FileInputStream in = new FileInputStream(classifierProperties);
37  properties.load(in);
38 
39  in.close();
40  properties.setProperty("applyChanges", String.valueOf(applyChanges));
41  String[] paramNames = properties.getProperty("parameters").split(",");
42  Parameter param;
43  String label, help, value;
44  params = new ArrayList<Classifier.Parameter>();
45  for(String paramName : paramNames)
46  {
47  label = properties.getProperty(paramName + ".label");
48  help = properties.getProperty(paramName + ".help");
49  value = properties.getProperty(paramName + ".value");
50  param = new Parameter(paramName, label, help, value);
51  params.add(param);
52  }
53  if (hasInitialCoordinates())
54  convert();
55  }
56  catch (Exception e)
57  {
58  throw new IllegalArgumentException(e.getMessage());
59  }
60  }
61 
63  private void execute(String name, String cmd, String runDir) throws Exception
64  {
65  if(cmd == null)
66  {
67  if (DEBUG.hasScipionDebug())
68  System.out.println(name + " command: NULL\n");
69  return;
70  }
71 
72  if (DEBUG.hasScipionDebug())
73  System.out.println(name + " command: \n" + cmd + "\n");
74 
75  String output = (runDir == null) ? XmippWindowUtil.executeCommand(cmd, true) :
76  XmippWindowUtil.executeCommand(cmd, true, runDir);
77  if (DEBUG.hasScipionDebug())
78  System.out.println(name + " output: \n" + output + "\n");
79  }
80 
81  private void convert() throws Exception {
82  String convertCommand = properties.getProperty("convertCommand");
83  execute("Convert", convertCommand, null);
84  }
85 
86  public void autopick(SupervisedPickerMicrograph micrograph)
87  {
88  String preprocessCommand = properties.getProperty("preprocessCommand");
89  String autopickCommand = properties.getProperty("autopickCommand");
90  String runDir = properties.getProperty("runDir");
91 
92  for(Classifier.Parameter param: params)
93  {
94  if(preprocessCommand != null)
95  preprocessCommand = preprocessCommand.replace("%(" + param.name + ")", param.value);
96  autopickCommand = autopickCommand.replace("%(" + param.name + ")", param.value);
97  }
98 
99  String micPath = micrograph.getFile();
100 
101  if (runDir != null)
102  micPath = new File(runDir).toURI().relativize(new File(micPath).toURI()).getPath();
103 
104  String name = micrograph.getName();
105  autopickCommand = autopickCommand.replace("%(micrograph)", micPath);
106  autopickCommand = autopickCommand.replace("%(micrographName)", name);
107 
108  try
109  {
110  execute("Preprocess", preprocessCommand, runDir);
111  execute("Autopick", autopickCommand, runDir);
112  convert();
113  writeProperties();
114  }
115  catch (Exception e)
116  {
117  // TODO Auto-generated catch block
118  e.printStackTrace();
119  }
120  }
121 
122  @Override
123  public int getTrainingParticlesMinimum()
124  {
125  // TODO Auto-generated method stub
126  return 0;
127  }
128 
129  @Override
130  public void setSize(int psize)
131  {
132  // TODO Auto-generated method stub
133  }
134 
135  @Override
136  public boolean needsTraining()
137  {
138  return false;
139  }
140 
141  public void writeProperties()
142  {
143  try
144  {
145  for(Classifier.Parameter param: params)
146  properties.setProperty(param.name + ".value", param.value);
147  properties.setProperty("applyChanges", String.valueOf(applyChanges));
148  File file = new File(classifierProperties);
149  FileOutputStream fileOut;
150  fileOut = new FileOutputStream(file);
151  properties.store(fileOut, "Favorite Things");
152  fileOut.close();
153  }
154  catch (Exception e)
155  {
156  // TODO Auto-generated catch block
157  e.printStackTrace();
158  if(!e.getMessage().isEmpty())
159  XmippDialog.showError(null,e.getMessage());
160  }
161  }
162 
163  public void setApplyChanges(boolean applyChanges) {
164  super.setApplyChanges(applyChanges);
165  writeProperties();
166  }
167 
168  public boolean hasInitialCoordinates() {
169  return properties.getProperty("hasInitialCoordinates", "").equals("true");
170  }
171 
172  public boolean doPickAll() {
173  return properties.getProperty("doPickAll", "").equals("true");
174  }
175 
176 }
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static boolean hasScipionDebug()
Definition: DEBUG.java:43
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static String executeCommand(String[] command, boolean wait)
Definition: XmippWindowUtil.java:276
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void autopick(SupervisedPickerMicrograph micrograph)
Definition: GenericClassifier.java:86
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List< Classifier.Parameter > params
Definition: Classifier.java:7
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boolean showError(String message)
Definition: XmippDialog.java:211
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.ij.commons;
8 
13  public class Geometry
14  {
15  public double shiftx, shifty, psiangle;
16  public boolean flip;
17  public double scaleFactor = 1;
18 
19  private String matrixString;
20 
21  public Geometry(double shiftx, double shifty, double psiangle, boolean flip, double scaleFactor)
22  {
23  this.shiftx = shiftx;
24  this.shifty = shifty;
25  this.psiangle = psiangle;
26  this.flip = flip;
27  this.matrixString = null;
28  this.scaleFactor = scaleFactor;
29  }
30 
31 
32  public Geometry(String matrixString)
33  {
34  this.matrixString = matrixString;
35  }
36 
37  public String getMatrix()
38  {
39  return this.matrixString;
40  }
41 
42  public boolean hasMatrix()
43  {
44  return this.matrixString != null;
45  }
46 
47 
48  }
49 
50 
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xmipp.ij.commons.Geometry.Geometry
Geometry(String matrixString)
Definition: Geometry.java:32
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xmipp.ij.commons.Geometry.Geometry
Geometry(double shiftx, double shifty, double psiangle, boolean flip, double scaleFactor)
Definition: Geometry.java:21
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1 import ij.*;
2 import ij.process.*;
3 import ij.gui.*;
4 import java.awt.*;
5 import java.awt.geom.*;
6 import java.util.*;
7 import ij.plugin.*;
8 import ij.measure.*;
9 
10 public class Grid_ implements PlugIn, DialogListener {
11  private static String[] colors = {"Red","Green","Blue","Magenta","Cyan","Yellow","Orange","Black","White"};
12  private static String color = "Cyan";
13  private final static int LINES=0, HLINES=1, CROSSES=2, POINTS=3, NONE=4;
14  private static String[] types = {"Lines","Horizontal Lines", "Crosses", "Points", "None"};
15  private static String type = types[LINES];
16  private static double areaPerPoint;
17  private static boolean randomOffset;
18  private Random random = new Random(System.currentTimeMillis());
19  private ImagePlus imp;
20  private double tileWidth, tileHeight;
21  private int xstart, ystart;
22  private int linesV, linesH;
23  private double pixelWidth=1.0, pixelHeight=1.0;
24  private String units = "pixels";
25 
26  public void run(String arg) {
27  if (IJ.versionLessThan("1.43u")) return;
28  imp = IJ.getImage();
29  showDialog();
30  }
31 
32  void drawPoints() {
33  int one = 1;
34  int two = 2;
35  GeneralPath path = new GeneralPath();
36  for(int h=0; h<linesV; h++) {
37  for(int v=0; v<linesH; v++) {
38  float x = (float)(xstart+h*tileWidth);
39  float y = (float)(ystart+v*tileHeight);
40  path.moveTo(x-two, y-one); path.lineTo(x-two, y+one);
41  path.moveTo(x+two, y-one); path.lineTo(x+two, y+one);
42  path.moveTo(x-one, y-two); path.lineTo(x+one, y-two);
43  path.moveTo(x-one, y+two); path.lineTo(x+one, y+two);
44  }
45  }
46  showGrid(path);
47  }
48 
49  void drawCrosses() {
50  GeneralPath path = new GeneralPath();
51  float arm = 5;
52  for(int h=0; h<linesV; h++) {
53  for(int v=0; v<linesH; v++) {
54  float x = (float)(xstart+h*tileWidth);
55  float y = (float)(ystart+v*tileHeight);
56  path.moveTo(x-arm, y);
57  path.lineTo(x+arm, y);
58  path.moveTo(x, y-arm);
59  path.lineTo(x, y+arm);
60  }
61  }
62  showGrid(path);
63  }
64 
65  void showGrid(Shape shape) {
66  if (shape==null)
67  imp.setOverlay(null);
68  else
69  imp.setOverlay(shape, getColor(), null);
70  }
71 
72  void drawLines() {
73  GeneralPath path = new GeneralPath();
74  int width = imp.getWidth();
75  int height = imp.getHeight();
76  for(int i=0; i<linesV; i++) {
77  float xoff = (float)(xstart+i*tileWidth);
78  path.moveTo(xoff,0f);
79  path.lineTo(xoff, height);
80  }
81  for(int i=0; i<linesH; i++) {
82  float yoff = (float)(ystart+i*tileHeight);
83  path.moveTo(0f, yoff);
84  path.lineTo(width, yoff);
85  }
86  showGrid(path);
87  }
88 
89  void drawHorizontalLines() {
90  GeneralPath path = new GeneralPath();
91  int width = imp.getWidth();
92  int height = imp.getHeight();
93  for(int i=0; i<linesH; i++) {
94  float yoff = (float)(ystart+i*tileHeight);
95  path.moveTo(0f, yoff);
96  path.lineTo(width, yoff);
97  }
98  showGrid(path);
99  }
100 
101  void showDialog() {
102  int width = imp.getWidth();
103  int height = imp.getHeight();
104  Calibration cal = imp.getCalibration();
105  int places;
106  if (cal.scaled()) {
107  pixelWidth = cal.pixelWidth;
108  pixelHeight = cal.pixelHeight;
109  units = cal.getUnits();
110  places = 2;
111  } else {
112  pixelWidth = 1.0;
113  pixelHeight = 1.0;
114  units = "pixels";
115  places = 0;
116  }
117  if (areaPerPoint==0.0)
118  areaPerPoint = (width*cal.pixelWidth*height*cal.pixelHeight)/81.0; // default to 9x9 grid
119  ImageWindow win = imp.getWindow();
120  GenericDialog gd = new GenericDialog("Grid...");
121  gd.addChoice("Grid Type:", types, type);
122  gd.addNumericField("Area per Point:", areaPerPoint, places, 6, units+"^2");
123  gd.addChoice("Color:", colors, color);
124  gd.addCheckbox("Random Offset", randomOffset);
125  gd.addDialogListener(this);
126  gd.showDialog();
127  if (gd.wasCanceled())
128  showGrid(null);
129  }
130 
131  public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
132  int width = imp.getWidth();
133  int height = imp.getHeight();
134  type = gd.getNextChoice();
135  areaPerPoint = gd.getNextNumber();
136  color = gd.getNextChoice();
137  randomOffset = gd.getNextBoolean();
138 
139  double minArea= (width*height)/50000.0;
140  if (type.equals(types[CROSSES])&&minArea<144.0)
141  minArea = 144.0;
142  else if (minArea<16)
143  minArea = 16.0;
144  if (areaPerPoint/(pixelWidth*pixelHeight)<minArea) {
145  String err = "\"Area per Point\" too small";
146  if (gd.wasOKed())
147  IJ.error("Grid", err);
148  else
149  IJ.showStatus(err);
150  return true;
151  }
152  double tileSize = Math.sqrt(areaPerPoint);
153  tileWidth = tileSize/pixelWidth;
154  tileHeight = tileSize/pixelHeight;
155  if (randomOffset) {
156  xstart = (int)(random.nextDouble()*tileWidth);
157  ystart = (int)(random.nextDouble()*tileHeight);
158  } else {
159  xstart = (int)(tileWidth/2.0+0.5);
160  ystart = (int)(tileHeight/2.0+0.5);
161  }
162  linesV = (int)((width-xstart)/tileWidth)+1;
163  linesH = (int)((height-ystart)/tileHeight)+1;
164  if (gd.invalidNumber())
165  return true;
166  if (type.equals(types[LINES]))
167  drawLines();
168  else if (type.equals(types[HLINES]))
169  drawHorizontalLines();
170  else if (type.equals(types[CROSSES]))
171  drawCrosses();
172  else if (type.equals(types[POINTS]))
173  drawPoints();
174  else
175  showGrid(null);
176  return true;
177  }
178 
179  Color getColor() {
180  Color c = Color.cyan;
181  if (color.equals(colors[0])) c = Color.red;
182  else if (color.equals(colors[1])) c = Color.green;
183  else if (color.equals(colors[2])) c = Color.blue;
184  else if (color.equals(colors[3])) c = Color.magenta;
185  else if (color.equals(colors[4])) c = Color.cyan;
186  else if (color.equals(colors[5])) c = Color.yellow;
187  else if (color.equals(colors[6])) c = Color.orange;
188  else if (color.equals(colors[7])) c = Color.black;
189  else if (color.equals(colors[8])) c = Color.white;
190  return c;
191  }
192 }
Grid_
Definition: Grid_.java:10
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Grid_.run
void run(String arg)
Definition: Grid_.java:26
-
Grid_.dialogItemChanged
boolean dialogItemChanged(GenericDialog gd, AWTEvent e)
Definition: Grid_.java:131
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package  xmipp.ij.plugins.maskstoolbar
 
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1 package xmipp.ij.plugins.maskstoolbar;
2 
3 /*
4  * To change this template, choose Tools | Templates
5  * and open the template in the editor.
6  */
7 import javax.swing.ImageIcon;
8 
9 import xmipp.jni.Filename;
10 
15 @SuppressWarnings("ResultOfObjectAllocationIgnored")
16 public class ICONS {
17 
18  public final static String PATH_ICONS = Filename.getXmippPath("resources/");
19  public final static String PATH_TOOL_RECTANGLE = PATH_ICONS + "rectangle.png";
20  public final static String PATH_TOOL_ROUNDRECTANGLE = PATH_ICONS + "roundrectangle.png";
21  public final static String PATH_TOOL_ELLIPSE = PATH_ICONS + "ellipse.png";
22  public final static String PATH_TOOL_OVAL = PATH_ICONS + "oval.png";
23  public final static String PATH_TOOL_POLYGON = PATH_ICONS + "polygon.png";
24  public final static String PATH_TOOL_FREEHAND = PATH_ICONS + "freehand.png";
25  public final static String PATH_TOOL_BRUSH = PATH_ICONS + "brush.png";
26  public final static String PATH_ACTION_CREATEMASK = PATH_ICONS + "create_mask.png";
27  public final static String PATH_ACTION_CREATESELECTION = PATH_ICONS + "create_selection.png";
28  public final static String PATH_ACTION_INVERTSELECTION = PATH_ICONS + "invert_selection.png";
29  public final static String PATH_ACTION_INVERTMASK = PATH_ICONS + "invert_mask.png";
30  public final static String PATH_ACTION_SPECIFYSELECTION = PATH_ICONS + "specify_selection.png";
31  public final static String PATH_ACTION_BRUSHSIZE = PATH_ICONS + "brush_size.png";
32  public final static String PATH_MASK_LOCKED = PATH_ICONS + "locked.png";
33  public final static String PATH_MASK_UNLOCKED = PATH_ICONS + "unlocked.png";
34  public static ImageIcon TOOL_RECTANGLE;
35  public static ImageIcon TOOL_ROUNDRECTANGLE;
36  public static ImageIcon TOOL_ELLIPSE;
37  public static ImageIcon TOOL_OVAL;
38  public static ImageIcon TOOL_POLYGON;
39  public static ImageIcon TOOL_FREEHAND;
40  public static ImageIcon TOOL_BRUSH;
41  public static ImageIcon ACTION_CREATEMASK;
42  public static ImageIcon ACTION_CREATESELECTION;
43  public static ImageIcon ACTION_INVERTSELECTION;
44  public static ImageIcon ACTION_INVERTMASK;
45  public static ImageIcon ACTION_SPECIFYSELECTION;
46  public static ImageIcon ACTION_BRUSHSIZE;
47  public static ImageIcon MASK_LOCKED;
48  public static ImageIcon MASK_UNLOCKED;
49 
50  static {
51  new ICONS(); // Auto-load.
52  }
53 
54  public ICONS() {
55 // TOOL_RECTANGLE = new ImageIcon(getClass().getResource(PATH_TOOL_RECTANGLE));
56 // TOOL_ROUNDRECTANGLE = new ImageIcon(getClass().getResource(PATH_TOOL_ROUNDRECTANGLE));
57 // TOOL_ELLIPSE = new ImageIcon(getClass().getResource(PATH_TOOL_ELLIPSE));
58 // TOOL_OVAL = new ImageIcon(getClass().getResource(PATH_TOOL_OVAL));
59 // TOOL_POLYGON = new ImageIcon(getClass().getResource(PATH_TOOL_POLYGON));
60 // TOOL_FREEHAND = new ImageIcon(getClass().getResource(PATH_TOOL_FREEHAND));
61 // TOOL_BRUSH = new ImageIcon(getClass().getResource(PATH_TOOL_BRUSH));
62 // ACTION_CREATEMASK = new ImageIcon(getClass().getResource(PATH_ACTION_CREATEMASK));
63 // ACTION_CREATESELECTION = new ImageIcon(getClass().getResource(PATH_ACTION_CREATESELECTION));
64 // ACTION_INVERTSELECTION = new ImageIcon(getClass().getResource(PATH_ACTION_INVERTSELECTION));
65 // ACTION_INVERTMASK = new ImageIcon(getClass().getResource(PATH_ACTION_INVERTMASK));
66 // ACTION_SPECIFYSELECTION = new ImageIcon(getClass().getResource(PATH_ACTION_SPECIFYSELECTION));
67 // ACTION_BRUSHSIZE = new ImageIcon(getClass().getResource(PATH_ACTION_BRUSHSIZE));
68 // MASK_LOCKED = new ImageIcon(getClass().getResource(PATH_MASK_LOCKED));
69 // MASK_UNLOCKED = new ImageIcon(getClass().getResource(PATH_MASK_UNLOCKED));
70  TOOL_RECTANGLE = new ImageIcon(PATH_TOOL_RECTANGLE);
71  TOOL_ROUNDRECTANGLE = new ImageIcon(PATH_TOOL_ROUNDRECTANGLE);
72  TOOL_ELLIPSE = new ImageIcon(PATH_TOOL_ELLIPSE);
73  TOOL_OVAL = new ImageIcon(PATH_TOOL_OVAL);
74  TOOL_POLYGON = new ImageIcon(PATH_TOOL_POLYGON);
75  TOOL_FREEHAND = new ImageIcon(PATH_TOOL_FREEHAND);
76  TOOL_BRUSH = new ImageIcon(PATH_TOOL_BRUSH);
77  ACTION_CREATEMASK = new ImageIcon(PATH_ACTION_CREATEMASK);
78  ACTION_CREATESELECTION = new ImageIcon(PATH_ACTION_CREATESELECTION);
79  ACTION_INVERTSELECTION = new ImageIcon(PATH_ACTION_INVERTSELECTION);
80  ACTION_INVERTMASK = new ImageIcon(PATH_ACTION_INVERTMASK);
81  ACTION_SPECIFYSELECTION = new ImageIcon(PATH_ACTION_SPECIFYSELECTION);
82  ACTION_BRUSHSIZE = new ImageIcon(PATH_ACTION_BRUSHSIZE);
83  MASK_LOCKED = new ImageIcon(PATH_MASK_LOCKED);
84  MASK_UNLOCKED = new ImageIcon(PATH_MASK_UNLOCKED);
85  }
86 }
87 
xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_RECTANGLE
static ImageIcon TOOL_RECTANGLE
Definition: ICONS.java:34
-
xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_ELLIPSE
static ImageIcon TOOL_ELLIPSE
Definition: ICONS.java:36
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_INVERTSELECTION
static ImageIcon ACTION_INVERTSELECTION
Definition: ICONS.java:43
-
xmipp.jni.Filename.getXmippPath
static native String getXmippPath()
- -
xmipp.ij.plugins.maskstoolbar.ICONS.MASK_UNLOCKED
static ImageIcon MASK_UNLOCKED
Definition: ICONS.java:48
-
xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_FREEHAND
static ImageIcon TOOL_FREEHAND
Definition: ICONS.java:39
-
xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_CREATESELECTION
static ImageIcon ACTION_CREATESELECTION
Definition: ICONS.java:42
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_CREATEMASK
static ImageIcon ACTION_CREATEMASK
Definition: ICONS.java:41
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xmipp.ij.plugins.maskstoolbar.ICONS.MASK_LOCKED
static ImageIcon MASK_LOCKED
Definition: ICONS.java:47
-
xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_INVERTMASK
static ImageIcon ACTION_INVERTMASK
Definition: ICONS.java:44
-
xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_SPECIFYSELECTION
static ImageIcon ACTION_SPECIFYSELECTION
Definition: ICONS.java:45
-
xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_POLYGON
static ImageIcon TOOL_POLYGON
Definition: ICONS.java:38
-
xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_ROUNDRECTANGLE
static ImageIcon TOOL_ROUNDRECTANGLE
Definition: ICONS.java:35
-
xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_BRUSHSIZE
static ImageIcon ACTION_BRUSHSIZE
Definition: ICONS.java:46
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1 package xmipp.ij.commons;
2 
3 public class IJCommand
4 {
5 
6  private String command;
7  private String options;
8 
9  public IJCommand(String command, String options)
10  {
11  this.command = command;
12  this.options = options;
13  }
14 
15  public String getCommand()
16  {
17  return command;
18  }
19  public void setCommand(String command)
20  {
21  this.command = command;
22  }
23  public String getOptions()
24  {
25  return options;
26  }
27  public void setOptions(String options)
28  {
29  this.options = options;
30  }
31 
32  public String getMdCommand()
33  {
34  return command.replace('_', '&').replace(' ', '_');
35  }
36 
37  public String getMdOptions()
38  {
39  return (options == null || options.equals("")) ? "NULL" :options.replace('_', '&').replace(' ', '_');
40  }
41 
42  public static String getString(String mdstring)
43  {
44  return mdstring.replace('_', ' ').replace('&', '_');
45  }
46 
47 
48  public String toString()
49  {
50  return command + " " + options;
51  }
52 
53 }
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Definition: IJCommand.java:19
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IJCommand(String command, String options)
Definition: IJCommand.java:9
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Definition: IJCommand.java:27
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Definition: IJCommand.java:42
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class  IPLab_Reader
 
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1 import ij.plugin.*;
2 import ij.*;
3 import ij.io.*;
4 import ij.process.*;
5 import java.io.*;
6 
8 public class IPLab_Reader extends ImagePlus implements PlugIn {
9 
10  boolean littleEndian;
11  RandomAccessStream f;
12  boolean isColor48;
13  int nextBlock;
14  int itag;
15 
16  public void run(String arg) {
17  OpenDialog od = new OpenDialog("Open IPLab...", arg);
18  String directory = od.getDirectory();
19  String name = od.getFileName();
20  if (name==null)
21  return;
22  IJ.showStatus("Opening: " + directory + name);
23  open(directory, name, arg);
24  }
25 
26  void open(String directory, String name, String arg) {
27  FileInfo fi = null;
28  try {
29  fi = getFileInfo(directory, name);
30  } catch (IOException e) {
31  IJ.showStatus("");
32  String error = e.getMessage();
33  if (error==null || error.equals(""))
34  error = ""+e;
35  IJ.showMessage("IPLab Reader", ""+error);
36  return;
37  }
38  if (fi!=null) {
39  FileOpener fo = new FileOpener(fi);
40  ImagePlus imp = fo.open(false);
41  if (imp==null)
42  return;
43  if (isColor48 && imp.getBitDepth()==16 && imp.getStackSize()==3)
44  handleColor48Image(imp);
45  setStack(name, imp.getStack());
46  setCalibration(imp.getCalibration());
47  if (arg.equals("")) show();
48  }
49  }
50 
51  void handleColor48Image(ImagePlus imp) {
52  ImageStack stack = imp.getStack();
53  stack.setSliceLabel( "Red", 1);
54  stack.setSliceLabel( "Green", 2);
55  stack.setSliceLabel( "Blue", 3);
56  convertColor48ToRGB(imp);
57  }
58 
59  void convertColor48ToRGB(ImagePlus imp) {
60  int width = imp.getWidth();
61  int height = imp.getHeight();
62  ImageProcessor ip;
63  ImageStack stack1 = imp.getStack();
64  ImageStack stack2 = new ImageStack(width, height);
65  for (int i=1; i<=stack1.getSize(); i++) {
66  ip = stack1.getProcessor(i);
67  ImageProcessor ip2 = ip.duplicate();
68  stack2.addSlice(null, ip2);
69  }
70  ImagePlus imp2 = imp.createImagePlus();
71  imp2.setStack("RGB of "+imp.getTitle(), stack2);
72  ImageProcessor ip2 = imp2.getProcessor();
73  StackConverter sc = new StackConverter(imp2);
74  sc.convertToGray8();
75  ImageConverter ic = new ImageConverter(imp2);
76  ic.convertRGBStackToRGB();
77  imp2.show();
78  }
79 
80  FileInfo getFileInfo(String directory, String name) throws IOException {
81  FileInfo fi = new FileInfo();
82  f = new RandomAccessStream(new RandomAccessFile(directory + name, "r"));
83  //f = new BufferedInputStream(new FileInputStream(directory+name));
84  int b0=getByte(), b1=getByte(), b2=getByte(), b3=getByte();
85  if (b0==105&&b1==105&&b2==105&&b3==105) // "iiii"
86  littleEndian = true;
87  else if (b0==109&&b1==109&&b2==109&&b3==109) // "mmmm"
88  littleEndian = false;
89  else
90  throw new IOException("This does not appear to be an IPLab/Windows (.IPL) file.");
91  f.skip(8);
92  if (!(getByte()==100&&getByte()==97&&getByte()==116&&getByte()==97)) // "data"
93  throw new IOException("This does not appear to be an IPLab/Windows (.IPL) file.");
94  int blockSize = getInt();
95  nextBlock = 16 + blockSize;
96  fi.width = getInt();
97  fi.height = getInt();
98  int nChannels = getInt();
99  int zPlanes = getInt();
100  int tVolumes = getInt();
101  int dataType = getInt();
102  fi.fileFormat = fi.RAW;
103  fi.fileName = name;
104  fi.directory = directory;
105  fi.nImages = zPlanes*tVolumes;
106  fi.intelByteOrder = littleEndian;
107  fi.offset = 44;
108  switch (dataType) {
109  case 0:
110  if (nChannels==3)
111  fi.fileType = FileInfo.RGB_PLANAR;
112  else
113  fi.fileType = FileInfo.GRAY8;
114  break;
115  case 1:
116  fi.fileType = FileInfo.GRAY16_SIGNED;
117  break;
118  case 2:
119  fi.fileType = FileInfo.GRAY16_UNSIGNED;
120  if (fi.nImages==1)
121  fi.nImages = nChannels;
122  isColor48 = nChannels==3;
123  break;
124  case 3:
125  fi.fileType = FileInfo.GRAY32_INT;
126  break;
127  case 4:
128  fi.fileType = FileInfo.GRAY32_FLOAT;
129  break;
130  }
131  String tag = null;
132  do {
133  tag = getNextBlock();
134  if (tag==null) break;
135  if (tag.equals("unit"))
136  getUnits(fi);
137  else if (itag==0x2d45c4f6)
138  decodeAcquireTag(fi);
139  } while (tag!=null);
140  f.close();
141  return fi;
142  }
143 
144  String getNextBlock() throws IOException {
145  f.seek(nextBlock);
146  String tag = getString();
147  int blockSize = getInt();
148  //IJ.log(blockSize+" " + nextBlock+" \""+tag+"\"" + " " +Integer.toHexString(itag));
149  nextBlock = nextBlock + 8 + blockSize;
150  if (blockSize==0)
151  return null;
152  else
153  return tag;
154  }
155 
156  void getUnits(FileInfo fi) throws IOException {
157  float[] unitsPerPixel = new float[5];
158  int[] unit = new int[5];
159  for (int i=0; i<4; i++) {
160  getInt();
161  unitsPerPixel[i] = getFloat();
162  unit[i] = getShort();
163  getShort(); // skip 2 filler bytes
164  //IJ.log(i+" "+unitsPerPixel[i]+" "+unit[i]);
165  }
166  if (unitsPerPixel[0]!=0.0) {
167  fi.pixelWidth = 1.0/unitsPerPixel[0];
168  fi.pixelHeight = fi.pixelWidth;
169  }
170  switch (unit[0]) {
171  case 1: fi.unit="um"; break;
172  case 2: fi.unit="mm"; break;
173  case 3: fi.unit="cm"; break;
174  case 4: fi.unit="m"; break;
175  case 5: fi.unit="inch"; break;
176  case 6: fi.unit="ft"; break;
177  }
178  }
179 
180  void decodeAcquireTag(FileInfo fi) throws IOException {
181  f.skip(1276);
182  double zSpacing = getFloat();
183  //IJ.log("decodeAcquireTag: "+zSpacing);
184  if (zSpacing>0.0)
185  fi.pixelDepth = zSpacing;
186  }
187 
188  int getByte() throws IOException {
189  int b = f.read();
190  if (b ==-1) throw new IOException("unexpected EOF");
191  return b;
192  }
193 
194  int getShort() throws IOException {
195  int b0 = getByte();
196  int b1 = getByte();
197  if (littleEndian)
198  return ((b1<<8) + b0);
199  else
200  return ((b0<<8) + b1);
201  }
202 
203  final int getInt() throws IOException {
204  int b0 = getByte();
205  int b1 = getByte();
206  int b2 = getByte();
207  int b3 = getByte();
208  if (littleEndian)
209  return ((b3<<24) + (b2<<16) + (b1<<8) + b0);
210  else
211  return ((b0<<24) + (b1<<16) + (b2<<8) + b3);
212  }
213 
214  float getFloat() throws IOException {
215  return Float.intBitsToFloat(getInt());
216  }
217 
218  String getString() throws IOException {
219  //reads next 4 bytes and returns them as a string
220  byte[] list = new byte[4];
221  f.read(list);
222  if (littleEndian)
223  itag = ((list[0]<<24) + (list[1]<<16) + (list[2]<<8) + list[3]);
224  else
225  itag = ((list[3]<<24) + (list[2]<<16) + (list[1]<<8) + list[0]);
226  return new String(list);
227  }
228 
229 }
230 
231 /*
232 #define kAcquireTagID 0xF6C5462D//TAG value use this to identify the tag
233 
234 struct AcquireXTag {
235  char cTag[4]; //0xF6C5462D //tag id //check first four bytes for this long hex value
236  long lSize; // 2016 bytes size of the tag without tag and size (2024 - 8)
237  float fVersion; //4
238  long lTime; //4 will cast to time_t structure for time extraction
239  char szExpName[32]; //32 Exp. Name
240  char cExpID[16]; //16 GUID per experiment
241  char cGeneralUnused[512]; //512 (568)
245  char szCameraName[32]; //32 Camera Name
246  long lXResolution; //4 CC X Max
247  long lYResolution; //4 CCD Y Max
248  long lLeft; //4 CCD Coordinates used
249  long lRight; //4
250  long lTop; //4
251  long lBottom; //4
252  long lBinX; //4 Binning in X direction
253  long lBinY; //4 Binning in Y Direction
254  float fExposure; //4 Exposure
255  float fCalibrationXY; //4 XY image calibration for current binn
256  long lCalibrationXYUnits; //4 Units for the XY calibration
257  long lGain; //4 Camera Gain
258  long lEGain; //4 Multiplicative/Intensifier Gain
259  long lCameraSpeed; //4 Speed setting for camera
260  char szCameraSpeed[32]; //32 Speed as string
261  long lCameraOffset; //4 Camera Offset
262  long lTriggerMode; //4 Trigger mode
263  char szTriggerMode[32]; //32 Trigger mode as string
264  long lBitDepth; //4
265  char cCameraUnused[508]; //508 (672)
269  //Z Axis Settings
270  char szZAxis[32]; //32 Z Axis Name
271  float fZStepsPerMicron; //4 Steps per micron for Z Axis
272  float fZSpacing; //4 Z Spacing //1276 (568+672+36)
273  float fZCurPos; //4 Z Current Position
274  //XY Stage Settings
275  char szXYStage[32]; //32 XY Stage Name
276  float fXStepsPerMicron; //4 X Steps per micron
277  float fYStepsPerMicron; //4 Y Steps per micron
278  float fXPosition; //4 X Current position
279  float fYPosition; //4 Y Current position
280  long lCurRow; //4 Current array row
281  long lCurCol; //4 Current array col
282  long lCurSuperRow; //4 Current super row
283  long lCurSuperCol; //4 Current super col
284  //Shutter Settings
285  char szShutterName[32]; //32 Shutter Name
286  float fShutterDelay; //4 Shutter Delay
287  //Filter Settings
288  char szFilterName[32]; //32 Filter Name
289  long lFilterPos; //4 Filter Position
290  long lFilterWavelength; //4 Filter Wavelength
291  char szFilterPosName[32]; //32 Filter Position Name
292  //Objective Settings
293  float fNA; //4 Numerical Aperature
294  float fRefactiveIndex; //4 Refractive Index
295  long lObjectivePos; //4 Objective Position
296  char szObjectiveName[32]; //32 Objective Name
297  char szObjectivePosName[32]; //32 Objective Position Name
298  //Other Settingsing
299  float fMagFactor; //4 Magnification factor other than objective
300 
301  char cMicUnused[480]; //480
303 };
304 */
305 
306 
IPLab_Reader.run
void run(String arg)
Definition: IPLab_Reader.java:16
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IPLab_Reader
Definition: IPLab_Reader.java:8
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1 import java.awt.*;
2 import java.awt.event.*;
3 import java.io.*;
4 import ij.plugin.frame.*;
5 import ij.*;
6 import ij.process.*;
7 import ij.gui.*;
8 
13 public class IP_Demo extends PlugInFrame implements ActionListener {
14  private Panel panel;
15  private int previousID;
16  private static Frame instance;
17 
18  public IP_Demo() {
19  super("IP Demo");
20  if (instance!=null) {
21  instance.toFront();
22  return;
23  }
24  instance = this;
25  addKeyListener(IJ.getInstance());
26 
27  setLayout(new FlowLayout());
28  panel = new Panel();
29  panel.setLayout(new GridLayout(4, 4, 5, 5));
30  addButton("Reset");
31  addButton("Flip");
32  addButton("Invert");
33  addButton("Rotate");
34  addButton("Lighten");
35  addButton("Darken");
36  addButton("Zoom In");
37  addButton("Zoom Out");
38  addButton("Smooth");
39  addButton("Sharpen");
40  addButton("Find Edges");
41  addButton("Threshold");
42  addButton("Add Noise");
43  addButton("Reduce Noise");
44  addButton("Macro1");
45  addButton("Macro2");
46  add(panel);
47 
48  pack();
49  GUI.center(this);
50  setVisible(true);
51  }
52 
53  void addButton(String label) {
54  Button b = new Button(label);
55  b.addActionListener(this);
56  b.addKeyListener(IJ.getInstance());
57  panel.add(b);
58  }
59 
60  public void actionPerformed(ActionEvent e) {
61  ImagePlus imp = WindowManager.getCurrentImage();
62  if (imp==null) {
63  IJ.beep();
64  IJ.showStatus("No image");
65  previousID = 0;
66  return;
67  }
68  if (!imp.lock())
69  {previousID = 0; return;}
70  int id = imp.getID();
71  if (id!=previousID)
72  imp.getProcessor().snapshot();
73  previousID = id;
74  String label = e.getActionCommand();
75  if (label==null)
76  return;
77  new Runner(label, imp);
78  }
79 
80  public void processWindowEvent(WindowEvent e) {
81  super.processWindowEvent(e);
82  if (e.getID()==WindowEvent.WINDOW_CLOSING) {
83  instance = null;
84  }
85  }
86 
87 
88  class Runner extends Thread { // inner class
89  private String command;
90  private ImagePlus imp;
91 
92  Runner(String command, ImagePlus imp) {
93  super(command);
94  this.command = command;
95  this.imp = imp;
96  setPriority(Math.max(getPriority()-2, MIN_PRIORITY));
97  start();
98  }
99 
100  public void run() {
101  try {
102  runCommand(command, imp);
103  } catch(OutOfMemoryError e) {
104  IJ.outOfMemory(command);
105  if (imp!=null) imp.unlock();
106  } catch(Exception e) {
107  CharArrayWriter caw = new CharArrayWriter();
108  PrintWriter pw = new PrintWriter(caw);
109  e.printStackTrace(pw);
110  IJ.log(caw.toString());
111  IJ.showStatus("");
112  if (imp!=null) imp.unlock();
113  }
114  }
115 
116  void runCommand(String command, ImagePlus imp) {
117  ImageProcessor ip = imp.getProcessor();
118  IJ.showStatus(command + "...");
119  long startTime = System.currentTimeMillis();
120  Roi roi = imp.getRoi();
121  if (command.startsWith("Zoom")||command.startsWith("Macro")||command.equals("Threshold"))
122  {roi = null; ip.resetRoi();}
123  ImageProcessor mask = roi!=null?roi.getMask():null;
124  if (command.equals("Reset"))
125  ip.reset();
126  else if (command.equals("Flip"))
127  ip.flipVertical();
128  else if (command.equals("Invert"))
129  ip.invert();
130  else if (command.equals("Lighten")) {
131  if (imp.isInvertedLut())
132  ip.multiply(0.9);
133  else
134  ip.multiply(1.1);
135  }
136  else if (command.equals("Darken")) {
137  if (imp.isInvertedLut())
138  ip.multiply(1.1);
139  else
140  ip.multiply(0.9);
141  }
142  else if (command.equals("Rotate"))
143  ip.rotate(30);
144  else if (command.equals("Zoom In"))
145  ip.scale(1.2, 1.2);
146  else if (command.equals("Zoom Out"))
147  ip.scale(.8, .8);
148  else if (command.equals("Threshold"))
149  ip.autoThreshold();
150  else if (command.equals("Smooth"))
151  ip.smooth();
152  else if (command.equals("Sharpen"))
153  ip.sharpen();
154  else if (command.equals("Find Edges"))
155  ip.findEdges();
156  else if (command.equals("Add Noise"))
157  ip.noise(20);
158  else if (command.equals("Reduce Noise"))
159  ip.medianFilter();
160  else if (command.equals("Macro1"))
161  macro1(imp, ip);
162  else if (command.equals("Macro2"))
163  macro2(imp, ip);
164  if (mask!=null) ip.reset(mask);
165  imp.updateAndDraw();
166  imp.unlock();
167  IJ.showStatus((System.currentTimeMillis()-startTime)+" milliseconds");
168  }
169 
170  void macro1(ImagePlus imp, ImageProcessor ip) {
171  IJ.resetEscape();
172  for (int i=10; i<=360; i+=10) {
173  ip.reset();
174  ip.rotate(i);
175  imp.updateAndDraw();
176  if (IJ.escapePressed()) return;
177  IJ.wait(10);
178  }
179  }
180 
181  void macro2(ImagePlus imp, ImageProcessor ip) {
182  IJ.resetEscape();
183  double scale = 1, m = 1.2;
184  for (int i=0; i<20; i++) {
185  ip.reset();
186  scale *= m;
187  ip.scale(scale, scale);
188  imp.updateAndDraw();
189  if (IJ.escapePressed()) return;
190  IJ.wait(10);
191  }
192  for (int i=0; i <20; i++) {
193  ip.reset();
194  scale /= m;
195  ip.scale(scale, scale);
196  imp.updateAndDraw();
197  if (IJ.escapePressed()) return;
198  IJ.wait(10);
199  }
200  }
201 
202  } // Runner inner class
203 
204 } //IP_Demo class
IP_Demo.IP_Demo
IP_Demo()
Definition: IP_Demo.java:18
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IP_Demo.actionPerformed
void actionPerformed(ActionEvent e)
Definition: IP_Demo.java:60
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void processWindowEvent(WindowEvent e)
Definition: IP_Demo.java:80
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IP_Demo
Definition: IP_Demo.java:13
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class  xmipp.viewer.ImageDimension
 
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package  xmipp.viewer
 
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ImageDimension.java
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1 /***************************************************************************
2  * Authors: Juanjo Vega
3  * J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
4  *
5  *
6  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
7  *
8  * This program is free software; you can redistribute it and/or modify
9  * it under the terms of the GNU General Public License as published by
10  * the Free Software Foundation; either version 2 of the License, or
11  * (at your option) any later version.
12  *
13  * This program is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  * GNU General Public License for more details.
17  *
18  * You should have received a copy of the GNU General Public License
19  * along with this program; if not, write to the Free Software
20  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
21  * 02111-1307 USA
22  *
23  * All comments concerning this program package may be sent to the
24  * e-mail address 'xmipp@cnb.csic.es'
25  ***************************************************************************/
26 
27 package xmipp.viewer;
28 
29 import ij.IJ;
30 import xmipp.jni.ImageGeneric;
31 
35 public class ImageDimension {
36 
37  private int xdim, ydim, zdim;
38  private long ndim;
39 
40  public ImageDimension() {
41  }
42 
43  public ImageDimension(int x){
44  this(x, x);
45  }
46 
47  public ImageDimension(int x, int y){
48  this(x, y, 1, 1);
49  }
50 
51  public ImageDimension(int x, int y, int z){
52  this(x, y, z, 1);
53  }
54 
55  public ImageDimension(int x, int y, int z, long n) {
56  this.xdim = x;
57  this.ydim = y;
58  this.zdim = z;
59  this.ndim = n;
60  }
61 
62  public ImageDimension(ImageGeneric image) {
63  try {
64  xdim = image.getXDim();
65  ydim = image.getYDim();
66  zdim = image.getZDim();
67  ndim = image.getNDim();
68  } catch (Exception ex) {
69  IJ.error("Retrieving image dimensions: "+ image);
70  }
71  }
72 
73  public int getXDim() {
74  return xdim;
75  }
76 
77  public int getYDim() {
78  return ydim;
79  }
80 
81  public int getZDim() {
82  return zdim;
83  }
84 
85  public long getNDim() {
86  return ndim;
87  }
88 
89  public void setXDim(int x) {
90  this.xdim = x;
91  }
92 
93  public void setYDim(int y) {
94  this.ydim = y;
95  }
96 
97  public void setZDim(int z) {
98  this.zdim = z;
99  }
100 
101  public void setNDim(long n) {
102  this.ndim = n;
103  }
104 }
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xmipp.jni.ImageGeneric.getNDim
native long getNDim()
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xmipp.viewer.ImageDimension.ImageDimension
ImageDimension(int x, int y, int z, long n)
Definition: ImageDimension.java:55
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xmipp.viewer.ImageDimension.ImageDimension
ImageDimension(int x, int y, int z)
Definition: ImageDimension.java:51
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native int getYDim()
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xmipp.viewer.ImageDimension.ImageDimension
ImageDimension(ImageGeneric image)
Definition: ImageDimension.java:62
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xmipp.jni.ImageGeneric.getZDim
native int getZDim()
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class  xmipp.viewer.models.ImageGalleryTableModel
 
class  xmipp.viewer.models.ImageGalleryTableModel.ImageItem
 
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package  xmipp.viewer.models
 
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- - diff --git a/html/ImageGalleryTableModel_8java_source.html b/html/ImageGalleryTableModel_8java_source.html deleted file mode 100644 index 1bb3499e..00000000 --- a/html/ImageGalleryTableModel_8java_source.html +++ /dev/null @@ -1,244 +0,0 @@ - - - - - - - -Xmipp: xmippViz/java/src/xmipp/viewer/models/ImageGalleryTableModel.java Source File - - - - - - - - - -
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.models;
27 
28 import ij.ImagePlus;
29 
30 import java.awt.Dimension;
31 import java.awt.Image;
32 import java.awt.Insets;
33 import java.awt.Point;
34 import java.util.ArrayList;
35 
36 import javax.swing.JTable;
37 import javax.swing.border.Border;
38 import javax.swing.table.AbstractTableModel;
39 import javax.swing.table.JTableHeader;
40 
41 import xmipp.ij.commons.ImagePlusLoader;
42 import xmipp.jni.MDLabel;
43 import xmipp.jni.MDRow;
44 import xmipp.jni.MetaData;
45 import xmipp.utils.Cache;
46 import xmipp.utils.DEBUG;
47 import xmipp.utils.XmippPopupMenuCreator;
48 import xmipp.viewer.ImageDimension;
49 import xmipp.viewer.ImageItemRenderer;
50 
51 public abstract class ImageGalleryTableModel extends AbstractTableModel {
52 
53  protected ArrayList<Integer> busyRows = new ArrayList<Integer>();
54 
55  private static final long serialVersionUID = 1L;
56  // Store the number of rows and columns
57  protected int rows, cols;
58  // Total number of elements and last width
59  protected int n, last_width;
60  // Image original dimensions
61  protected int image_width, image_height;
62  // Thumbnails dimensions
63  protected int thumb_width, thumb_height, font_height;
64  // Table cell dimensions, this is redundant, but to avoid to be recalculated
65  public Dimension cellDim = new Dimension();
66 
67  // Relation between real dimensions and thumbnails dimensions
68  // scale = image_width / thumb_width
69  protected float scale = (float) 1.;
70  // protected int zoom = 100;
71  // Cache class to reuse of already loaded items
72  protected Cache<String, ImageItem> cache;
73  // Filename
74  // Hold gallery dimensions
75  protected ImageDimension dimension;
76  // Renderer to display images
77  protected ImageItemRenderer renderer = new ImageItemRenderer();
78  // Column model
79  protected GalleryColumnModel columnModel;
80  // Where to show labels
81  // protected boolean showLabel = false;
82  // Whether to autoadjust columns
83  // Flags and variables to control global normalization
84  protected boolean normalize_calculated = false;
85  protected double normalize_min = Double.POSITIVE_INFINITY,
86  normalize_max = Double.NEGATIVE_INFINITY;
87 
88  public GalleryData data; // information about the gallery
89 
90  public boolean adjustWidth = true;
91  protected boolean[] selection;
92 
93  // Initiazation function
94  public ImageGalleryTableModel(GalleryData data, boolean[] selection) throws Exception {
95  this.data = data;
96  cols = 0;
97  dimension = loadDimension();
98  columnModel = createColumnModel();
99 
100  int zoom = 100;
101  if(data.getZoom() != null)
102  zoom = data.getZoom();
103  setZoomValue(zoom);
104  // This should be changed later after a call to
105  // setColumns or adjustColumns
106  if (cols < 1) {
107  cols = 1;
108  rows = n;
109  }
110  // DEBUG.printMessage(String.format("col: %d, rows: %d", cols, rows));
111  //resizeCache(); NOw this is done when setZoomValue
112  //might be that the number of items is the same and we keep selection, although it is a different metadata
113  if(selection == null)
114  this.selection = new boolean[data.ids.length];
115  else
116  this.selection = selection;
117 
118  }
119 
120 
121 
122  public int getImageWidth()
123  {
124  return image_width;
125  }
126 
127  public int getImageHeight()
128  {
129  return image_height;
130  }
131 
132  // Load initial dimensions
133  protected abstract ImageDimension loadDimension() throws Exception;
134 
139  protected void resizeCache() {
140  int limit = Cache.getLimit(thumb_width, thumb_height);
141  if(cache == null)
142  cache = new Cache(limit);
143  else
144  cache.resize(limit > 0 ? limit : 1);
145  }
146 
147  @Override
148  public int getColumnCount() {
149  return cols;
150  }
151 
152  @Override
153  public int getRowCount() {
154  return rows;
155  }
156 
157  @Override
158  public String getColumnName(int column) {
159  return String.format("%d", column + 1);
160  }
161 
162  @Override
163  public Class getColumnClass(int c) {
164  return ImageItem.class;
165  }
166 
167  @Override
168  public Object getValueAt(int row, int col) {
169  int index = getIndex(row, col);
170  if (isValidIndex(index)) {
171  try {
172  String key = getItemKey(index);
173  ImageItem item;
174  // If the element is on cache, just return it
175  if (cache.containsKey(key))
176  item = cache.get(key);
177  else {
178 // // If not, create the item and store it for future
179  item = createItem(index, key, getColumn(row, col));
180  cache.put(key, item);
181  }
182  setupItem(item);
183  return item;
184  } catch (Exception e) {
185  e.printStackTrace();
186  }
187  }
188 
189  return null;
190  }
191 
193  public void refreshAt(int row, int col) {
194 
195  int index = getIndex(row, col);
196 
197  if (isValidIndex(index)) {
198  try {
199  String key = getItemKey(index, data.getLabelFromCol(col));
200  // Clear cache entry
201  cache.remove(key);
202  fireTableRowsUpdated(row, row);
203  } catch (Exception e) {
204  e.printStackTrace();
205  }
206  }
207  }
208 
209 
210 
211  protected void setupItem(ImageItem item) {
212  ImagePlus imp = item.getImagePlus();
213  if (imp != null && imp.getProcessor() != null) { // When image is missing this will be null
214  if (data.normalize)
215  imp.getProcessor().setMinAndMax(normalize_min, normalize_max);
216  else
217  imp.getProcessor().resetMinAndMax();
218  imp.updateImage();
219  }
220  }
221 
222  public void setRows(int rows) {
223  if (rows != this.rows) {
224  this.rows = rows;
225  cols = n / rows + (n % rows == 0 ? 0 : 1);
226  fireTableStructureChanged();
227  }
228  }
229 
230  protected void setColumnsValue(int cols) {
231  this.cols = cols;
232  rows = n / cols + (n % cols == 0 ? 0 : 1);
233  fireTableStructureChanged();
234  }
235 
236  public void setColumns(int cols) {
237  if (cols != this.cols) {
238  setColumnsValue(cols);
239  }
240  }
241 
242  // Return True if columns were changed
243  public boolean adjustColumn(int width) {
244  last_width = width;
245  int new_cols = Math.max(Math.min(width / cellDim.width, n), 1);
246  if (new_cols != cols) {
247  setColumnsValue(new_cols);
248  return true;
249  }
250  return false;
251  }
252 
253  public int getSize() {
254  return n;
255  }
256 
257  public Dimension getCellSize() {
258  return cellDim;
259  }// function getCellSize
260 
268  protected void calculateCellSize() {
269  thumb_width = (int) (image_width * scale);
270  thumb_height = (int) (image_height * scale);
271 
272  font_height = 0;
273  if (data.isDisplayLabel()) {
274  font_height = renderer.getFontMetrics(renderer.getFont())
275  .getHeight();
276  font_height += renderer.getIconTextGap(); // Adds the extra gap.
277  // font_height -= table.getIntercellSpacing().height; // Removes
278  }
279 
280  int borderHeight = 0, borderWidth = 0;
281  Border border = renderer.getBorder();
282 
283  if (border != null) {
284  Insets insets = renderer.getBorder().getBorderInsets(renderer);
285  borderWidth = insets.left + insets.right;
286  borderHeight = insets.bottom + insets.top;
287  }
288  cellDim.setSize(thumb_width + 1 * borderWidth, thumb_height + 1
289  * borderHeight + font_height);
290  adjustColumnsWidth();
291  }
292 
296  public void setupTable(JTable table) {
297  table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
298  table.setDefaultRenderer(ImageItem.class, renderer);
299  }
300 
302  public void updateTableSelection(JTable table) {
303  // For now do nothing, overrided in MetadataTable
304  }
305 
307  protected void adjustColumnsWidth() {
308  // renderer.setPreferredSize(cellDim);
309  columnModel.setWidth(cellDim.width);
310  }
311 
313  public ImageItemRenderer getRenderer() {
314  return renderer;
315  }
316 
318  public GalleryColumnModel getColumnModel() {
319  return columnModel;
320  }
321 
322  public JTableHeader getTableHeaderModel(){
323  return new JTableHeader(columnModel);
324  }
325 
327  protected GalleryColumnModel createColumnModel() {
328  return new GalleryColumnModel(cellDim.width);
329  }
330 
331  protected void setZoomValue(int z) {
332  data.setZoom(z);
333  scale = (float) (z / 100.0);
334  calculateCellSize();
335  resizeCache();
336  }
337 
338  public void setZoom(int z) {
339 
340  if (data.getZoom() != null || data.getZoom() != z) {
341  setZoomValue(z);
342  fireTableDataChanged();
343  if (data.isAutoAdjust())
344  adjustColumn(last_width);
345  }
346  }
347 
357  public int getIndex(int row, int col) {
358 
359  return row * cols + col;
360  }
361 
362 
363 
364  public long getId(int row, int col) {
365  int index = getIndex(row, col);
366  return data.ids[index];
367 
368  }
369 
371  public boolean isValidIndex(int index){
372  return index >= 0 && index < n;
373  }
374 
376  public abstract String getLabel(int row, int col);
377 
384  public Point getCoords(int index) {
385  Point p = new Point();
386  p.y = index / cols;
387  p.x = index % cols;
388  return p;
389  }
390 
394  public void setSelectionEnabled(boolean value) {
395  try {
396  int from = getSelFrom(), to = getSelTo();
397  for (int i = from; i <= to; i++)
398  if (selection[i])
399  data.setEnabled(i, value);
400 
401  if(from != -1)
402  {
403  from = getCoords(from).y;
404  to = getCoords(to).y;
405  fireTableRowsUpdated(from, to);
406  }
407 
408  } catch (Exception e) {
409  // TODO Auto-generated catch block
410  e.printStackTrace();
411  }
412  }
413 
414 
415 
416  public int getFirstSelectedIndex(){
417  return getSelFrom();
418  }
419 
421  public void selectRange(int first_index, int last_index, boolean value) {
422  for (int i = first_index; i <= last_index; ++i)
423  setSelected(i, value);
424  int from = getCoords(first_index).y;
425  int to = getCoords(last_index).y;
426  fireTableRowsUpdated(from, to);
427  }
428 
430  public void selectRange(int first_row, int first_col, int last_row, int last_col) {
431  int i1 = getIndex(first_row, first_col);
432  int i2 = getIndex(last_row, last_col);
433  int i = Math.min(i1, i2);
434  i2 = Math.max(i1, i2);
435  for (; i <= i2; ++i)
436  setSelected(i, true);
437  fireTableRowsUpdated(first_row, last_row);
438  }
439 
441  public void setSelectionClass(int classNumber) {
442  ClassInfo cli = data.getClassInfo(classNumber);
443  for (int i = getSelFrom(); i <= getSelTo(); ++i)
444  if (selection[i]) {
445  data.setItemClass(i, cli);
446  }
447  clearSelection();
448  fireTableDataChanged();
449  }
450 
452  public void removeClass(int classNumber) {
453  data.removeClass(classNumber);
454  fireTableDataChanged();
455  }
456 
458  public void touchItem(int row, int col) {
459  setSelected(row, col, !isSelected(row, col));
460  adjustWidth = false;
461  fireTableCellUpdated(row, col);
462  }
463 
465  public void touchItem(int row, int col, boolean isselected) {
466 
467  setSelected(row, col, isselected);
468  adjustWidth = false;
469  fireTableCellUpdated(row, col);
470  }
471 
472 
477  public void gotoItem(int i) {
478  clearSelection();
479  setSelected(i, !isSelected(i));
480  Point coords = getCoords(i);
481  fireTableCellUpdated(coords.y, coords.x);
482  }
483 
484 
485 
487  public void setNormalized(boolean normalize) {
488 
489  if (normalize != data.normalize) {
490  data.normalize = normalize;
491  if (normalize)
492  calculateMinAndMax();
493  fireTableDataChanged();
494  }
495  }
496 
497 
498 
500  public void calculateMinAndMax() {
501  if (!normalize_calculated) {
502  double[] mm = getMinAndMax();
503  normalize_min = mm[0];
504  normalize_max = mm[1];
505  normalize_calculated = true;
506  }
507  }
508 
515  public abstract boolean handleRightClick(int row, int col,
516  XmippPopupMenuCreator xpopup);
517 
522  public abstract boolean handleDoubleClick(int row, int col) ;
523 
525  public void setShowLabels() {
526 
527  calculateCellSize();
528  fireTableStructureChanged();
529 
530  }
531 
532 
533 
535  protected abstract double[] getMinAndMax();
536 
537  // /** Retrieve the image filename, return null if error */
538  // protected abstract String getImageFilenameAt(int row, int col);
539 
543  public abstract String getItemKey(int index) throws Exception;
544 
548  public String getItemKey(int index, int label) throws Exception {
549  Object value = data.getValueFromLabel(index, label);
550 
551  String format = value + "_%d_%d(%d,%d)";
552  if (data.useGeo)
553  format += "_geo";
554  if (data.wrap)
555  format += "_wrap";
556  // String key = String.format(format, thumb_width, thumb_height);
557  // DEBUG.printMessage(String.format("key: %s", key));
558  String key = String.format(format, index, label, thumb_width, thumb_height);
559  return key;
560  }
561 
562 
566  public abstract String getTitle();
567 
572  public abstract ImagePlusLoader getImageLoader();
573 
582  protected abstract ImageItem createItem(int index, String key, ColumnInfo ci)
583  throws Exception;
584 
585  public boolean isSelected(int row, int col) {
586  int index = getIndex(row, col);
587  return isSelected(index);
588  }
589 
590  public abstract boolean showLabels() ;
591 
592  public void setInvertY(boolean itemSelected) {
593  data.inverty = itemSelected;
594  cache.clear();
595  fireTableDataChanged();
596  }
597 
598 
599 
604  public class ImageItem {
605 
606  protected ImagePlus image = null;
607  protected int index;
608 
612  public ImageItem(int row, int col) {
613  index = ImageGalleryTableModel.this.getIndex(row, col);
614  }
615 
616  public ImageItem(int index, ImagePlus imp) {
617  this.index = index;
618  this.image = imp;
619  }
620 
621  public int getIndex() {
622  return index;
623  }
624 
625  public ImagePlus getImagePlus() {
626  return image;
627  }
628 
629  public void setImagePlus(ImagePlus value) {
630  image = value;
631  }
632 
633  public Image getImage() {
634  if (image != null)
635  return image.getImage();
636  return null;
637  }
638 
639  public boolean getShowLabel() {
640  return data.isDisplayLabel();
641  }
642 
643  public Dimension getCellDim() {
644  return cellDim;
645  }
646 
647  public String getLabel() {
648  Point coords = getCoords(index);
649  return ImageGalleryTableModel.this.getLabel(coords.y, coords.x);
650  }
651 
652  public String getKey() {
653  try {
654  return getItemKey(index);
655  } catch (Exception e) {
656  // TODO Auto-generated catch block
657  e.printStackTrace();
658  }
659  return null;
660  }
661 
662  public boolean isSelected() {
663  return ImageGalleryTableModel.this.isSelected(index);
664  }
665 
666  public boolean isEnabled() {
667  return data.isEnabled(index);
668  }
669 
670  public boolean isBusy() {
671  return ImageGalleryTableModel.this.isBusy(index, 0);
672  }
673 
674  public ClassInfo getClassInfo() {
675  return data.getItemClassInfo(index);
676  }
677 
678  @Override
679  public String toString() {
680  return image != null ? image.getFileInfo().fileName : null;
681  }
682  }// class ImageItem
683 
684  public int getRows()
685  {
686  return rows;
687  }
688 
689 
690  public int getColumns()
691  {
692  return cols;
693  }
694 
695 
697  public boolean isBusy(int row, int col){
698  return busyRows.contains(row);
699  }
700 
701  public void setRowBusy(int row) {
702  DEBUG.printFormat("setting busy row: %d", row);
703  busyRows.add(new Integer(row));
704  fireTableRowsUpdated(row, row);
705  }
706 
707  public void setRowIdle(int row) {
708  DEBUG.printFormat("setting idle row: %d", row);
709  busyRows.remove(new Integer(row));
710  long objId = data.ids[row];
711  String psdFile = data.md.getValueString(MDLabel.MDL_PSD, objId);
712  String sortFn = psdFile.replace(".psd", ".xmd");
713  MetaData mdRow = new MetaData(sortFn);
714  MDRow row2 = new MDRow();
715  mdRow.getRow(row2, mdRow.firstObject());
716  data.setRow(row2, objId);
717  mdRow.destroy();
718  refreshRow(row);
719  }
720 
722  public void refreshRow(int row) {
723  try {
724  int n = getColumnCount();
725  int index;
726  String key;
727  ColumnInfo ci;
728  for (int col = 0; col < n; ++col) {
729  ci = data.getColumnInfo(col);
730  if (ci.allowRender){
731  key = getItemKey(row, ci.label);
732  DEBUG.printFormat("Removing item: %s from cache", key);
733  cache.remove(key);
734  }
735  }
736  fireTableRowsUpdated(row, row);
737  } catch (Exception e) {
738  e.printStackTrace();
739  }
740  }
741 
742  public void clearSelection() {
743  for (int i = 0; i < selection.length; ++i) {
744  selection[i] = false;
745  }
746 
747  }
748 
752  public int getSelectionCount() {
753  int count = 0;
754 
755  if (!data.isVolumeMode() && hasSelection()) {
756  for (int i = 0; i < selection.length; i++) {
757  if (selection[i]) {
758  count++;
759  }
760  }
761  }
762  return count;
763  }
764 
765  public boolean[] getSelection()
766  {
767  return selection;
768  }
769 
770  public void setSelected(int index, boolean isselected) {
771 
772 
773  selection[index] = isselected;
774 
775  if (data.isVolumeMd && data.isTableMode())
776  data.selectedVolFn = isselected? data.getVolumeAt(index): data.getVolumeAt(0);
777 
778  }
779 
780  public boolean isSelected(int index) {
781 
782  return selection[index];
783  }
784 
785  public int getSelFrom()
786  {
787  for(int i = 0; i < selection.length; i ++)
788  {
789  if(selection[i])
790  return i;
791  }
792  return -1;
793  }
794 
795  public int getSelTo()
796  {
797  int selto = -1;
798  for(int i = 0; i < selection.length; i ++)
799  {
800  if(selection[i])
801  selto = i;
802  }
803  return selto;
804  }
805 
806  public boolean hasSelection() {
807  if(getSelFrom() == -1)
808  return false;
809  return true;
810  }
811 
812  public void setSelected(int row, int col, boolean b) {
813  setSelected(getIndex(row, col), b);
814  }
815 
816  public ColumnInfo getColumn(int row, int col)
817  {
818  return data.ciFirstRender;
819  }
820 
821 }
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void selectRange(int first_index, int last_index, boolean value)
Definition: ImageGalleryTableModel.java:421
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ImageGalleryTableModel(GalleryData data, boolean[] selection)
Definition: ImageGalleryTableModel.java:94
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Definition: GalleryData.java:892
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Definition: GalleryData.java:1190
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Definition: ImageGalleryTableModel.java:812
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Definition: GalleryData.java:923
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  * Roberto Marabini (roberto@cnb.csic.es)
4  *
5  *
6  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
7  *
8  * This program is free software; you can redistribute it and/or modify
9  * it under the terms of the GNU General Public License as published by
10  * the Free Software Foundation; either version 2 of the License, or
11  * (at your option) any later version.
12  *
13  * This program is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  * GNU General Public License for more details.
17  *
18  * You should have received a copy of the GNU General Public License
19  * along with this program; if not, write to the Free Software
20  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
21  * 02111-1307 USA
22  *
23  * All comments concerning this program package may be sent to the
24  * e-mail address 'xmipp@cnb.csic.es'
25  ***************************************************************************/
26 package xmipp.test;
27 
28 import ij.ImagePlus;
29 import ij.gui.Roi;
30 import ij.io.FileSaver;
31 import ij.process.ImageProcessor;
32 
33 import java.awt.Rectangle;
34 import java.io.File;
35 import org.junit.After;
36 import org.junit.AfterClass;
37 import org.junit.Before;
38 import org.junit.BeforeClass;
39 import org.junit.Test;
40 
41 import xmipp.ij.commons.XmippImageConverter;
42 import xmipp.jni.Filename;
43 import xmipp.jni.ImageGeneric;
44 import xmipp.jni.MetaData;
45 import static org.junit.Assert.*;
46 import java.util.Arrays;
47 
52 public class ImageGenericTest {
53 
54  // Filenames to test.
55  static String filename = XmippTest.getTestFilename("singleImage.spi");
56  static String filename2 = XmippTest.getTestFilename("singleImage2.spi");
57  // Indexes for arrays.
58  final static int X = 0;
59  final static int Y = 1;
60  final static int Z = 2;
61  // Predefined dimension of 'singleImage.spi' to test
62  int xdim = 3;
63  int ydim = 3;
64  int zdim = 1;
65  int ndim = 1;
66  // Image pixels values
67  float[] imagePixels = { 1.0f, 2.0f, 3.0f, 4.0f, 5.0f, 6.0f, 7.0f, 8.0f,
68  9.0f };
69  // Images statistics.
70  // min, max, avg, std dev
71  double[] imageStats = { 1.0, 9.0, 5.0, 2.5820 };
72  // Image datatype
73  int imageDatatype = ImageGeneric.Float;
74 
75  public ImageGenericTest() {
76 
77  }
78 
79  @BeforeClass
80  public static void setUpClass() throws Exception {
81  }
82 
83  @AfterClass
84  public static void tearDownClass() throws Exception {
85  }
86 
87  @Before
88  public void setUp() {
89  }
90 
91  @After
92  public void tearDown() {
93  }
94 
98  @Test
99  public void testGetFilename() throws Exception {
100  ImageGeneric image = new ImageGeneric(filename);
101  String imageFn = image.getFilename();
102  assertEquals(filename, imageFn);
103  }
104 
108  @Test
109  public void testGetDimensions() throws Exception {
110  ImageGeneric image = new ImageGeneric(filename);
111  assertEquals(xdim, image.getXDim());
112  assertEquals(ydim, image.getYDim());
113  assertEquals(zdim, image.getZDim());
114  assertEquals(ndim, image.getNDim());
115  }
116 
120  @Test
121  public void testGetDataType() throws Exception {
122  ImageGeneric image = new ImageGeneric(filename);
123  assertEquals(imageDatatype, image.getDataType());
124  }
125 
129  @Test
130  public void testGetArrayFloat() throws Exception {
131  ImageGeneric image = XmippTest.getImageGeneric(filename);
132 
133  float[] result = image.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE);
134  for (int i = 0; i < imagePixels.length; i++)
135  assertEquals(imagePixels[i], result[i], XmippTest.EQUAL_ACCURACY);
136  }
137 
141  @Test
142  public void testEqual() throws Exception {
143  ImageGeneric image = XmippTest.getImageGeneric(filename);
144  ImageGeneric image2 = XmippTest.getImageGeneric(filename2);
145 
146  assertTrue(image.equal(image, XmippTest.EQUAL_ACCURACY));
147  assertFalse(image.equal(image2, XmippTest.EQUAL_ACCURACY));
148  }
149 
153  @Test
154  public void testSubtract() throws Exception {
155  ImageGeneric image = XmippTest.getImageGeneric(filename);
156  ImageGeneric image2 = XmippTest.getImageGeneric(filename2);
157  ImageGeneric image3 = new ImageGeneric();
158  image2.subtract(image,image3);
159  float[] result = image3.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE);
160  for (int i = 0; i < imagePixels.length -1; i++)
161  assertEquals(result[i],0., XmippTest.EQUAL_ACCURACY);
162  assertEquals(result[8],27.0, XmippTest.EQUAL_ACCURACY);
163  }
164 
168  @Test
169  public void testGetStatistics() throws Exception {
170  ImageGeneric image = XmippTest.getImageGeneric(filename);
171  double[] stats = image.getStatistics();
172  for (int i = 0; i < stats.length; i++) {
173  assertEquals(imageStats[i], stats[i], XmippTest.EQUAL_ACCURACY);
174  }
175  }
176 
180  @Test
181  public void testSetArrayFloat() throws Exception {
182  //PENDING TO CHANGE IMAGE GENERIC TO ALLOW WRITE MODE ON MEMORY MAPPED TO DISK
183  System.out.println("TestSetArrayFloat");
184  int size = 100;
185  String templatesfile = "imagegeneric.stk";
186  ImageGeneric templates = new ImageGeneric(templatesfile);
187  XmippImageConverter.readToImagePlus(templates);//to load templates on memory
188 
189 
190  String micrographfile = XmippTest.getTestFilename("BPV_1386.mrc");
191  ImagePlus mimage = new ImagePlus(micrographfile);
192  Rectangle r = new Rectangle(0, 0, size, size);
193  mimage.setRoi(r);
194  ImageProcessor processor = mimage.getProcessor().crop();
195  ImagePlus particleimg = new ImagePlus("particle", processor);
196  //new FileSaver(particleimg).save();
197  ImageGeneric particleig = XmippImageConverter.convertToImageGeneric(particleimg);
198  float[] matrix = particleig.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.ALL_SLICES);
199  templates.setArrayFloat(matrix, ImageGeneric.FIRST_IMAGE, ImageGeneric.ALL_SLICES);
200  templates.write(templatesfile);
201  }
202 
206  // /@Test
207  public void testWhatIs() throws Exception {
208  ImageGeneric image = new ImageGeneric(filename);
209  assertTrue(image.isSingleImage());
210  assertFalse(image.isStackOrVolume());
211  assertFalse(image.isPSD());
212  }
213 
214 }//class ImageGenericTest
xmipp.jni.ImageGeneric.FIRST_SLICE
static final int FIRST_SLICE
Definition: ImageGeneric.java:9
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xmipp.jni.ImageGeneric.getNDim
native long getNDim()
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Definition: XmippImageConverter.java:297
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Definition: ImageGeneric.java:11
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Definition: XmippTest.java:40
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Definition: ImageGeneric.java:8
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Definition: XmippImageConverter.java:82
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xmipp.test.XmippTest.getImageGeneric
static ImageGeneric getImageGeneric(String filename)
Definition: XmippTest.java:45
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Definition: ImageGeneric.java:24
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1 package xmipp.jni;
2 
3 import java.io.File;
4 
5 public class ImageGeneric {
6 
7  //Constants to image selection indexes
8  public final static long FIRST_IMAGE = 1;
9  public final static int FIRST_SLICE = 1;
10  public final static long ALL_IMAGES = 0;
11  public final static int ALL_SLICES = 0;
12  public final static int MID_SLICE = -1;
13  //Datatypes constants
14  public final static int Default = -1; // For writing purposes
15  public final static int Unknown_Type = 0; // Undefined data type
16  public final static int UChar = 1; // Unsigned character or byte type
17  public final static int SChar = 2; // Signed character (for CCP4)
18  public final static int UShort = 3; // Unsigned integer (2-byte)
19  public final static int Short = 4; // Signed integer (2-byte)
20  public final static int UInt = 5; // Unsigned integer (4-byte)
21  public final static int Int = 6; // Signed integer (4-byte)
22  public final static int ULong = 7; // Unsigned integer (4 or 8 byte; depending on system)
23  public final static int Long = 8; // Signed integer (4 or 8 byte; depending on system)
24  public final static int Float = 9; // Floating point (4-byte)
25  public final static int Double = 10; // Double precision floating point (8-byte)
26  public final static int ComplexShort = 11; // Complex two-byte integer (4-byte)
27  public final static int ComplexInt = 12; // Complex integer (8-byte)
28  public final static int ComplexFloat = 13; // Complex floating point (8-byte)
29  public final static int ComplexDouble = 14; // Complex floating point (16-byte)
30  public final static int Bool = 15; // Boolean (1-byte?)
31  public final static int UHalfByte = 16 ; // 4 bits per pixel
32  public final static int LastEntry = 17; // This must be the last entry
33 
34  //AxisView constants for volume reslice
35  public final static int Z_NEG = 0;
36  public final static int Z_POS = 1;
37  public final static int Y_NEG = 2; // Align -Y axis to Z axis, rotating 90 degrees around X axis");
38  public final static int Y_POS = 3; // Align Y axis to Z axis, rotating -90 degrees around X axis");
39  public final static int X_NEG = 4; // Align -X axis to Z axis, rotating -90 degrees around Y axis");
40  public final static int X_POS = 5; // Align X axis to Z axis, rotating 90 degrees around Y axis");
41 
42  public final static int VIEWS[] = {Z_NEG, Y_NEG, X_NEG, Y_POS, X_POS };
43 
44 
45 
46  // Associated filename.
47  private String filename;
48  private boolean useLogarithm = true; // To convert PSD images.
49  // pointer to Image class in C++ space. Needed by native library.
50  long peer;
51 
52  // Initialize library.
53  static {
54  System.loadLibrary("XmippJNI");
55  //storeIds();
56  }
57 
58  // Catching some ids
59  //private static native void storeIds();
60  // Functions to create objects.
61  private native void create();
62 
63  // Destructor.
64  public synchronized native void destroy();
65 
66  //non-native functions
67  //constructor
68  public ImageGeneric() throws Exception {
69  create();
70  }
71 
72  public ImageGeneric(int datatype) throws Exception {
73  this();
74 
75  setDataType(datatype);
76  }
77 
78  public ImageGeneric(String filename) throws Exception {
79  this();
80  setFilename(filename);
81 
82  }
83 
85  public void setFilename(String filename) throws Exception {
86  this.filename = filename;
87  readHeader(filename);//Filename.getFilename(filename));
88  }
89 
90  public void resize(int w, int h) throws Exception {
91  resize(w, h, 1);
92  }
93 
94  public void resize(int w, int h, int d) throws Exception {
95  resize(w, h, d, 1);
96  }
97 
98  public native void resize(int h, int w, int d, long n) throws Exception;
99 
100  public String getFilename() {
101  return filename;
102  }
103 
104  public native int getXDim() throws Exception;
105 
106  public native int getYDim() throws Exception;
107 
108  public native int getZDim() throws Exception;
109 
110  public native long getNDim() throws Exception;
111 
112  public native int getDataType() throws Exception;
113 
114  public boolean getUseLogarithm() {
115  return useLogarithm;
116  }
117 
118  public void setUseLogarithm(boolean useLogarithm) {
119  this.useLogarithm = useLogarithm;
120  }
121 
122  // Header reader.
123  private native void readHeader(String filename) throws Exception;
124 
125  // Data readers.
126  public void read(int slice) throws Exception {
127  read(slice, FIRST_IMAGE);
128  }
129 
130  public void read(int width, int height, int slice) throws Exception {
131  read(width, height, slice, FIRST_IMAGE);
132  }
133 
134  public void read(int slice, long image) throws Exception {
135  read(getXDim(), getYDim(), slice, image);
136  }
137 
138  public void read(long image) throws Exception {
139  read(ALL_SLICES, image);
140  }
141 
142  public void read(int width, int height, long image) throws Exception {
143  read(width, height, ALL_SLICES, image);
144  }
145 
146  public void read(int width, int height, int slice, long image) throws Exception {
147  read(filename, width, height, slice, image, true);
148  // At this moment we don't know why
149 // read(Filename.getFilename(filename), width, height, slice, image, true);
150  }
151 
152  public void read(String filename, boolean map) throws Exception {
153  setFilename(filename);
154  read(filename, getXDim(), getYDim(), MID_SLICE, ALL_IMAGES, map);//image in filename will be used
155  }
156 
157  public void read(String filename, int width, int height) throws Exception {
158  this.filename = filename;
159  read(filename, width, height, MID_SLICE, ALL_IMAGES, true);//image in filename will be used
160  }
161 
162  public void read(int width, int height) throws Exception {
163  read(filename, width, height, MID_SLICE, ALL_IMAGES, true);//image in filename will be used
164  }
165 
166  private native void read(String filename, int width, int height, int slice, long nimage, boolean map) throws Exception;
167 
168  public void readApplyGeo(String filename, MetaData metadata, long id) throws Exception {
169  readApplyGeo(filename, metadata, id, true);
170  }
171 
172  public void readApplyGeo(String filename, MetaData metadata, long id, boolean wrap) throws Exception {
173  //ImageGeneric image = new ImageGeneric(filename);
174  readHeader(filename);
175  readApplyGeo(filename, metadata, id, getXDim(), getYDim(), wrap);
176  }
177 
178  public void readApplyGeo(String filename, MetaData metadata, long id, int w, int h) throws Exception {
179  this.filename = filename;
180  readApplyGeo_(filename, metadata, id, w, h, true);
181  }
182 
183  public void readApplyGeo(String filename, MetaData metadata, long id, int w, int h, boolean wrap) throws Exception {
184  this.filename = filename;
185  readApplyGeo_(filename, metadata, id, w, h, wrap);
186  }
187 
188  public void readApplyGeo(MetaData metadata, long id, int w, int h) throws Exception {
189  readApplyGeo_(filename, metadata, id, w, h, true);
190  }
191 
192  public void readApplyGeo(MetaData metadata, long id, int w, int h, boolean wrap) throws Exception {
193  readApplyGeo_(filename, metadata, id, w, h, wrap);
194  }
195 
196  private native void readApplyGeo_(String filename, MetaData metadata, long id, int w, int h, boolean wrap) throws Exception;
197 
198  // Getters for data arrays.
199  public native byte[] getArrayByte(long select_image, int slice) throws Exception;
200 
201  public native short[] getArrayShort(long select_image, int slice) throws Exception;
202 
203  public native float[] getArrayFloat(long select_image, int slice) throws Exception;
204 
205  // Setters for data arrays.
206  public native void setArrayByte(byte data[], long select_image, int slice) throws Exception;
207 
208  public native void setArrayShort(short data[], long select_image, int slice) throws Exception;
209 
210  public native void setArrayFloat(float data[], long select_image, int slice) throws Exception;
211 
212  //Some others image generic utilities
213  public final native void setDataType(int dataType) throws Exception;
214 
215  public final native void convert2Datatype(int dataType) throws Exception;
216 
217  public native void mapFile2Write(int xDim, int yDim, int zDim, String filename, long nimage) throws Exception;
218 
219  public native void write(String filename) throws Exception;
220 
221  public native void printShape() throws Exception;
222 
223  public native double[] getStatistics() throws Exception;
224 
225  public native void setXmippOrigin() throws Exception;
226 
227  public native void convertPSD(boolean useLogarithm) throws Exception;
228 
229  public native void generatePSDCTF(MetaData md) throws Exception;
230 
231  public native void generateImageWithTwoCTFs(MetaData md1, MetaData md2, int xdim) throws Exception;
232 
233  public native void getReslice(ImageGeneric imgOut, int view) throws Exception;
234 
235  public native void reslice(int view) throws Exception;
236 
237 
238  public native void getPreview(ImageGeneric imgOut, int xdim, int ydim,
239  int select_slice, long select_image) throws Exception;
240 
241 
242  public synchronized native double[] alignImage(ImageGeneric img) throws Exception;
243 
244  public synchronized native void getRadialAvg(ImageGeneric radialimg) throws Exception;
245 
246  public native void applyAlignment(ImageGeneric img, int index, double rot, double tilt, double psi) throws Exception;
247 
248 
249  public native void removeAlignment(ImageGeneric img, int index, double rot, double tilt, double psi) throws Exception;
250 
251  public native Particle bestShift(ImageGeneric img) throws Exception;
252 
253 
254  //Check if two images have same values to some accuracy
255  public native boolean equal(ImageGeneric img, double accuracy) throws Exception;
256 
257  //subtract two imageGeneric. calling image minuend
258  public native void subtract(ImageGeneric imgSubtrahend, ImageGeneric imgResult) throws Exception;
259 
260  //Smooth image generic by color dithering
261  public native void smooth(ImageGeneric imgResult) throws Exception;
262 
263  public boolean isPSD() {
264  return Filename.isPSD(filename);
265  }
266 
267  public boolean isStack() throws Exception {
268  return getNDim() > 1;
269  }
270 
271  public boolean isVolume() throws Exception {
272  return getZDim() > 1;
273  }
274 
275  public boolean isStackOrVolume() throws Exception {
276  return isStack() || isVolume();
277  }
278 
279  public boolean isSingleImage() throws Exception {
280  return !isStackOrVolume();
281  }
282 
283  // Should be called by GarbageCollector before destroying
284  @Override
285  @SuppressWarnings("FinalizeDeclaration")
286  protected void finalize() throws Throwable {
287  super.finalize();
288  destroy();
289  }
290 
291  public static boolean exists(String imagepath)
292  {
293  if(imagepath == null || imagepath.isEmpty())
294  return false;
295  String prefix = Filename.getPrefix(imagepath);
296  if(prefix == null)
297  return new File(imagepath).exists();
298  try
299  {
300 
301  int index = Integer.parseInt(prefix);
302  String file = Filename.removePrefix(imagepath);
303  ImageGeneric ig = new ImageGeneric(file);
304  ig.readHeader(file);
305  if(index < 0 || index > ig.getNDim())
306  return false;
307  return true;
308 
309  }
310  catch (Exception e)
311  {
312  return false;
313  }
314  }
315 
316  public native void applyGeo(double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap, double scaleFactor);
317 
318  public void applyGeo(double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap)
319  {
320  applyGeo(shiftX, shiftY, anglepsi, flip, wrap, 1.);
321  }
328  public void applyGeoMatrix(String matrixString, boolean wrap)
329  {
330  applyGeoMatrix(matrixString, 1, wrap);
331  }
332 
333 
334  public native void applyGeoMatrix(String matrixString, double scaleFactor, boolean wrap);
335 
336 
337 
338 }
xmipp.jni.ImageGeneric.SChar
static final int SChar
Definition: ImageGeneric.java:17
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xmipp.jni.ImageGeneric.smooth
native void smooth(ImageGeneric imgResult)
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xmipp.jni.ImageGeneric.ComplexFloat
static final int ComplexFloat
Definition: ImageGeneric.java:28
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xmipp.jni.ImageGeneric.FIRST_SLICE
static final int FIRST_SLICE
Definition: ImageGeneric.java:9
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xmipp.jni.ImageGeneric.mapFile2Write
native void mapFile2Write(int xDim, int yDim, int zDim, String filename, long nimage)
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xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(String filename, MetaData metadata, long id)
Definition: ImageGeneric.java:168
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xmipp.jni.ImageGeneric.destroy
synchronized native void destroy()
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xmipp.jni.ImageGeneric.getNDim
native long getNDim()
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xmipp.jni.ImageGeneric.applyGeoMatrix
void applyGeoMatrix(String matrixString, boolean wrap)
Definition: ImageGeneric.java:328
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xmipp.jni.ImageGeneric.reslice
native void reslice(int view)
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xmipp.jni.ImageGeneric.read
void read(int width, int height)
Definition: ImageGeneric.java:162
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xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(MetaData metadata, long id, int w, int h, boolean wrap)
Definition: ImageGeneric.java:192
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xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(MetaData metadata, long id, int w, int h)
Definition: ImageGeneric.java:188
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xmipp.jni.ImageGeneric.subtract
native void subtract(ImageGeneric imgSubtrahend, ImageGeneric imgResult)
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xmipp.jni.ImageGeneric.convert2Datatype
final native void convert2Datatype(int dataType)
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xmipp.jni.ImageGeneric.Long
static final int Long
Definition: ImageGeneric.java:23
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xmipp.jni.ImageGeneric.ImageGeneric
ImageGeneric(int datatype)
Definition: ImageGeneric.java:72
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xmipp.jni.Filename.isPSD
static boolean isPSD(String filename)
Definition: Filename.java:82
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xmipp.jni.ImageGeneric.read
void read(int width, int height, int slice)
Definition: ImageGeneric.java:130
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xmipp.jni.ImageGeneric.exists
static boolean exists(String imagepath)
Definition: ImageGeneric.java:291
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xmipp.jni.ImageGeneric.ALL_SLICES
static final int ALL_SLICES
Definition: ImageGeneric.java:11
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xmipp.jni.ImageGeneric.generatePSDCTF
native void generatePSDCTF(MetaData md)
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xmipp.jni.ImageGeneric.getArrayShort
native short [] getArrayShort(long select_image, int slice)
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xmipp.jni.ImageGeneric.ComplexInt
static final int ComplexInt
Definition: ImageGeneric.java:27
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xmipp.jni.ImageGeneric.read
void read(int width, int height, long image)
Definition: ImageGeneric.java:142
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xmipp.jni.ImageGeneric.write
native void write(String filename)
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xmipp.jni.Filename.removePrefix
static String removePrefix(String filename)
Definition: Filename.java:373
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xmipp.jni.ImageGeneric.Y_POS
static final int Y_POS
Definition: ImageGeneric.java:38
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xmipp.jni.ImageGeneric.convertPSD
native void convertPSD(boolean useLogarithm)
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xmipp.jni.ImageGeneric.setArrayShort
native void setArrayShort(short data[], long select_image, int slice)
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xmipp.jni.ImageGeneric.getYDim
native int getYDim()
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xmipp.jni.ImageGeneric.printShape
native void printShape()
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xmipp.jni.ImageGeneric.X_NEG
static final int X_NEG
Definition: ImageGeneric.java:39
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xmipp.jni.ImageGeneric.getDataType
native int getDataType()
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xmipp.jni.ImageGeneric.getStatistics
native double [] getStatistics()
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xmipp.jni.ImageGeneric.setArrayFloat
native void setArrayFloat(float data[], long select_image, int slice)
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xmipp.jni.ImageGeneric.read
void read(String filename, int width, int height)
Definition: ImageGeneric.java:157
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xmipp.jni.ImageGeneric.getXDim
native int getXDim()
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xmipp.jni.ImageGeneric.setXmippOrigin
native void setXmippOrigin()
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xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(String filename, MetaData metadata, long id, int w, int h, boolean wrap)
Definition: ImageGeneric.java:183
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xmipp.jni.ImageGeneric.resize
void resize(int w, int h, int d)
Definition: ImageGeneric.java:94
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xmipp.jni.ImageGeneric.UShort
static final int UShort
Definition: ImageGeneric.java:18
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xmipp.jni.ImageGeneric.Unknown_Type
static final int Unknown_Type
Definition: ImageGeneric.java:15
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xmipp.jni.ImageGeneric.removeAlignment
native void removeAlignment(ImageGeneric img, int index, double rot, double tilt, double psi)
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xmipp.jni.ImageGeneric.ULong
static final int ULong
Definition: ImageGeneric.java:22
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xmipp.jni.ImageGeneric.UChar
static final int UChar
Definition: ImageGeneric.java:16
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.ImageGeneric.setArrayByte
native void setArrayByte(byte data[], long select_image, int slice)
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xmipp.jni.ImageGeneric.Bool
static final int Bool
Definition: ImageGeneric.java:30
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xmipp.jni.ImageGeneric.read
void read(int width, int height, int slice, long image)
Definition: ImageGeneric.java:146
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xmipp.jni.ImageGeneric.resize
void resize(int w, int h)
Definition: ImageGeneric.java:90
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xmipp.jni.ImageGeneric.read
void read(long image)
Definition: ImageGeneric.java:138
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xmipp.jni.ImageGeneric.setDataType
final native void setDataType(int dataType)
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xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(String filename, MetaData metadata, long id, boolean wrap)
Definition: ImageGeneric.java:172
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xmipp.jni.ImageGeneric.Z_NEG
static final int Z_NEG
Definition: ImageGeneric.java:35
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xmipp.jni.ImageGeneric.applyGeo
void applyGeo(double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap)
Definition: ImageGeneric.java:318
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xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(String filename, MetaData metadata, long id, int w, int h)
Definition: ImageGeneric.java:178
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xmipp.jni.ImageGeneric.applyAlignment
native void applyAlignment(ImageGeneric img, int index, double rot, double tilt, double psi)
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xmipp.jni.ImageGeneric.getRadialAvg
synchronized native void getRadialAvg(ImageGeneric radialimg)
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xmipp.jni.ImageGeneric.Z_POS
static final int Z_POS
Definition: ImageGeneric.java:36
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xmipp.jni.ImageGeneric.ALL_IMAGES
static final long ALL_IMAGES
Definition: ImageGeneric.java:10
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xmipp.jni.ImageGeneric.setFilename
void setFilename(String filename)
Definition: ImageGeneric.java:85
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xmipp.jni.ImageGeneric.Default
static final int Default
Definition: ImageGeneric.java:14
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xmipp.jni.ImageGeneric.ComplexDouble
static final int ComplexDouble
Definition: ImageGeneric.java:29
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xmipp.jni.ImageGeneric.applyGeo
native void applyGeo(double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap, double scaleFactor)
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xmipp.jni.ImageGeneric.bestShift
native Particle bestShift(ImageGeneric img)
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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xmipp.jni.ImageGeneric.UHalfByte
static final int UHalfByte
Definition: ImageGeneric.java:31
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xmipp.jni.ImageGeneric.getArrayByte
native byte [] getArrayByte(long select_image, int slice)
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xmipp.jni.ImageGeneric.MID_SLICE
static final int MID_SLICE
Definition: ImageGeneric.java:12
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xmipp.jni.ImageGeneric.LastEntry
static final int LastEntry
Definition: ImageGeneric.java:32
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xmipp.jni.ImageGeneric.ImageGeneric
ImageGeneric(String filename)
Definition: ImageGeneric.java:78
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xmipp.jni.ImageGeneric.read
void read(int slice, long image)
Definition: ImageGeneric.java:134
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xmipp.jni.ImageGeneric.getZDim
native int getZDim()
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xmipp.jni.ImageGeneric.Int
static final int Int
Definition: ImageGeneric.java:21
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xmipp.jni.ImageGeneric.read
void read(String filename, boolean map)
Definition: ImageGeneric.java:152
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xmipp.jni.ImageGeneric.Short
static final int Short
Definition: ImageGeneric.java:19
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xmipp.jni.Filename.getPrefix
static String getPrefix(String filename)
Definition: Filename.java:339
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xmipp.jni.ImageGeneric.setUseLogarithm
void setUseLogarithm(boolean useLogarithm)
Definition: ImageGeneric.java:118
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xmipp.jni.ImageGeneric.generateImageWithTwoCTFs
native void generateImageWithTwoCTFs(MetaData md1, MetaData md2, int xdim)
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xmipp.jni.ImageGeneric.getArrayFloat
native float [] getArrayFloat(long select_image, int slice)
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xmipp.jni.ImageGeneric.Y_NEG
static final int Y_NEG
Definition: ImageGeneric.java:37
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xmipp.jni.ImageGeneric.VIEWS
static final int VIEWS[]
Definition: ImageGeneric.java:42
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xmipp.jni.ImageGeneric.Double
static final int Double
Definition: ImageGeneric.java:25
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xmipp.jni.ImageGeneric.equal
native boolean equal(ImageGeneric img, double accuracy)
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xmipp.jni.ImageGeneric.UInt
static final int UInt
Definition: ImageGeneric.java:20
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xmipp.jni.ImageGeneric.ComplexShort
static final int ComplexShort
Definition: ImageGeneric.java:26
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xmipp.jni.ImageGeneric.getReslice
native void getReslice(ImageGeneric imgOut, int view)
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xmipp.jni.ImageGeneric.alignImage
synchronized native double [] alignImage(ImageGeneric img)
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xmipp.jni.ImageGeneric.X_POS
static final int X_POS
Definition: ImageGeneric.java:40
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xmipp.jni.ImageGeneric.Float
static final int Float
Definition: ImageGeneric.java:24
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xmipp.jni.ImageGeneric.getPreview
native void getPreview(ImageGeneric imgOut, int xdim, int ydim, int select_slice, long select_image)
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1 package xmipp.viewer;
2 
3 
4 import java.awt.Color;
5 import java.awt.Component;
6 import java.awt.Font;
7 import java.awt.Image;
8 
9 import javax.swing.BorderFactory;
10 import javax.swing.Icon;
11 import javax.swing.ImageIcon;
12 import javax.swing.JLabel;
13 import javax.swing.JTable;
14 import javax.swing.border.Border;
15 import javax.swing.table.DefaultTableCellRenderer;
16 
17 import xmipp.utils.CompoundIcon;
18 import xmipp.utils.XmippResource;
19 import xmipp.viewer.models.ImageGalleryTableModel;
20 import xmipp.viewer.models.ClassInfo;
21 
26 public class ImageItemRenderer extends DefaultTableCellRenderer {
27  private static final long serialVersionUID = 1L;
28 
29  Border BORDER_SELECTED = new StrokeBorder(Color.RED, 3);
30  Border BORDER_FOCUSED = BorderFactory.createLineBorder(Color.RED, 3);
31  public boolean hackBorders = true;
32 
33  public ImageItemRenderer() {
34  super();
35  setOpaque(true);
36  setHorizontalAlignment(JLabel.CENTER);
37  setHorizontalTextPosition(JLabel.CENTER);
38  setVerticalTextPosition(JLabel.BOTTOM);
39  }
40 
41  public ImageItemRenderer(boolean hackBorders) {
42  this();
43  this.hackBorders = false;//no use of parameter provided???
44  }
45 
46  @Override
47  public Component getTableCellRendererComponent(JTable table, Object object,
48  boolean isSelected, boolean hasFocus, int row, int column) {
49  ImageGalleryTableModel.ImageItem item = (ImageGalleryTableModel.ImageItem) object;
50  // DEBUG.printMessage("*** 1. Rendering: " + item.getLabel());
51  // DEBUG.printFormat("*** 1. Rendering: item: %s, index: %d, row: %d, col: %d",
52  // item.getLabel(), item.getIndex(), row, column);
53 // Calls super class so foreground, background, borders and rest of
54 // stuff is set.
55  super.getTableCellRendererComponent(table, null, item != null
56  && item.isSelected(), item != null && hasFocus, row, column);
57 
58  if (item != null) {
59  // DEBUG.printMessage("*** 2. Rendering: " + item.getLabel());
60  // AbstractXmippTableModel tableModel = (AbstractXmippTableModel)
61  // table.getModel();
62 
63  setPreferredSize(item.getCellDim());
64 
65  // Loads image...
66 
67  Image image = item.getImage();
68  Icon icon;
69 
70  if (image != null)
71  icon = new ImageIcon(image);
72  else
73  icon = XmippResource.MISSING_ICON;
74 
75  if (!item.isEnabled()){
76  icon = new CompoundIcon(CompoundIcon.Axis.Z_AXIS, 0,
77  CompoundIcon.RIGHT, CompoundIcon.BOTTOM, icon,
78  XmippResource.DELETE_ICON);
79  //new ColoredRectangleIcon(Color.red, 16, 16));
80  }
81 
82  if (item.isBusy()) {
83  icon = new CompoundIcon(CompoundIcon.Axis.Z_AXIS, 0,
84  CompoundIcon.RIGHT, CompoundIcon.BOTTOM, icon,
85  XmippResource.LOCK_ICON);
86  }
87  ClassInfo cli = item.getClassInfo();
88  if (cli != null){
89  icon = new CompoundIcon(CompoundIcon.Axis.Z_AXIS, 0,
90  CompoundIcon.RIGHT, CompoundIcon.BOTTOM, icon,
91  cli.getIcon());
92 
93  }
94  setIcon(icon);
95  // Tooltip.
96  setToolTipText(item.getLabel());
97 
98  // (Shows label only when required).
99  if (item.getShowLabel()) {
100  String label = cutString(item.getLabel(), table
101  .getColumnModel().getColumn(column).getWidth());
102  setText(label);
103  } else {
104  setText(null);
105  }
106 
107  if (hackBorders) {
108  // Hacking borders to enhance the default one.
109  if (item.isSelected()) {
110  setBorder(BORDER_SELECTED);
111  }
112 
113  // if (hasFocus) {
114  // setBorder(BORDER_FOCUSED);
115  // }
116  }
117  } else {
118  setIcon(null);
119  setText(null);
120  setToolTipText(null);
121  }
122 
123  return this;
124  }
125 
126  protected String cutString(String string, int columnWidth) {
127  StringBuilder sb = new StringBuilder(string);
128  String str = sb.toString();
129 
130  Font font = getFont();
131  int w = getFontMetrics(font).stringWidth(str);
132 
133  int i = 0;
134  while (w > columnWidth) {
135  str = "..." + sb.substring(i++);
136  w = getFontMetrics(font).stringWidth(str);
137  }
138 
139  return str;
140  }
141 }
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xmipp.utils.XmippResource.DELETE_ICON
static ImageIcon DELETE_ICON
Definition: XmippResource.java:45
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xmipp.viewer.ImageItemRenderer.getTableCellRendererComponent
Component getTableCellRendererComponent(JTable table, Object object, boolean isSelected, boolean hasFocus, int row, int column)
Definition: ImageItemRenderer.java:47
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xmipp.utils.XmippResource.LOCK_ICON
static ImageIcon LOCK_ICON
Definition: XmippResource.java:44
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xmipp.utils.CompoundIcon.BOTTOM
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Definition: CompoundIcon.java:33
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xmipp.viewer.ImageItemRenderer.ImageItemRenderer
ImageItemRenderer(boolean hackBorders)
Definition: ImageItemRenderer.java:41
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xmipp.utils.CompoundIcon.RIGHT
static final float RIGHT
Definition: CompoundIcon.java:34
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xmipp.viewer.ImageItemRenderer.cutString
String cutString(String string, int columnWidth)
Definition: ImageItemRenderer.java:126
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xmipp.utils.XmippResource.MISSING_ICON
static ImageIcon MISSING_ICON
Definition: XmippResource.java:50
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.ij.commons;
8 
9 import ij.ImagePlus;
10 import java.awt.Dimension;
11 import java.awt.Graphics;
12 import java.awt.Image;
13 import java.awt.event.MouseEvent;
14 import java.awt.event.MouseMotionListener;
15 import javax.swing.JPanel;
16 
21 public class ImageJPanel extends JPanel{
22 
23  protected ImagePlus imp;
24  protected int width, height;
25 
26  public ImageJPanel(ImagePlus image, int width, int height) {
27  this.imp = image;
28  this.width = width;
29  this.height = height;
30  }
31 
32  @Override
33  public Dimension getPreferredSize()
34  {
35  return new Dimension(width, height);
36 
37  }
38 
39  @Override
40  protected void paintComponent(Graphics g) {
41  super.paintComponent(g);
42 
43  g.drawImage(imp.getImage().getScaledInstance(width, height, Image.SCALE_SMOOTH), 0, 0, null); // see javadoc for more info on the parameters
44  }
45 
46  public void setMask(ImagePlus mask, int width, int height)
47  {
48  this.imp = mask;
49  this.width = width;
50  this.height = height;
51  setSize(new Dimension(width, height));
52  repaint();
53 
54  }
55 
56 
57 
58 }
xmipp.ij.commons.ImageJPanel.paintComponent
void paintComponent(Graphics g)
Definition: ImageJPanel.java:40
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xmipp.ij.commons.ImageJPanel.setMask
void setMask(ImagePlus mask, int width, int height)
Definition: ImageJPanel.java:46
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xmipp.ij.commons.ImageJPanel.ImageJPanel
ImageJPanel(ImagePlus image, int width, int height)
Definition: ImageJPanel.java:26
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.ij.commons;
8 
9 import ij.ImagePlus;
10 import java.io.File;
11 import xmipp.jni.Filename;
12 import xmipp.jni.ImageGeneric;
13 
18 public class ImagePlusFromFile extends ImagePlusReader{
19 
20 
21  private String fileName;
22  private long modified;
23 
24  public ImagePlusFromFile(String fileName)
25  {
26  if (fileName == null || fileName.equals(""))
27  throw new IllegalArgumentException("empty file");
28  this.fileName = fileName;
29  this.modified = new File(fileName).lastModified();
30 
31  }
32 
33  public ImagePlusFromFile(String fileName, ImagePlus imp, ImageGeneric ig)
34  {
35  this(fileName);
36  this.imp = imp;
37  this.ig = ig;
38  }
39 
40 
41  @Override
42  public ImagePlus loadImagePlus()
43  {
44 
45  imp = null;
46  try
47  {
48  if (ig == null || hasChanged())
49  {
50  if(Filename.isXmippSupported(fileName))
51  try
52  {
53  ig = new ImageGeneric(fileName);//to read again file
54  }
55  catch(Exception e)
56  {
57  imp = new ImagePlus(fileName);
58  }
59  else
60  imp = new ImagePlus(fileName);
61  if(ig != null && !hasIndex())
62  {
63  imp = XmippImageConverter.readToImagePlus(ig);
64  }
65  else if(ig != null)
66  {
67  if(ig.isStack())
68  imp = XmippImageConverter.readToImagePlus(ig, index, ImageGeneric.ALL_SLICES);//read image or volume on indexn
69  else
70  imp = XmippImageConverter.readToImagePlus(ig, (int)index);//read image slice on volume
71  }
72  }
73  else if(ig != null)
74  {
75  if(index == -2 || !ig.isStackOrVolume())//if index is not -2 ig read it already
76  imp = XmippImageConverter.convertToImagePlus(ig);
77  else
78  {
79  if(ig.isStack())
80  imp = XmippImageConverter.convertToImagePlus(ig, index);//read image or volume on index
81  else
82  imp = XmippImageConverter.convertToImagePlus(ig, ImageGeneric.FIRST_IMAGE, (int)index);//read image slice on volume
83  }
84  }
85  checkResizeAndGeo();
86  checkInvertY();
87  if(normalize)
88  {
89  imp.getProcessor().setMinAndMax(normalize_min, normalize_max);
90  imp.updateImage();
91  }
92  return imp;
93 
94  }
95  catch (Exception e)
96  {
97  e.printStackTrace();
98  }
99  return imp;
100  }
101 
102 
103 
104  public boolean hasChanged()
105  {
106  return new File(fileName).lastModified() > modified;
107  }
108 
109 
110  public String getFileName()
111  {
112  return fileName;
113  }
114 
115  @Override
116  public boolean getAllowsPoll() {
117  return true;
118  }
119 
120  @Override
121  public String getName() {
122 
123  String name = fileName;
124  if(!name.contains("@"))
125  name = Filename.getBaseName(name);
126  else
127  name = Filename.getPrefix(name) + Filename.SEPARATOR + Filename.getBaseName(Filename.getFilename(name));
128 
129  if(index != -2)
130  name = String.format("%d@%s", index, name);
131  return name;
132 
133  }
134 
135 
136 
137 
138 
139 
140 }
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xmipp.jni.Filename.getBaseName
static String getBaseName(String path)
Definition: Filename.java:458
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xmipp.jni.ImageGeneric.ALL_SLICES
static final int ALL_SLICES
Definition: ImageGeneric.java:11
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xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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ImagePlusFromFile(String fileName, ImagePlus imp, ImageGeneric ig)
Definition: ImagePlusFromFile.java:33
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xmipp.jni.Filename.isXmippSupported
static boolean isXmippSupported(String filename)
Definition: Filename.java:502
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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static String getFilename(String filename)
Definition: Filename.java:302
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xmipp.jni.Filename.getPrefix
static String getPrefix(String filename)
Definition: Filename.java:339
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static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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static final String SEPARATOR
Definition: Filename.java:8
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1 
26 package xmipp.ij.commons;
27 
28 import ij.ImagePlus;
29 import java.io.File;
30 import xmipp.jni.Filename;
31 import xmipp.jni.ImageGeneric;
32 import xmipp.utils.XmippMessage;
33 
34 public class ImagePlusLoader {
35 
36  protected ImagePlusReader impreader;
37  private boolean existsfile;
38 
39  public ImagePlusLoader(ImagePlus imp) {
40  this(getFile(imp), imp, null, false, false, false, -2);
41  }
42 
43  public ImagePlusLoader(ImagePlus imp, boolean inverty) {
44  this(getFile(imp), imp, null, false, false, inverty, -2);
45  }
46 
47  public ImagePlusLoader(ImageGeneric ig, boolean inverty) {
48  this(getFile(ig), null, ig, false, false, inverty, -2);
49  }
50 
51  public ImagePlusLoader(int index, ImageGeneric ig) {
52  this(getFile(ig), null, ig, false, false, false, index);
53  }
54 
55  public ImagePlusLoader(int index, ImageGeneric ig, boolean inverty) {
56  this(getFile(ig), null, ig, false, false, inverty, index);
57  }
58 
59  public ImagePlusLoader(String fileName, boolean inverty) {
60  this(fileName, null, null, false, false, inverty, -2);
61  }
62 
63  public ImagePlusLoader(String fileName) {
64  this(fileName, null, null, false, false, false, -2);
65  }
66 
67  public ImagePlusLoader(String fileName, boolean useGeometry, boolean wrap, boolean inverty) {
68  this(fileName, null, null, useGeometry, wrap, inverty, -2);
69  }
70 
71  public ImagePlusLoader(String fileName, ImagePlus imp, ImageGeneric ig, boolean useGeo, boolean wrap, boolean inverty, int index) {
72 
73  if (fileName != null) {
74  String path = Filename.findImagePath(fileName, null, true);//check if file exists dismissing preffix and suffix
75  existsfile = path != null;
76  }
77  if (existsfile)
78  impreader = new ImagePlusFromFile(fileName, imp, ig);
79  else
80  {
81 
82  if(fileName != null)
83  throw new IllegalArgumentException(XmippMessage.getPathNotExistsMsg(fileName));
84  impreader = new ImagePlusNotFromFile(imp, ig);
85  }
86 //
87  impreader.setIndex(index);
88  impreader.setUseGeometry(useGeo);
89  setWrap(wrap);
90  setInvertY(inverty);
91  }
92 
93  public ImagePlusLoader(ImageGeneric ig) {
94  this(-1, ig);
95  }
96 
97  public void setNormalize(double normalize_min, double normalize_max) {
98  impreader.setNormalize(normalize_min, normalize_max);
99 
100  }
101 
102  public void setInvertY(boolean invert) {
103  impreader.setInvertY(invert);
104 
105  }
106 
107  public ImagePlus getImagePlus() {
108  return impreader.getImagePlus();
109  }
110 
111  public void setWrap(boolean value) {
112  impreader.setWrap(value);
113 
114  }
115 
116  public boolean isWrap() {
117  return impreader.isWrap();
118  }
119 
120  public static String getFile(ImagePlus imp) {
121  String file = null;
122 
123  if (imp != null && imp.getOriginalFileInfo() != null) {
124  file = imp.getOriginalFileInfo().directory + File.separator + imp.getOriginalFileInfo().fileName;
125  }
126 
127  return file;
128  }
129 
130  public static String getFile(ImageGeneric ig) {
131  String file = null;
132  if (ig != null && ig.getFilename() != null) {
133  file = ig.getFilename();
134  }
135  return file;
136  }
137 
138  public boolean allowsPoll() {
139  return impreader.getAllowsPoll();
140  }
141 
142  public String getName() {
143  return impreader.getName();
144  }
145 
146  public ImagePlus loadImagePlus() {
147  return impreader.loadImagePlus();
148  }
149 
150  public boolean existsFile() {
151  return existsfile;
152  }
153 
154  public boolean isVolume() {
155  return impreader.isVolume();
156  }
157 
158 
159  public boolean isStackOrVolume() {
160  return impreader.isStackOrVolume();
161  }
162 
163  public boolean getUseGeometry() {
164  return impreader.getUseGeometry();
165  }
166 
167  public void setUseGeometry(boolean value) {
168  impreader.setUseGeometry(value);
169 
170  }
171 
172  public void setGeometry(Geometry geometry)
173  {
174  impreader.setGeometry(geometry);
175  }
176 
177  public boolean hasGeometry()
178  {
179  return impreader.geometry != null;
180  }
181 
182 
183  public void setDimension(int width, int height)
184  {
185  impreader.setDimension(width, height);
186  }
187 
188  public boolean isInvertY() {
189  return impreader.isInvertY();
190  }
191 
192 
193 
194 }
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void setNormalize(double normalize_min, double normalize_max)
Definition: ImagePlusLoader.java:97
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xmipp.ij.commons.ImagePlusLoader.ImagePlusLoader
ImagePlusLoader(String fileName, ImagePlus imp, ImageGeneric ig, boolean useGeo, boolean wrap, boolean inverty, int index)
Definition: ImagePlusLoader.java:71
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ImagePlusLoader(int index, ImageGeneric ig)
Definition: ImagePlusLoader.java:51
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void setNormalize(double normalize_min, double normalize_max)
Definition: ImagePlusReader.java:115
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ImagePlusLoader(int index, ImageGeneric ig, boolean inverty)
Definition: ImagePlusLoader.java:55
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ImagePlusLoader(String fileName, boolean inverty)
Definition: ImagePlusLoader.java:59
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static String findImagePath(String filename, String mdFilename, boolean shouldExist)
Definition: Filename.java:225
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ImagePlusLoader(ImagePlus imp, boolean inverty)
Definition: ImagePlusLoader.java:43
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void setGeometry(Geometry geometry)
Definition: ImagePlusReader.java:165
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ImagePlusLoader(String fileName, boolean useGeometry, boolean wrap, boolean inverty)
Definition: ImagePlusLoader.java:67
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ImagePlusLoader(ImageGeneric ig, boolean inverty)
Definition: ImagePlusLoader.java:47
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static String getFile(ImageGeneric ig)
Definition: ImagePlusLoader.java:130
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void setDimension(int width, int height)
Definition: ImagePlusReader.java:179
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void setDimension(int width, int height)
Definition: ImagePlusLoader.java:183
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static String getPathNotExistsMsg(String path)
Definition: XmippMessage.java:71
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xmipp.ij.commons.ImagePlusLoader.getFile
static String getFile(ImagePlus imp)
Definition: ImagePlusLoader.java:120
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void setGeometry(Geometry geometry)
Definition: ImagePlusLoader.java:172
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.ij.commons;
8 
9 import ij.ImagePlus;
10 import xmipp.jni.Filename;
11 import xmipp.jni.ImageGeneric;
12 import xmipp.utils.XmippMessage;
13 
18 public class ImagePlusNotFromFile extends ImagePlusReader{
19 
20 
21  public ImagePlusNotFromFile(ImagePlus imp, ImageGeneric ig) {
22  if(imp == null && ig == null)
23  throw new IllegalArgumentException(XmippMessage.getEmptyFieldMsg("image") );
24  this.imp = imp;
25  this.ig = ig;
26  }
27 
28 
29 
30  @Override
31  public boolean getAllowsPoll() {
32  return false;
33  }
34 
35 
36 
37  @Override
38  public String getName() {
39 
40  if(imp == null && ig == null)
41  return null;
42  String name = (ig != null)? Filename.getBaseName(ig.getFilename()): imp.getTitle();
43 
44  if(index != -2)
45  name = String.format("%d@%s", index, name);
46  return name;
47  }
48 
49 
50 }
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xmipp.jni.Filename.getBaseName
static String getBaseName(String path)
Definition: Filename.java:458
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ImagePlusNotFromFile(ImagePlus imp, ImageGeneric ig)
Definition: ImagePlusNotFromFile.java:21
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static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 package xmipp.ij.commons;
7 
8 import ij.ImagePlus;
9 import ij.process.ImageProcessor;
10 import java.util.logging.Level;
11 import java.util.logging.Logger;
12 import xmipp.jni.ImageGeneric;
13 
18 public abstract class ImagePlusReader {
19 
20  protected ImagePlus imp;
21  protected ImageGeneric ig;
22  protected boolean useGeometry;
23  protected boolean wrap;
24  protected long modified;
25 
26  protected long index = -2;
27  protected boolean normalize;
28  protected double normalize_min;
29  protected double normalize_max;
30  protected Geometry geometry;
31  protected int width, height;
32  protected boolean inverty;
33 
34 
35  public abstract boolean getAllowsPoll();
36 
37  public ImagePlus getImagePlus() {
38  if (imp == null) {
39  imp = loadImagePlus();
40  }
41  return imp;
42  }
43 
44  public ImagePlus loadImagePlus()
45  {
46  imp = null;
47  try
48  {
49  if(ig != null)
50  {
51 
52  if(!hasIndex() )
53  imp = XmippImageConverter.convertToImagePlus(ig);
54  else
55  {
56  if(ig.isStack())
57  imp = XmippImageConverter.convertToImagePlus(ig, index);//read image or volume on index
58  else
59  imp = XmippImageConverter.convertToImagePlus(ig, ImageGeneric.FIRST_IMAGE, (int)index);//read image slice on volume
60  }
61  }
62  checkResizeAndGeo();
63  checkInvertY();
64  if(normalize)
65  {
66  imp.getProcessor().setMinAndMax(normalize_min, normalize_max);
67  imp.updateImage();
68  }
69 
70  return imp;
71  }
72  catch (Exception e)
73  {
74  e.printStackTrace();
75  throw new IllegalArgumentException(e);
76  }
77 
78  }
79 
80  public void checkResizeAndGeo()
81  {
82  if(useGeometry && geometry != null)
83  {
84  try {
85 
86  ImageGeneric tempig = XmippImageConverter.convertToImageGeneric(imp);
87  if (geometry.hasMatrix())
88  tempig.applyGeoMatrix(geometry.getMatrix(), wrap);
89  else
90  tempig.applyGeo(geometry.shiftx, geometry.shifty, geometry.psiangle, geometry.flip, wrap, geometry.scaleFactor);
91  imp = XmippImageConverter.convertToImagePlus(tempig);
92  } catch (Exception ex) {
93  Logger.getLogger(ImagePlusReader.class.getName()).log(Level.SEVERE, null, ex);
94  }
95  }
96  ImageProcessor processor = imp.getProcessor();
97  if(width != 0 && height != 0 && imp != null && processor != null)
98  {
99  processor.setInterpolate(true);
100  processor = processor.resize(width, height);
101  imp = new ImagePlus("", processor);
102  }
103  }
104 
105 
106  protected void checkInvertY() {
107  if(inverty)
108  {
109  imp.getProcessor().flipVertical();
110  imp.updateImage();
111  }
112  }
113 
114 
115  public void setNormalize(double normalize_min, double normalize_max)
116  {
117  this.normalize = true;
118  this.normalize_min = normalize_min;
119  this.normalize_max = normalize_max;
120 
121  }
122 
123  public void setInvertY(boolean inverty)
124  {
125  this.inverty = inverty;
126 
127  }
128 
129  public boolean isVolume()
130  {
131  try
132  {
133  if(imp != null)
134  return imp.getStackSize() > 1;
135  loadImagePlus();
136  return isVolume();
137 
138  }
139  catch (Exception e)
140  {
141  throw new IllegalArgumentException(e.getMessage());
142  }
143  }
144 
145  void setIndex(int index) {
146 
147  this.index = index;
148  }
149 
150  public boolean hasIndex()
151  {
152  return index != -2;
153  }
154 
155  public abstract String getName() ;
156 
157 
158  boolean isStackOrVolume() {
159  if(imp == null)
160  loadImagePlus();
161  return imp.getStackSize() > 1;
162  }
163 
164 
165  public void setGeometry(Geometry geometry)
166  {
167  this.geometry = geometry;
168  }
169 
170  public boolean getUseGeometry() {
171  return useGeometry;
172  }
173 
174  public void setUseGeometry(boolean value) {
175  useGeometry = value;
176 
177  }
178 
179  public void setDimension(int width, int height) {
180  this.width = width;
181  this.height = height;
182  }
183 
184  public void setWrap(boolean value) {
185  wrap = value;
186 
187  }
188 
189  public boolean isWrap() {
190  return wrap;
191  }
192 
193  public boolean isInvertY() {
194  return inverty;
195  }
196 
197 
198 }
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xmipp.jni.ImageGeneric.applyGeoMatrix
void applyGeoMatrix(String matrixString, boolean wrap)
Definition: ImageGeneric.java:328
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xmipp.ij.commons.XmippImageConverter.convertToImageGeneric
static ImageGeneric convertToImageGeneric(ImagePlus imp)
Definition: XmippImageConverter.java:297
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xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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xmipp.ij.commons.ImagePlusReader.setNormalize
void setNormalize(double normalize_min, double normalize_max)
Definition: ImagePlusReader.java:115
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xmipp.ij.commons.ImagePlusReader.setGeometry
void setGeometry(Geometry geometry)
Definition: ImagePlusReader.java:165
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xmipp.ij.commons.ImagePlusReader.setDimension
void setDimension(int width, int height)
Definition: ImagePlusReader.java:179
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xmipp.jni.ImageGeneric.applyGeo
native void applyGeo(double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap, double scaleFactor)
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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xmipp.ij.commons.ImagePlusReader.getAllowsPoll
abstract boolean getAllowsPoll()
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.utils;
8 
9 import java.awt.Component;
10 import java.awt.Image;
11 import javax.swing.ImageIcon;
12 import javax.swing.JLabel;
13 import javax.swing.JTable;
14 import javax.swing.table.DefaultTableCellRenderer;
15 
20 public class ImageRenderer extends DefaultTableCellRenderer {
21  JLabel lbl = new JLabel();
22 
23 
24 
25  public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected,
26  boolean hasFocus, int row, int column) {
27  lbl.setIcon((ImageIcon)value);
28  return lbl;
29  }
30 }
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xmipp.utils.ImageRenderer.getTableCellRendererComponent
Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)
Definition: ImageRenderer.java:25
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1 package xmipp.jni;
2 
3 public class ImageWriteMode {
4  public static final int WRITE_READONLY = 0; //only can read the file ///
5  public static final int WRITE_OVERWRITE = 1; //forget about the old file and overwrite it ///
6  public static final int WRITE_REPLACE = 2; //replace a particular object by another ///
7  public static final int WRITE_APPEND = 3; //append and object at the end of a stack = 3; so far can not append stacks ///
8  public static final int WRITE_LAST_LABEL = 4; // **** NOTE ****: Do keep this label always at the end ///
9 }
xmipp.jni.ImageWriteMode.WRITE_REPLACE
static final int WRITE_REPLACE
Definition: ImageWriteMode.java:6
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xmipp.jni.ImageWriteMode.WRITE_LAST_LABEL
static final int WRITE_LAST_LABEL
Definition: ImageWriteMode.java:8
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xmipp.jni.ImageWriteMode.WRITE_APPEND
static final int WRITE_APPEND
Definition: ImageWriteMode.java:7
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xmipp.jni.ImageWriteMode.WRITE_READONLY
static final int WRITE_READONLY
Definition: ImageWriteMode.java:4
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xmipp.jni.ImageWriteMode.WRITE_OVERWRITE
static final int WRITE_OVERWRITE
Definition: ImageWriteMode.java:5
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1 import ij.*;
2 import ij.plugin.filter.PlugInFilter;
3 import ij.process.*;
4 import java.awt.*;
5 
27 public class Image_Inverter implements PlugInFilter {
28 
29  public int setup(String arg, ImagePlus imp) {
30  return DOES_ALL+DOES_STACKS+SUPPORTS_MASKING;
31  }
32 
33  public void run(ImageProcessor ip) {
34  Rectangle r = ip.getRoi();
35  for (int y=r.y; y<(r.y+r.height); y++)
36  for (int x=r.x; x<(r.x+r.width); x++)
37  ip.set(x, y, ~ip.get(x,y));
38  }
39 
40 }
41 
Image_Inverter.run
void run(ImageProcessor ip)
Definition: Image_Inverter.java:33
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Image_Inverter.setup
int setup(String arg, ImagePlus imp)
Definition: Image_Inverter.java:29
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Image_Inverter
Definition: Image_Inverter.java:27
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class  xmipp.viewer.windows.ImagesWindowFactory
 
class  xmipp.viewer.windows.ImagesWindowFactory.Worker
 
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package  xmipp.viewer.windows
 
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1 /*
2  * To change this template, choose Tools | Templates
3  * and openTableFileImageItem the template in the editor.
4  */
5 package xmipp.viewer.windows;
6 
7 import ij.IJ;
8 import ij.ImagePlus;
9 import ij.gui.ImageWindow;
10 import ij.process.StackConverter;
11 import ij3d.Content;
12 import ij3d.Image3DUniverse;
13 import java.awt.Component;
14 import java.awt.FontMetrics;
15 import java.awt.Frame;
16 import java.awt.Window;
17 import javax.swing.SwingUtilities;
18 import javax.vecmath.Color3f;
19 import xmipp.ij.commons.ImagePlusLoader;
20 import xmipp.ij.commons.XmippIJWindow;
21 import xmipp.ij.commons.XmippImageCanvas;
22 import xmipp.ij.commons.XmippImageConverter;
23 import xmipp.ij.commons.XmippImageWindow;
24 import xmipp.ij.commons.XmippMenuBar;
25 import xmipp.ij.commons.XmippStackWindow;
26 import xmipp.jni.Filename;
27 import xmipp.jni.ImageGeneric;
28 import xmipp.jni.MDLabel;
29 import xmipp.jni.MetaData;
30 import xmipp.utils.DEBUG;
31 import xmipp.utils.Params;
32 import xmipp.utils.ScipionParams;
33 import xmipp.utils.XmippDialog;
34 import xmipp.utils.XmippMessage;
35 import xmipp.viewer.scipion.ScipionGalleryData;
36 import xmipp.viewer.scipion.ScipionGalleryJFrame;
37 import xmipp.viewer.scipion.ScipionMetaData;
38 
43 public class ImagesWindowFactory {
44 
45  private final static int UNIVERSE_W = 400, UNIVERSE_H = 400;
46 
47  public static void openFilesAsDefault(String filenames[], Params parameters) {
48  for (int i = 0; i < filenames.length; i++) {
49  openFileAsDefault(filenames[i], parameters);
50  }
51  }
52 
53  public static void openFileAsDefault(String filename) {
54 
55  Params params = new Params();
56 
57  if (ScipionMetaData.isScipionMetaData(filename)) {
58  params = new ScipionParams();
59  }
60 
61  openFileAsDefault(filename, params);
62  }
63 
64  public static void openFileAsDefault(String filename, Params parameters) {
65  try {
66  if (Filename.isMetadata(filename)) {
67  if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_IMAGE))
68  openFileAsImage(null, filename, parameters);
69  else
70  openMetadata(filename, parameters,
71  Params.OPENING_MODE_GALLERY);
72  } else {
73  ImageGeneric img = new ImageGeneric(filename);
74 
75  if (img.isSingleImage()) {
76  openFileAsImage(null, filename, parameters);
77  } else if (img.isStackOrVolume()) {
78  if (parameters.mode
79  .equalsIgnoreCase(Params.OPENING_MODE_IMAGE))
80  openFileAsImage(null, filename, parameters);
81  else
82  openMetadata(filename, parameters, Params.OPENING_MODE_GALLERY);
83  }
84  }
85  } catch (Exception e) {
86  XmippDialog.showError(null, String.format(
87  "Couldn't open file: '%s'\nError: %s", filename,
88  e.getMessage()));
89  e.printStackTrace();
90  }
91  }
92 
93  public static void openFilesAsImages(String filenames[], Params parameters) {
94  for (int i = 0; i < filenames.length; i++) {
95  openFileAsImage(null, filenames[i], parameters);
96  }
97  }
98 
99  public static void openFileAsImage(String path) {
100  openFileAsImage(null, path, new Params());
101  }
102 
103  public static void openFileAsImage(Frame pframe, String filename,
104  Params parameters) {
105  try {
106  ImagePlusLoader ipl = new ImagePlusLoader(filename, false);
107  XmippIJWindow xiw = openXmippImageWindow(ipl,
108  parameters);
109  if (parameters.mask_toolbar)
110  xiw.openMaskToolbar();
111  } catch (Exception e) {
112  XmippDialog.showError(null, String.format(
113  "Couldn't open file: '%s'\nError: %s", filename,
114  e.getMessage()));
115  e.printStackTrace();
116  }
117  }
118 
119  public static ImagePlus openFileAsImagePlus(String path, Params parameters)
120  throws Exception {
121  ImagePlus imp;
122  if (Filename.isMetadata(path)) {
123  MetaData md = new MetaData(path);
124  imp = XmippImageConverter.readMetadataToImagePlus(
125  MDLabel.MDL_IMAGE, md, parameters.useGeo, parameters.wrap, parameters.inverty);
126  md.destroy();
127  } else {
128  imp = XmippImageConverter.loadImage(path,
129  parameters.zoom != null ? parameters.zoom : 100);
130  }
131  return imp;
132  }
133 
134  public static XmippIJWindow openXmippImageWindow(
135  ImagePlus imp, Params params) {
136  return openXmippImageWindow(new ImagePlusLoader(imp), params);
137  }
138 
139  public static XmippIJWindow openXmippImageWindow(
140  ImagePlusLoader impLoader, Params parameters) {
141  return openXmippImageWindow(impLoader, impLoader.getName(), parameters);
142 
143  }
144  public static XmippIJWindow openXmippImageWindow(
145  ImagePlusLoader impLoader, String title, Params parameters) {
146 
147  XmippIJWindow iw;
148 
149  if (impLoader.isStackOrVolume())
150  iw = (title != null)? new XmippStackWindow(impLoader, title, parameters): new XmippStackWindow(impLoader, parameters);
151  else
152  iw = (title != null )? new XmippImageWindow(impLoader, title, parameters): new XmippImageWindow(impLoader, parameters);
153 
154  SwingUtilities.invokeLater(new Worker(iw));
155  return iw;
156  }
157 
158  public static class Worker implements Runnable {
159 
160  XmippIJWindow iw;
161 
162  public Worker(XmippIJWindow iw) {
163  this.iw = iw;
164  }
165 
166  @Override
167  public void run() {
168  ((XmippImageCanvas) iw.getCanvas()).adjustMagnification();
169  Frame frame = (ImageWindow) iw;
170  frame.setVisible(true);
171 
172  }
173  }
174 
180  public static GalleryJFrame openMetadata(String filename, MetaData md,
181  Params parameters, String mode) {
182 
183  if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_DEFAULT))
184  parameters.mode = mode;
185  return new GalleryJFrame(md, parameters);
186  }
187 
188  public static void openMetadata(String filename, Params parameters,
189  String mode) throws Exception
190  {
191  if(filename.endsWith(".sqlite") || filename.endsWith(".db"))
192  openScipionMetadata(filename, parameters);
193  else
194  openMetadata(filename, new MetaData(filename), parameters, mode);
195  }
196 
197  public static void openScipionMetadata(String filename, Params parameters) throws Exception
198  {
199  if(!(filename.endsWith(".sqlite") || filename.endsWith(".db")))
200  throw new IllegalArgumentException(XmippMessage.getIllegalValueMsg("scipion metadata", filename));
201  else
202  {
203  ScipionMetaData md;
204  if(filename.contains("@"))
205  {
206  int sep = filename.indexOf('@');
207  final String preffix = filename.substring(0, sep);
208  filename = filename.substring(sep + 1);
209  md = new ScipionMetaData(filename);
210  final ScipionGalleryData data = new ScipionGalleryData(null, parameters, md);
211  SwingUtilities.invokeLater(new Runnable() {
212 
213  @Override
214  public void run() {
215  ScipionGalleryJFrame frame = new ScipionGalleryJFrame(data);
216  frame.selectBlock(preffix);
217  }
218  });
219 
220  }
221  else
222  {
223  md = new ScipionMetaData(filename);
224  ScipionGalleryData data = new ScipionGalleryData(null, parameters, md);
225  new ScipionGalleryJFrame(data);
226  }
227  }
228  }
229 
230 
231 
232 
233  public static void openFilesAsGallery(String filenames[],
234  boolean useSameTable) throws Exception {
235  openFilesAsGallery(filenames, useSameTable, new Params());
236  }
237 
238  public static void openFilesAsGallery(String filenames[],
239  boolean useSameTable, Params parameters) throws Exception {
240  GalleryJFrame gallery = null;
241 
242  if (useSameTable) {
243  MetaData md = new MetaData();
244  for (int i = 0; i < filenames.length; ++i)
245  md.setValueString(MDLabel.MDL_IMAGE, filenames[i],
246  md.addObject());
247  openMetadata(null, md, parameters, null);
248  } else {
249  for (int i = 0; i < filenames.length; i++) {
250  openMetadata(filenames[i], parameters,
251  Params.OPENING_MODE_GALLERY);
252  }
253  }
254 
255  }
256 
257  public static void openImagePlusAs3D(ImagePlus ip) {
258  try {
259  // Checks if java3D is available or not.
260  Class.forName("javax.media.j3d.J3DBuffer");
261 
262  new StackConverter(ip).convertToRGB();
263 
264  Image3DUniverse universe = new Image3DUniverse(UNIVERSE_W,
265  UNIVERSE_H);
266 
267  // Adds the sphere image plus to universe.
268  Content c = universe.addSurfacePlot(ip, new Color3f(1f, 165f / 255,
269  82f / 255), "1", 50, new boolean[] { true, true, true }, 1);
270  c.displayAs(Content.SURFACE);
271  c.setColor(new Color3f(1f, 165f / 255, 82f / 255));
272 
273  universe.show(); // Shows...
274  } catch (final ClassNotFoundException e) {
275  IJ.error("Java 3D not found. Please, check your installation.");
276  }
277  }
278 
279 
280 
281  public static void openFileAsText(String filename, Component parent) {
282  TextfileJFrame frameText = new TextfileJFrame(filename);
283  if (parent != null)
284  frameText.setLocationRelativeTo(null);
285  frameText.setVisible(true);
286  }
287 
288 
289  public static String getSortTitle(String title, int width,
290  FontMetrics fontMetrics) {
291  String sort = title;
292  int strlenght = fontMetrics.stringWidth(sort);
293  int index = 0;
294 
295  while (strlenght > width) {
296  index++;
297  sort = "..." + title.substring(index);
298  strlenght = fontMetrics.stringWidth(sort);
299  }
300 
301  return sort;
302  }
303 }
xmipp.jni.MetaData.addObject
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xmipp.jni.MetaData.setValueString
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xmipp.viewer.windows.ImagesWindowFactory.openFileAsDefault
static void openFileAsDefault(String filename)
Definition: ImagesWindowFactory.java:53
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static ImagePlus readMetadataToImagePlus(int label, MetaData md, boolean useGeo, boolean wrap, boolean inverty)
Definition: XmippImageConverter.java:226
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xmipp.viewer.windows.ImagesWindowFactory.openFilesAsDefault
static void openFilesAsDefault(String filenames[], Params parameters)
Definition: ImagesWindowFactory.java:47
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xmipp.viewer.windows.ImagesWindowFactory.openXmippImageWindow
static XmippIJWindow openXmippImageWindow(ImagePlusLoader impLoader, String title, Params parameters)
Definition: ImagesWindowFactory.java:144
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static void openMetadata(String filename, Params parameters, String mode)
Definition: ImagesWindowFactory.java:188
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xmipp.ij.commons.XmippImageConverter.loadImage
static ImagePlus loadImage(String filename)
Definition: XmippImageConverter.java:49
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xmipp.utils.Params.mask_toolbar
boolean mask_toolbar
Definition: Params.java:68
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xmipp.viewer.windows.ImagesWindowFactory.getSortTitle
static String getSortTitle(String title, int width, FontMetrics fontMetrics)
Definition: ImagesWindowFactory.java:289
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xmipp.viewer.windows.ImagesWindowFactory.openFilesAsGallery
static void openFilesAsGallery(String filenames[], boolean useSameTable)
Definition: ImagesWindowFactory.java:233
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.viewer.windows.ImagesWindowFactory.openFileAsText
static void openFileAsText(String filename, Component parent)
Definition: ImagesWindowFactory.java:281
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xmipp.jni.Filename.isMetadata
static boolean isMetadata(String filename)
Definition: Filename.java:165
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static GalleryJFrame openMetadata(String filename, MetaData md, Params parameters, String mode)
Definition: ImagesWindowFactory.java:180
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xmipp.utils.Params.OPENING_MODE_DEFAULT
static final String OPENING_MODE_DEFAULT
Definition: Params.java:27
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static void openScipionMetadata(String filename, Params parameters)
Definition: ImagesWindowFactory.java:197
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xmipp.jni.MDLabel.MDL_IMAGE
static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
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xmipp.utils.Params.OPENING_MODE_GALLERY
static final String OPENING_MODE_GALLERY
Definition: Params.java:29
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xmipp.utils.Params.OPENING_MODE_IMAGE
static final String OPENING_MODE_IMAGE
Definition: Params.java:28
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xmipp.viewer.windows.ImagesWindowFactory.openFileAsImagePlus
static ImagePlus openFileAsImagePlus(String path, Params parameters)
Definition: ImagesWindowFactory.java:119
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xmipp.viewer.scipion.ScipionMetaData.isScipionMetaData
static boolean isScipionMetaData(String filename)
Definition: ScipionMetaData.java:1227
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xmipp.viewer.windows.ImagesWindowFactory.openFileAsDefault
static void openFileAsDefault(String filename, Params parameters)
Definition: ImagesWindowFactory.java:64
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xmipp.viewer.windows.ImagesWindowFactory.openFilesAsGallery
static void openFilesAsGallery(String filenames[], boolean useSameTable, Params parameters)
Definition: ImagesWindowFactory.java:238
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xmipp.viewer.windows.ImagesWindowFactory.openXmippImageWindow
static XmippIJWindow openXmippImageWindow(ImagePlus imp, Params params)
Definition: ImagesWindowFactory.java:134
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.viewer.windows.ImagesWindowFactory.openFilesAsImages
static void openFilesAsImages(String filenames[], Params parameters)
Definition: ImagesWindowFactory.java:93
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xmipp.utils.XmippMessage.getIllegalValueMsg
static String getIllegalValueMsg(String field, Object value)
Definition: XmippMessage.java:66
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static void openFileAsImage(Frame pframe, String filename, Params parameters)
Definition: ImagesWindowFactory.java:103
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xmipp.viewer.windows.ImagesWindowFactory.openXmippImageWindow
static XmippIJWindow openXmippImageWindow(ImagePlusLoader impLoader, Params parameters)
Definition: ImagesWindowFactory.java:139
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class  xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog
 
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package  xmipp.viewer.particlepicker.tiltpair.gui
 
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ImportParticlesFromFilesTiltPairJDialog.java
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1 package xmipp.viewer.particlepicker.tiltpair.gui;
2 
3 import java.awt.GridBagConstraints;
4 import java.awt.GridBagLayout;
5 import java.awt.Insets;
6 import java.awt.event.ActionEvent;
7 import java.awt.event.ActionListener;
8 import java.text.NumberFormat;
9 import java.util.Locale;
10 
11 import javax.swing.JButton;
12 import javax.swing.JCheckBox;
13 import javax.swing.JComboBox;
14 import javax.swing.JFormattedTextField;
15 import javax.swing.JLabel;
16 import javax.swing.JPanel;
17 import javax.swing.JTextField;
18 import xmipp.utils.XmippFileChooser;
19 
20 import xmipp.utils.XmippMessage;
21 import xmipp.utils.XmippWindowUtil;
22 import xmipp.viewer.particlepicker.ImportParticlesJDialog;
23 
24 
25 public class ImportParticlesFromFilesTiltPairJDialog extends ImportParticlesJDialog {
26 
27 
28 
29  private JTextField sourcetf2;
30  private JButton browsebt2;
31  private String path2;
32 
33  public ImportParticlesFromFilesTiltPairJDialog(TiltPairPickerJFrame parent) {
34  super(parent);
35  }
36 
37 
38 
39 
40 
41  @Override
42  protected void createContent(JPanel panel) {
43  setResizable(false);
44  panel.setLayout(new GridBagLayout());
45  GridBagConstraints gbc = new GridBagConstraints();
46  gbc.insets = new Insets(5, 5, 5, 5);
47 
48  gbc.anchor = GridBagConstraints.EAST;
49  panel.add(new JLabel("Format:"),
50  XmippWindowUtil.getConstraints(gbc, 0, 0, 1));
51  panel.add(new JLabel("Untilted:"),
52  XmippWindowUtil.getConstraints(gbc, 0, 1, 1));
53 
54  panel.add(new JLabel("Tilted:"),
55  XmippWindowUtil.getConstraints(gbc, 0, 2, 1));
56 
57  gbc.anchor = GridBagConstraints.WEST;
59  jcbFormat = new JComboBox(formatsString);
60  jcbFormat.addActionListener(new ActionListener() {
61 
62  @Override
63  public void actionPerformed(ActionEvent arg0) {
64  format = formatsList[jcbFormat.getSelectedIndex()];
65 
66  }
67  });
68  panel.add(jcbFormat, XmippWindowUtil.getConstraints(gbc, 1, 0, 1));
69  sourcetf = new JTextField(20);
70  panel.add(sourcetf, XmippWindowUtil.getConstraints(gbc, 1, 1, 1));
71 
72  sourcetf2 = new JTextField(20);
73  panel.add(sourcetf2, XmippWindowUtil.getConstraints(gbc, 1, 2, 1));
74  browsebt = XmippWindowUtil.getIconButton("folderopen.gif", this);
75  browsebt2 = XmippWindowUtil.getIconButton("folderopen.gif", this);
76  browsebt2.setActionCommand("browse2");
77  panel.add(browsebt, XmippWindowUtil.getConstraints(gbc, 2, 1, 1));
78  panel.add(browsebt2, XmippWindowUtil.getConstraints(gbc, 2, 2, 1));
79  panel.add(new JLabel("Scale To:"),
80  XmippWindowUtil.getConstraints(gbc, 0, 3, 1));
81  scaletf = new JFormattedTextField(NumberFormat.getNumberInstance(Locale.ENGLISH));
82  scaletf.setColumns(3);
83  scaletf.setValue(1);
84  panel.add(scaletf, XmippWindowUtil.getConstraints(gbc, 1, 3));
85 
86  panel.add(new JLabel("Invert X:"),
87  XmippWindowUtil.getConstraints(gbc, 0, 4));
88  invertxcb = new JCheckBox();
89  panel.add(invertxcb, XmippWindowUtil.getConstraints(gbc, 1, 4));
90 
91  panel.add(new JLabel("Invert Y:"),
92  XmippWindowUtil.getConstraints(gbc, 0, 5));
93  invertycb = new JCheckBox();
94  panel.add(invertycb, XmippWindowUtil.getConstraints(gbc, 1, 5));
95 
96 
97  }// function createContent
98 
99  @Override
100  public void handleActionPerformed(ActionEvent evt) {
101  Object o = evt.getSource();
102  if (o == browsebt)
103  browseDirectory(sourcetf);
104  else
105  browseDirectory(sourcetf2);
106  }// function actionPerformed
107 
108  protected void browseDirectory(JTextField sourcetf) {
109  int returnVal = xfc.showOpenDialog(this);
110  try {
111  if (returnVal == XmippFileChooser.APPROVE_OPTION) {
112  path = xfc.getSelectedPath();
113  sourcetf.setText(path);
114  }
115  } catch (Exception ex) {
116  showException(ex);
117  }
118 
119  }
120 
121 
122  protected String importParticles() {
123  path = sourcetf.getText().trim();
124 
125  if (path == null || path.equals("") )
126  showError(XmippMessage.getEmptyFieldMsg("Untilted"));
127  path2 = sourcetf2.getText().trim();
128 
129  if (path2 == null || path2.equals("") )
130  showError(XmippMessage.getEmptyFieldMsg("Tilted"));
131  return ((TiltPairPickerJFrame)parent).importParticlesFromFiles(format, path, path2, ((Number)scaletf.getValue()).floatValue(), invertxcb.isSelected(), invertycb.isSelected());
132 
133  }
134 
135 }
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Definition: XmippDialog.java:217
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Definition: XmippDialog.java:163
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Definition: XmippDialog.java:211
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static JButton getIconButton(String icon, ActionListener listener)
Definition: XmippWindowUtil.java:124
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static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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Definition: XmippWindowUtil.java:105
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package  xmipp.viewer.particlepicker
 
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ImportParticlesJDialog.java
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1 package xmipp.viewer.particlepicker;
2 
3 import java.awt.GridBagConstraints;
4 import java.awt.GridBagLayout;
5 import java.awt.Insets;
6 import java.awt.event.ActionEvent;
7 import java.awt.event.ActionListener;
8 import java.io.File;
9 import java.text.NumberFormat;
10 import java.util.Arrays;
11 import java.util.Locale;
12 
13 import javax.swing.JButton;
14 import javax.swing.JCheckBox;
15 import javax.swing.JComboBox;
16 import javax.swing.JFormattedTextField;
17 import javax.swing.JLabel;
18 import javax.swing.JPanel;
19 import javax.swing.JTextField;
20 
21 import xmipp.jni.Filename;
22 import xmipp.utils.XmippDialog;
23 import xmipp.utils.XmippFileChooser;
24 import xmipp.utils.XmippMessage;
25 import xmipp.utils.XmippWindowUtil;
26 import xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog;
27 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame;
28 
29 public class ImportParticlesJDialog extends XmippDialog {
30 
31  protected ParticlePickerJFrame parent;
32  protected JTextField sourcetf;
33  protected JButton browsebt;
34  protected JComboBox jcbFormat;
35  public Format format = Format.Auto;
36  protected XmippFileChooser xfc = null;
37  protected String path;
38  protected JFormattedTextField scaletf;
39  protected JCheckBox invertxcb;
40  protected JCheckBox invertycb;
41 
42  public static final String[] formatsString = new String[]{Format.Auto.toString(), Format.Xmipp24.toString(), Format.Xmipp30.toString(), Format.Xmipp301.toString(), Format.Eman.toString(), Format.Relion.toString()};
43  public static final Format[] formatsList = { Format.Auto, Format.Xmipp24,
44  Format.Xmipp30, Format.Xmipp301, Format.Eman, Format.Relion };
45  private JTextField preffixtf;
46  private JTextField suffixtf;
47 
48  public ImportParticlesJDialog(ParticlePickerJFrame parent) {
49  super(parent, "Import Particles", true);
50  this.parent = parent;
51  xfc = new XmippFileChooser();
52  if(parent instanceof SupervisedPickerJFrame)
53  xfc.setFileSelectionMode(XmippFileChooser.FILES_AND_DIRECTORIES);
54  else if (this instanceof ImportParticlesFromFilesTiltPairJDialog)
55  xfc.setFileSelectionMode(XmippFileChooser.FILES_ONLY);
56  else
57  xfc.setFileSelectionMode(XmippFileChooser.DIRECTORIES_ONLY);
58 
59  xfc.setMultiSelectionEnabled(false);
60  initComponents();
61  }// constructor
62 
63 
64 
65  @Override
66  protected void createContent(JPanel panel) {
67  setResizable(false);
68  panel.setLayout(new GridBagLayout());
69  GridBagConstraints gbc = new GridBagConstraints();
70  gbc.insets = new Insets(5, 5, 5, 5);
71 
72  gbc.anchor = GridBagConstraints.WEST;
73  panel.add(new JLabel("Format:"),
74  XmippWindowUtil.getConstraints(gbc, 0, 0));
75  panel.add(new JLabel("Source:"),
76  XmippWindowUtil.getConstraints(gbc, 0, 1));
77 
78 
80  jcbFormat = new JComboBox(formatsString);
81  jcbFormat.addActionListener(new ActionListener() {
82 
83  @Override
84  public void actionPerformed(ActionEvent arg0) {
85  int index = jcbFormat.getSelectedIndex();
86  format = formatsList[index];
87  suffixtf.setText(parent.getParticlePicker().emextensions.get(formatsList[index]));
88 
89  }
90  });
91  panel.add(jcbFormat, XmippWindowUtil.getConstraints(gbc, 1, 0));
92 
93  sourcetf = new JTextField(20);
94  panel.add(sourcetf, XmippWindowUtil.getConstraints(gbc, 1, 1));
95 
96  browsebt = XmippWindowUtil.getIconButton("folderopen.gif", this);
97  panel.add(browsebt, XmippWindowUtil.getConstraints(gbc, 2, 1));
98 
99  String tooltip = "Preffix added to micrograph name in coordinates file";
100  JLabel preffixlb = new JLabel("Preffix:");
101  preffixlb.setToolTipText(tooltip);
102  panel.add(preffixlb, XmippWindowUtil.getConstraints(gbc, 0, 2));
103  preffixtf = new JTextField(20);
104  preffixtf.setToolTipText(tooltip);
105  panel.add(preffixtf, XmippWindowUtil.getConstraints(gbc, 1, 2));
106  tooltip = "Suffix added to micrograph name in coordinates file (eg:_filt.pos)";
107  JLabel suffixlb = new JLabel("Suffix:");
108  panel.add(suffixlb, XmippWindowUtil.getConstraints(gbc, 0, 3));
109  suffixlb.setToolTipText(tooltip);
110  suffixtf = new JTextField(20);
111  suffixtf.setToolTipText(tooltip);
112  panel.add(suffixtf, XmippWindowUtil.getConstraints(gbc, 1, 3));
113 
114  panel.add(new JLabel("Scale To:"), XmippWindowUtil.getConstraints(gbc, 0, 4));
115  scaletf = new JFormattedTextField(NumberFormat.getNumberInstance(Locale.ENGLISH));
116  scaletf.setColumns(3);
117  scaletf.setValue(1);
118  panel.add(scaletf, XmippWindowUtil.getConstraints(gbc, 1, 4));
119 
120  panel.add(new JLabel("Invert X:"),
121  XmippWindowUtil.getConstraints(gbc, 0, 5));
122  invertxcb = new JCheckBox();
123  panel.add(invertxcb, XmippWindowUtil.getConstraints(gbc, 1, 5));
124 
125  panel.add(new JLabel("Invert Y:"),
126  XmippWindowUtil.getConstraints(gbc, 0, 6));
127  invertycb = new JCheckBox();
128  panel.add(invertycb, XmippWindowUtil.getConstraints(gbc, 1, 6));
129 
130  sourcetf.addActionListener(new ActionListener()
131  {
132 
133  @Override
134  public void actionPerformed(ActionEvent e)
135  {
136  String path = sourcetf.getText();
137  boolean isDir = new File(path).isDirectory();
138  preffixtf.setEnabled(isDir);
139  suffixtf.setEnabled(isDir);
140 
141  }
142  });
143 
144  }// function createContent
145 
146  @Override
147  public void handleActionPerformed(ActionEvent evt) {
148  browseDirectory(sourcetf);
149 
150  }// function actionPerformed
151 
152  protected void browseDirectory(JTextField sourcetf) {
153  int returnVal = xfc.showOpenDialog(this);
154  try {
155  if (returnVal == XmippFileChooser.APPROVE_OPTION) {
156  path = xfc.getSelectedPath();
157  sourcetf.setText(path);
158  preffixtf.setEnabled(xfc.getSelectedFile().isDirectory());
159  suffixtf.setEnabled(xfc.getSelectedFile().isDirectory());
160 
161  }
162  } catch (Exception ex) {
163  showException(ex);
164  }
165 
166  }
167 
168  @Override
169  public void handleOk() {
170 
171  path = sourcetf.getText().trim();
172 
173  if (path == null || path.equals(""))
174  showError(XmippMessage.getEmptyFieldMsg("source"));
175  else if (!existsSelectedPath())
176  showError(XmippMessage.getPathNotExistsMsg(path));
177  else
178  {
179  String result = importParticles();
180  if(result != null && !result.equals(""))
181  XmippDialog.showInfo(this.parent, result);
182 
183  }
184 
185  }
186 
187  protected String importParticles()
188  {
189  try {
190  return parent.importParticles(format, path, preffixtf.getText(), suffixtf.getText(), ((Number)scaletf.getValue()).floatValue(), invertxcb.isSelected(), invertycb.isSelected());
191  } catch (Exception e) {
192  XmippDialog.showInfo(parent, e.getMessage());
193  }
194  return null;
195 
196  }
197 
198 
199 
200  private boolean existsSelectedPath(){
201  return Filename.exists(path);
202 
203  }//function existsSelectedPaths
204 
205 
206 
207 
208 
209 }
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boolean showException(Exception e)
Definition: XmippDialog.java:217
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xmipp.viewer.particlepicker.ParticlePicker.emextensions
final HashMap< Format, String > emextensions
Definition: ParticlePicker.java:60
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boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.jni.Filename.exists
static boolean exists(String path)
Definition: Filename.java:266
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xmipp.utils.XmippDialog.actionPerformed
void actionPerformed(ActionEvent evt)
Definition: XmippDialog.java:163
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xmipp.viewer.particlepicker.ParticlePickerJFrame.importParticles
abstract String importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
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xmipp.utils.XmippMessage.getPathNotExistsMsg
static String getPathNotExistsMsg(String path)
Definition: XmippMessage.java:71
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boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.utils.XmippWindowUtil.getIconButton
static JButton getIconButton(String icon, ActionListener listener)
Definition: XmippWindowUtil.java:124
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xmipp.utils.XmippMessage.getEmptyFieldMsg
static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
-
xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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1 package xmipp.utils;
2 
8 import java.awt.Color;
9 import java.awt.Frame;
10 import java.awt.Graphics;
11 import java.awt.Graphics2D;
12 import java.awt.RenderingHints;
13 import java.awt.Window;
14 import java.awt.event.MouseEvent;
15 import java.awt.event.MouseListener;
16 import java.awt.font.FontRenderContext;
17 import java.awt.font.TextLayout;
18 import java.awt.geom.AffineTransform;
19 import java.awt.geom.Area;
20 import java.awt.geom.Ellipse2D;
21 import java.awt.geom.Point2D;
22 import java.awt.geom.Rectangle2D;
23 
24 import javax.swing.JComponent;
25 
58 public class InfiniteProgressPanel extends JComponent implements MouseListener {
59 
61  protected Area[] ticker = null;
63  protected Thread animation = null;
65  protected boolean started = false;
67  protected int alphaLevel = 0;
69  protected int rampDelay = 300;
71  protected float shield = 0.70f;
73  protected String text = "";
75  protected int barsCount = 14;
77  protected float fps = 15.0f;
79  protected RenderingHints hints = null;
80  private Window window;
81 
92  public InfiniteProgressPanel() {
93  this("");
94  }
95 
106  public InfiniteProgressPanel(String text) {
107  this(text, 14);
108  }
109 
110  public InfiniteProgressPanel(Window window, String text) {
111 
112  this(text, 14);
113  this.window = window;
114  }
115 
126  public InfiniteProgressPanel(String text, int barsCount) {
127  this(text, barsCount, 0.70f);
128  }
129 
141  public InfiniteProgressPanel(String text, int barsCount, float shield) {
142  this(text, barsCount, shield, 15.0f);
143  }
144 
157  public InfiniteProgressPanel(String text, int barsCount, float shield, float fps) {
158  this(text, barsCount, shield, fps, 300);
159  }
160 
172  public InfiniteProgressPanel(String text, int barsCount, float shield, float fps, int rampDelay) {
173  this.text = text;
174  this.rampDelay = rampDelay >= 0 ? rampDelay : 0;
175  this.shield = shield >= 0.0f ? shield : 0.0f;
176  this.fps = fps > 0.0f ? fps : 15.0f;
177  this.barsCount = barsCount > 0 ? barsCount : 14;
178 
179  this.hints = new RenderingHints(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
180  this.hints.put(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
181  this.hints.put(RenderingHints.KEY_FRACTIONALMETRICS, RenderingHints.VALUE_FRACTIONALMETRICS_ON);
182  }
183 
189  public void setText(String text) {
190  this.text = text;
191  repaint();
192  }
193 
197  public String getText() {
198  return text;
199  }
200 
206  public void start() {
207  addMouseListener(this);
208  setVisible(true);
209  ticker = buildTicker();
210  animation = new Thread(new Animator(true),"Progress panel");
211  animation.start();
212  }
213 
219  public void stop() {
220  if (animation != null) {
221  animation.interrupt();
222  animation = null;
223  animation = new Thread(new Animator(false));
224  animation.start();
225  }
226  }
227 
234  public void interrupt() {
235  if (animation != null) {
236  animation.interrupt();
237  animation = null;
238 
239  removeMouseListener(this);
240  setVisible(false);
241  }
242  }
243 
244 
245 
246  @Override
247  public void paintComponent(Graphics g) {
248  if (started) {
249  int width = (window != null)? window.getWidth(): getWidth();
250  int height = (window != null)? window.getHeight(): getHeight();
251  double maxY = 0.0;
252 
253  Graphics2D g2 = (Graphics2D) g;
254  g2.setRenderingHints(hints);
255 
256  g2.setColor(new Color(255, 255, 255, (int) (alphaLevel * shield)));
257  g2.fillRect(0, 0, width, height);
258 
259  AffineTransform oCenterT = AffineTransform.getTranslateInstance(
260  (double) width / 2.,
261  (double) height / 2.);
262 
263  g2.transform(oCenterT);
264 
265  for (int i = 0; i < ticker.length; i++) {
266  int channel = 224 - 128 / (i + 1);
267  g2.setColor(new Color(channel, channel, channel, alphaLevel));
268  g2.fill(ticker[i]);
269 
270  Rectangle2D bounds = ticker[i].getBounds2D();
271  if (bounds.getMaxY() > maxY) {
272  maxY = bounds.getMaxY();
273  }
274  }
275 
276  try {
277  g2.transform(oCenterT.createInverse());
278  } catch (Exception e) {
279  }
280 
281  if (text != null && text.length() > 0) {
282  FontRenderContext context = g2.getFontRenderContext();
283  TextLayout layout = new TextLayout(text, getFont(), context);
284  Rectangle2D bounds = layout.getBounds();
285  g2.setColor(getForeground());
286  layout.draw(g2, (float) (width - bounds.getWidth()) / 2,
287  (float) (maxY + layout.getLeading() + 2 * layout.getAscent()));
288  }
289  }
290  }
291 
297  private Area[] buildTicker() {
298  Area[] ticker = new Area[barsCount];
299  Point2D.Double center = new Point2D.Double((double) getWidth() / 2, (double) getHeight() / 2);
300  double fixedAngle = 2.0 * Math.PI / ((double) barsCount);
301 
302  for (double i = 0.0; i < (double) barsCount; i++) {
303  Area primitive = buildPrimitive();
304 
305  AffineTransform toCenter = AffineTransform.getTranslateInstance(center.getX(), center.getY());
306  AffineTransform toBorder = AffineTransform.getTranslateInstance(45.0, -6.0);
307  AffineTransform toCircle = AffineTransform.getRotateInstance(-i * fixedAngle, center.getX(), center.getY());
308 
309  AffineTransform toWheel = new AffineTransform();
310  toWheel.concatenate(toCenter);
311  toWheel.concatenate(toBorder);
312 
313  primitive.transform(toWheel);
314  primitive.transform(toCircle);
315 
316  ticker[(int) i] = primitive;
317  }
318 
319  return ticker;
320  }
321 
325  private Area buildPrimitive() {
326  Rectangle2D.Double body = new Rectangle2D.Double(6, 0, 30, 12);
327  Ellipse2D.Double head = new Ellipse2D.Double(0, 0, 12, 12);
328  Ellipse2D.Double tail = new Ellipse2D.Double(30, 0, 12, 12);
329 
330  Area tick = new Area(body);
331  tick.add(new Area(head));
332  tick.add(new Area(tail));
333 
334  return tick;
335  }
336 
340  private class Animator implements Runnable {
341 
342  private boolean rampUp = true;
343 
344  protected Animator(boolean rampUp) {
345  this.rampUp = rampUp;
346  }
347 
348  public void run() {
349  Point2D.Double center = new Point2D.Double((double) getWidth() / 2, (double) getHeight() / 2);
350  double fixedIncrement = 2.0 * Math.PI / ((double) barsCount);
351  AffineTransform toCircle = AffineTransform.getRotateInstance(fixedIncrement, center.getX(), center.getY());
352 
353  long start = System.currentTimeMillis();
354  if (rampDelay == 0) {
355  alphaLevel = rampUp ? 255 : 0;
356  }
357 
358  started = true;
359  boolean inRamp = rampUp;
360 
361  while (!Thread.interrupted()) {
362  if (!inRamp) {
363  for (int i = 0; i < ticker.length; i++) {
364  ticker[i].transform(toCircle);
365  }
366  }
367 
368  repaint();
369 
370  if (rampUp) {
371  if (alphaLevel < 255) {
372  alphaLevel = (int) (255 * (System.currentTimeMillis() - start) / rampDelay);
373  if (alphaLevel >= 255) {
374  alphaLevel = 255;
375  inRamp = false;
376  }
377  }
378  } else if (alphaLevel > 0) {
379  alphaLevel = (int) (255 - (255 * (System.currentTimeMillis() - start) / rampDelay));
380  if (alphaLevel <= 0) {
381  alphaLevel = 0;
382  break;
383  }
384  }
385 
386  try {
387  Thread.sleep(inRamp ? 10 : (int) (1000 / fps));
388  } catch (InterruptedException ie) {
389  break;
390  }
391  Thread.yield();
392  }
393 
394  if (!rampUp) {
395  started = false;
396  repaint();
397 
398  setVisible(false);
399  removeMouseListener(InfiniteProgressPanel.this);
400  }
401  }
402  }
403 
404  public void mouseClicked(MouseEvent e) {
405  }
406 
407  public void mousePressed(MouseEvent e) {
408  }
409 
410  public void mouseReleased(MouseEvent e) {
411  }
412 
413  public void mouseEntered(MouseEvent e) {
414  }
415 
416  public void mouseExited(MouseEvent e) {
417  }
418 }
419 /* Swing Hacks
420  * Tips and Tools for Killer GUIs
421  * By Joshua Marinacci, Chris Adamson
422  * First Edition June 2005
423  * Series: Hacks
424  * ISBN: 0-596-00907-0
425  * http://www.oreilly.com/catalog/swinghks/
426  */
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xmipp.utils.InfiniteProgressPanel.InfiniteProgressPanel
InfiniteProgressPanel(String text, int barsCount, float shield)
Definition: InfiniteProgressPanel.java:141
-
xmipp.utils.InfiniteProgressPanel.InfiniteProgressPanel
InfiniteProgressPanel(String text, int barsCount, float shield, float fps)
Definition: InfiniteProgressPanel.java:157
-
xmipp.utils.InfiniteProgressPanel.InfiniteProgressPanel
InfiniteProgressPanel(String text, int barsCount)
Definition: InfiniteProgressPanel.java:126
- -
xmipp.utils.InfiniteProgressPanel.InfiniteProgressPanel
InfiniteProgressPanel(String text, int barsCount, float shield, float fps, int rampDelay)
Definition: InfiniteProgressPanel.java:172
-
xmipp.utils.InfiniteProgressPanel.InfiniteProgressPanel
InfiniteProgressPanel(Window window, String text)
Definition: InfiniteProgressPanel.java:110
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.ij.commons;
8 
9 import java.awt.Color;
10 import java.awt.GridBagConstraints;
11 import java.awt.GridBagLayout;
12 import java.awt.Insets;
13 import java.awt.event.ActionEvent;
14 import java.awt.event.ActionListener;
15 import java.util.ArrayList;
16 import java.util.Dictionary;
17 import java.util.Enumeration;
18 import java.util.HashMap;
19 import java.util.List;
20 import java.util.Map;
21 import javax.swing.JButton;
22 import javax.swing.JDialog;
23 import javax.swing.JFrame;
24 import javax.swing.JLabel;
25 import javax.swing.JOptionPane;
26 import javax.swing.JPanel;
27 import javax.swing.JTextField;
28 import xmipp.utils.XmippWindowUtil;
29 
34 public class InputFieldsMessageDialog extends JDialog implements ActionListener {
35 
36  private String msg;
37  private JButton cancelbt;
38  private JButton okbt;
39  public int action;
40 
41  public static final int OK_OPTION = 1;
42  public static final int CANCEL_OPTION = 0;
43  private Map<String, String> fields;
44  Map<String, JTextField> fieldstfs;
45 
46 
47  public InputFieldsMessageDialog(JFrame parent, String title, String msg, Map<String, String> fields)
48  {
49  super(parent, true);
50  this.msg = msg;
51  this.fields = fields;
52  fieldstfs = new HashMap<String, JTextField>();
53  initComponents(title);
54 
55  }
56 
57  public InputFieldsMessageDialog(JFrame parent, String title, String msg)
58  {
59  this(parent, title, msg, null);
60  }
61 
62  protected void initComponents(String title)
63  {
64  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
65  setTitle(title);
66  setLayout(new GridBagLayout());
67  GridBagConstraints constraints = new GridBagConstraints();
68  constraints.insets = new Insets(5, 5, 5, 5);
69  JLabel msgLb = new JLabel(msg);
70  add(msgLb, XmippWindowUtil.getConstraints(constraints, 0, 0, 2));
71  int index = 1;
72  JTextField tf;
73  if(fields != null)
74  for(Map.Entry<String, String> e: fields.entrySet())
75  {
76 
77  add(new JLabel(e.getKey()), XmippWindowUtil.getConstraints(constraints, 0, index));
78  tf = new JTextField(e.getValue());
79  tf.setColumns(20);
80  fieldstfs.put(e.getKey(), tf);
81  add(tf, XmippWindowUtil.getConstraints(constraints, 1, index));
82  index ++;
83  }
84  JPanel buttonspn = new JPanel();
85  cancelbt = new JButton("Cancel");
86  cancelbt.addActionListener(new ActionListener() {
87 
88  @Override
89  public void actionPerformed(ActionEvent ae) {
90  action = CANCEL_OPTION;
91  close();
92  }
93  });
94  buttonspn.add(cancelbt);
95  okbt = new JButton("Ok");
96  okbt.setBackground(XmippWindowUtil.firebrick);
97  okbt.setForeground(Color.WHITE);
98  okbt.addActionListener(this);
99 
100  buttonspn.add(okbt);
101  add(buttonspn, XmippWindowUtil.getConstraints(constraints, 0, index, GridBagConstraints.HORIZONTAL));
102  pack();
103  if (getParent() != null)
104  XmippWindowUtil.centerWindows(this, getParent());
105  setVisible(true);
106 
107  }
108 
109 
110 
111 
112  public void close()
113  {
114  setVisible(false);
115  dispose();
116  }
117 
118  @Override
119  public void actionPerformed(ActionEvent ae) {
120  action = OK_OPTION;
121  close();
122  }
123 
124  public String getFieldValue(String field)
125  {
126  return fieldstfs.get(field).getText();
127  }
128 
129 
130 
131 }
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xmipp.utils.XmippWindowUtil.firebrick
static final Color firebrick
Definition: XmippWindowUtil.java:57
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xmipp.utils.XmippWindowUtil.centerWindows
static void centerWindows(Window w)
Definition: XmippWindowUtil.java:94
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InputFieldsMessageDialog(JFrame parent, String title, String msg)
Definition: InputFieldsMessageDialog.java:57
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InputFieldsMessageDialog(JFrame parent, String title, String msg, Map< String, String > fields)
Definition: InputFieldsMessageDialog.java:47
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.viewer;
8 
9 import java.io.BufferedWriter;
10 import java.io.File;
11 import java.io.FileWriter;
12 import java.util.logging.Level;
13 
14 import xmipp.ij.commons.IJCommand;
15 import xmipp.jni.MDLabel;
16 import xmipp.jni.MetaData;
17 import static xmipp.viewer.particlepicker.ParticlePicker.getLogger;
18 import xmipp.viewer.particlepicker.training.model.AutomaticParticle;
19 import xmipp.viewer.particlepicker.training.model.ManualParticle;
20 import xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker;
21 import xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph;
22 
27 public class JMetaDataIO {
28 
29 
30  public static void saveData(SupervisedPickerMicrograph m, String path)
31  {
32  //System.out.println("saving data on JMetaDataIO");
33  try
34  {
35  if (!m.hasData())
36  new File(path).delete();
37  else
38  {
39  FileWriter fstream = new FileWriter(path);
40  BufferedWriter out = new BufferedWriter(fstream);
41  out.write("# XMIPP_STAR_1 * \n#\ndata_header\nloop_\n");
42  String cformat = "_%s\n";
43  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_MICROGRAPH_STATE)));
44  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_AUTOPICKPERCENT)));
45  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_COST)));
46  String vformat = "%20s";
47  out.write(String.format(vformat, m.getState().toString()));
48  out.write(String.format(vformat, m.getAutopickpercent()));
49  out.write(String.format(vformat, m.getThreshold()));
50  out.newLine();
51  out.write("data_particles\nloop_\n");
52  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_XCOOR)));
53  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_YCOOR)));
54 
55  for (ManualParticle p : m.getManualParticles())
56  {
57  out.write(String.format(vformat, p.getX()));
58  out.write(String.format(vformat, p.getY()));
59  out.newLine();
60  }
61  if(m.hasAutomaticParticles())
62  {
63  out.write("data_particles_auto\nloop_\n");
64  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_XCOOR)));
65  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_YCOOR)));
66  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_COST)));
67  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_ENABLED)));
68  int enabled;
69  for (AutomaticParticle p : m.getAutomaticParticles())
70  {
71  out.write(String.format(vformat, p.getX()));
72  out.write(String.format(vformat, p.getY()));
73  out.write(String.format(vformat, p.getCost()));
74 // enabled = !p.isDeleted()? 1 : -1;
75  enabled = !p.isUnavailable() ? 1 : -1;
76  out.write(String.format(vformat, enabled));
77  out.newLine();
78  }
79  }
80  out.close();
81  }
82  }
83  catch (Exception e)
84  {
85  getLogger().log(Level.SEVERE, e.getMessage(), e);
86  throw new IllegalArgumentException(e.getMessage());
87  }
88 
89  }
90 
91 
92  public static void saveConfig(SupervisedParticlePicker picker, String path)
93  {
94  //System.out.println("saving data on JMetaDataIO");
95  long id;
96  try
97  {
98 
99  FileWriter fstream = new FileWriter(path);
100  BufferedWriter out = new BufferedWriter(fstream);
101  out.write("# XMIPP_STAR_1 * \n#\ndata_properties\nloop_\n");
102  String cformat = "_%s\n";
103  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_MICROGRAPH)));
104  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_COLOR)));
105  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_PARTICLE_SIZE)));
106  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_AUTOPICKPERCENT)));
107  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_TEMPLATES)));
108  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_STATE)));
109  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE)));
110  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE)));
111 
112  String vformat = "%20s";
113  out.write(String.format(vformat, picker.getMicrograph().getName()));
114  out.write(String.format(vformat, picker.getColor().getRGB()));
115  out.write(String.format(vformat, picker.getSize()));
116  out.write(String.format(vformat, picker.getAutopickpercent()));
117  out.write(String.format(vformat, picker.getTemplatesNumber()));
118  out.write(String.format(vformat, picker.getMode().toString()));
119  out.write(String.format(vformat, picker.getManualParticlesNumber()));
120  out.write(String.format(vformat, picker.getAutomaticParticlesNumber()));
121  out.newLine();
122  String optionsFormat = "%80s";
123  out.write("data_filters\nloop_\n");
124  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_MACRO_CMD)));
125  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_MACRO_CMD_ARGS)));
126  String options;
127  for (IJCommand f : picker.getFilters()) {
128  out.write(String.format(vformat, f.getMdCommand()));
129  options = f.getMdOptions();
130  out.write(String.format(optionsFormat, options));
131  out.newLine();
132 
133  }
134  out.close();
135  }
136  catch (Exception e)
137  {
138  getLogger().log(Level.SEVERE, e.getMessage(), e);
139  throw new IllegalArgumentException(e.getMessage());
140  }
141 
142  }
143 
144 }
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xmipp.jni.MDLabel.MDL_MACRO_CMD
static final int MDL_MACRO_CMD
< Number which will multiply all features (double)
Definition: MDLabel.java:280
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xmipp.jni.MDLabel.MDL_PICKING_AUTOPICKPERCENT
static final int MDL_PICKING_AUTOPICKPERCENT
< Micrograph state for particle picking
Definition: MDLabel.java:286
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xmipp.jni.MDLabel.MDL_PICKING_MICROGRAPH_STATE
static final int MDL_PICKING_MICROGRAPH_STATE
< State for particle picking
Definition: MDLabel.java:285
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xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MDLabel.MDL_COST
static final int MDL_COST
< Store a score for the coords. consensus (it will change the behavoir of the viewer) ...
Definition: MDLabel.java:46
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xmipp.jni.MetaData.getLabelName
static String getLabelName(int label)
Definition: MetaData.java:247
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xmipp.jni.MDLabel.MDL_PICKING_TEMPLATES
static final int MDL_PICKING_TEMPLATES
< Color for particle picking
Definition: MDLabel.java:283
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xmipp.jni.MDLabel.MDL_MACRO_CMD_ARGS
static final int MDL_MACRO_CMD_ARGS
Definition: MDLabel.java:281
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xmipp.viewer.JMetaDataIO.saveData
static void saveData(SupervisedPickerMicrograph m, String path)
Definition: JMetaDataIO.java:30
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xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.viewer.JMetaDataIO.saveConfig
static void saveConfig(SupervisedParticlePicker picker, String path)
Definition: JMetaDataIO.java:92
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xmipp.jni.MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE
static final int MDL_PICKING_AUTOPARTICLES_SIZE
< Particle size for particle picking
Definition: MDLabel.java:288
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xmipp.jni.MDLabel.MDL_PICKING_STATE
static final int MDL_PICKING_STATE
< Number of templates
Definition: MDLabel.java:284
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xmipp.jni.MDLabel.MDL_COLOR
static final int MDL_COLOR
Definition: MDLabel.java:282
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xmipp.jni.MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE
static final int MDL_PICKING_MANUALPARTICLES_SIZE
< Number of automatic particles picked
Definition: MDLabel.java:289
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xmipp.jni.MDLabel.MDL_PICKING_PARTICLE_SIZE
static final int MDL_PICKING_PARTICLE_SIZE
Definition: MDLabel.java:287
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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- - diff --git a/html/Kalman__Stack__Filter_8java.html b/html/Kalman__Stack__Filter_8java.html deleted file mode 100644 index 6bdfeac5..00000000 --- a/html/Kalman__Stack__Filter_8java.html +++ /dev/null @@ -1,89 +0,0 @@ - - - - - - - -Xmipp: xmippViz/external/imagej/plugins/Stacks/Kalman_Stack_Filter.java File Reference - - - - - - - - - -
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class  Kalman_Stack_Filter
 
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1 import ij.*;
2 import ij.plugin.*;
3 import ij.plugin.filter.RGBStackSplitter;
4 import ij.process.*;
5 import ij.gui.*;
6 import java.awt.*;
7 
8 /* The author of this software is Christopher Philip Mauer. Copyright (c) 2003.
9 Permission to use, copy, modify, and distribute this software for any purpose
10 without fee is hereby granted, provided that this entire notice is included in
11 all copies of any software which is or includes a copy or modification of this
12 software and in all copies of the supporting documentation for such software.
13 Any for profit use of this software is expressly forbidden without first
14 obtaining the explicit consent of the author.
15 THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED WARRANTY.
16 IN PARTICULAR, THE AUTHOR DOES NOT MAKE ANY REPRESENTATION OR WARRANTY
17 OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR ITS FITNESS FOR ANY
18 PARTICULAR PURPOSE.
19 */
20 /* This PlugInFilter implements a recursive prediction/correction
21 algorithm based on the Kalman Filter. The application for which
22 it was designed is cleaning up timelapse image streams. It operates
23 in linear space by filtering a previously opened stack of images and
24 producing a new filtered stack.
25  Christopher Philip Mauer
26  cpmauer@northwestern.edu
27 */
28 public class Kalman_Stack_Filter implements PlugIn {
29  private static double percentvar = 0.05;
30  private static double gain = 0.8;;
31 
32  public void run (String arg) {
33  ImagePlus imp = IJ.getImage();
34  if (imp.getStackSize()==1)
35  {IJ.error("Stack required"); return;}
36  String ErrorMessage = new String("One of your values was not properly formatted.\nThe default values will be used.");
37  GenericDialog d = new GenericDialog("Kalman Stack Filter");
38  d.addNumericField("Acquisition_noise variance estimate:", percentvar, 2);
39  d.addNumericField("Bias to be placed on the prediction:", gain, 2);
40  d.showDialog();
41  if(d.wasCanceled()) return;
42  double percentvar = d.getNextNumber();
43  gain = d.getNextNumber();
44  if(d.invalidNumber())
45  {IJ.error("Invalid input Number"); return;}
46  if(percentvar>1.0||gain>1.0||percentvar<0.0||gain<0.0){
47  IJ.error(ErrorMessage);
48  percentvar = 0.05;
49  gain = 0.8;
50  }
51  ImageStack stack = imp.getStack();
52  if (imp.getBitDepth()==24)
53  stack = filterRGB(stack, percentvar, gain);
54  else
55  filter(stack, percentvar, gain);
56  imp.setStack(null, stack);
57  }
58 
59  public void filter(ImageStack stack, double percentvar, double gain) {
60  ImageProcessor ip = stack.getProcessor(1);
61  int bitDepth = 0;
62  if (ip instanceof ByteProcessor)
63  bitDepth = 8;
64  else if (ip instanceof ShortProcessor)
65  bitDepth = 16;
66  else if (ip instanceof FloatProcessor)
67  bitDepth = 32;
68  else
69  throw new IllegalArgumentException("RGB stacks not supported");
70 
71  int width = stack.getWidth();
72  int height = stack.getHeight();
73  int dimension = width*height;
74  int stacksize = stack.getSize();
75  double[] stackslice = new double[dimension];
76  double[] filteredslice = new double[dimension];
77  double[] noisevar = new double[dimension];
78  double[] average = new double[dimension];
79  double[] predicted = new double[dimension];
80  double[] predictedvar = new double[dimension];
81  double[] observed = new double[dimension];
82  double[] Kalman = new double[dimension];
83  double[] corrected = new double[dimension];
84  double[] correctedvar = new double[dimension];
85 
86  for (int i=0; i<dimension; ++i)
87  noisevar[i] = percentvar;
88  predicted = toDouble(stack.getPixels(1), bitDepth);
89  predictedvar = noisevar;
90 
91  for(int i=1; i<stacksize; ++i) {
92  IJ.showProgress(i, stacksize);
93  stackslice = toDouble(stack.getPixels(i+1), bitDepth);
94  observed = toDouble(stackslice, 64);
95  for(int k=0;k<Kalman.length;++k)
96  Kalman[k] = predictedvar[k]/(predictedvar[k]+noisevar[k]);
97  for(int k=0;k<corrected.length;++k)
98  corrected[k] = gain*predicted[k]+(1.0-gain)*observed[k]+Kalman[k]*(observed[k] - predicted[k]);
99  for(int k=0;k<correctedvar.length;++k)
100  correctedvar[k] = predictedvar[k]*(1.0 - Kalman[k]);
101  predictedvar = correctedvar;
102  predicted = corrected;
103  stack.setPixels(fromDouble(corrected, bitDepth), i+1);
104  }
105  }
106 
107  public ImageStack filterRGB(ImageStack stack, double percentvar, double gain) {
108  RGBStackSplitter splitter = new RGBStackSplitter();
109  splitter.split(stack, false);
110  filter(splitter.red, percentvar, gain);
111  filter(splitter.green, percentvar, gain);
112  filter(splitter.blue, percentvar, gain);
113  RGBStackMerge merge = new RGBStackMerge();
114  ImageProcessor ip = splitter.red.getProcessor(1);
115  return merge.mergeStacks(ip.getWidth(), ip.getHeight(), splitter.red.getSize(), splitter.red, splitter.green, splitter.blue, false);
116  }
117 
118  public Object fromDouble(double[] array, int bitDepth) {
119  switch (bitDepth) {
120  case 8:
121  byte[] bytes = new byte[array.length];
122  for(int i=0; i<array.length; i++)
123  bytes[i] = (byte)array[i];
124  return bytes;
125  case 16:
126  short[] shorts = new short[array.length];
127  for(int i=0; i<array.length; i++)
128  shorts[i] = (short)array[i];
129  return shorts;
130  case 32:
131  float[] floats = new float[array.length];
132  for(int i=0; i<array.length; i++)
133  floats[i] = (float)array[i];
134  return floats;
135  }
136  return null;
137  }
138 
139  public double[] toDouble(Object array, int bitDepth) {
140  double[] doubles = null;
141  switch (bitDepth) {
142  case 8:
143  byte[] bytes = (byte[])array;
144  doubles = new double[bytes.length];
145  for(int i=0; i<doubles.length; i++)
146  doubles[i] = (bytes[i]&0xff);
147  break;
148  case 16:
149  short[] shorts = (short[])array;
150  doubles = new double[shorts.length];
151  for(int i=0; i<doubles.length; i++)
152  doubles[i] = (shorts[i]&0xffff);
153  break;
154  case 32:
155  float[] floats = (float[])array;
156  doubles = new double[floats.length];
157  for(int i=0; i<doubles.length; i++)
158  doubles[i] = floats[i];
159  break;
160  case 64:
161  double[] doubles0 = (double[])array;
162  doubles = new double[doubles0.length];
163  for(int i=0; i<doubles.length; i++)
164  doubles[i] = doubles0[i];
165  break;
166  }
167  return doubles;
168  }
169 
170 }
Kalman_Stack_Filter.filter
void filter(ImageStack stack, double percentvar, double gain)
Definition: Kalman_Stack_Filter.java:59
-
Kalman_Stack_Filter
Definition: Kalman_Stack_Filter.java:28
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Kalman_Stack_Filter.run
void run(String arg)
Definition: Kalman_Stack_Filter.java:32
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Kalman_Stack_Filter.filterRGB
ImageStack filterRGB(ImageStack stack, double percentvar, double gain)
Definition: Kalman_Stack_Filter.java:107
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Kalman_Stack_Filter.toDouble
double [] toDouble(Object array, int bitDepth)
Definition: Kalman_Stack_Filter.java:139
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Kalman_Stack_Filter.fromDouble
Object fromDouble(double[] array, int bitDepth)
Definition: Kalman_Stack_Filter.java:118
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1 package xmipp.ij.plugins.maskstoolbar;
2 
3 /*
4  * To change this template, choose Tools | Templates
5  * and open the template in the editor.
6  */
11 public class LABELS {
12 
13  public final static String TITLE = "Masks Tool Bar";
14  public final static String TOOLTIP_RECTANGLE = "Rectangle";
15  public final static String TOOLTIP_ROUNDRECTANGLE = "Round Rectangle";
16  public final static String TOOLTIP_ELLIPSE = "Ellipse";
17  public final static String TOOLTIP_OVAL = "Oval";
18  public final static String TOOLTIP_POLYGON = "Polygon";
19  public final static String TOOLTIP_FREEHAND = "Freehand";
20  public final static String TOOLTIP_BRUSH = "Brush";
21  public final static String TOOLTIP_SETBRUSHSIZE = "Set Brush Size";
22  public final static String TOOLTIP_CREATEMASK = "Create Mask";
23  public final static String TOOLTIP_CREATESELECTION = "Create Selection";
24  public final static String TOOLTIP_INVERTSELECTION = "Invert Selection";
25  public final static String TOOLTIP_INVERTMASK = "Invert Mask";
26  public final static String TOOLTIP_SPECIFYSELECTION = "Specify Selection";
27  public final static String TOOLTIP_MASK_LOCKED = "Unlock Mask";
28  public final static String TOOLTIP_MASK_UNLOCKED = "Lock Mask";
29  public final static String ABOUT_TITLE = "About Xmipp Browser plugin...";
30  public final static String ABOUT_TEXT =
31  "<html>"
32  + "Masks Tool Bar for ImageJ"
33  + "<hr>"
34  + "Juanjo Vega.<br>"
35  + "Biocomputing Unit.<br>"
36  + "National Center for Biotechnology (CNB/CSIC).<br>"
37  + "Madrid. May 2011."
38  + "</html>";
39 }
xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_ROUNDRECTANGLE
static final String TOOLTIP_ROUNDRECTANGLE
Definition: LABELS.java:15
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static final String TOOLTIP_CREATEMASK
Definition: LABELS.java:22
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static final String TOOLTIP_INVERTSELECTION
Definition: LABELS.java:24
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static final String TOOLTIP_MASK_UNLOCKED
Definition: LABELS.java:28
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static final String ABOUT_TEXT
Definition: LABELS.java:30
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static final String TOOLTIP_POLYGON
Definition: LABELS.java:18
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static final String TOOLTIP_OVAL
Definition: LABELS.java:17
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static final String TOOLTIP_CREATESELECTION
Definition: LABELS.java:23
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static final String TOOLTIP_RECTANGLE
Definition: LABELS.java:14
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static final String TOOLTIP_BRUSH
Definition: LABELS.java:20
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static final String TOOLTIP_ELLIPSE
Definition: LABELS.java:16
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static final String TOOLTIP_MASK_LOCKED
Definition: LABELS.java:27
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static final String TOOLTIP_FREEHAND
Definition: LABELS.java:19
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static final String TOOLTIP_INVERTMASK
Definition: LABELS.java:25
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Definition: LABELS.java:26
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static final String TOOLTIP_SETBRUSHSIZE
Definition: LABELS.java:21
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Definition: LABELS.java:29
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1 package xmipp.jni;
2 
3 public class LinearAlgebra {
4 
5  //Load the native library
6  static
7  {
8  System.loadLibrary("XmippJNI");
9  storeIds();
10  }
11  // hold pointer to Image class in C++ space
12  private long peer;
13 
14  public native void solveLinearSystem();
15 
16  // caching some ids
17  private static native void storeIds();
18 
19  public native void clear();
20 
21  // functions to create images
22  private native void create();
23 
24  // destructor
25  private synchronized native void destroy();
26 
27  // non-native functions
28  // constructor
29  public LinearAlgebra()
30  {
31  create();
32  }
33 
34  // Should be called by GarbageCollector before destroying
35  @Override
36  protected void finalize() throws Throwable
37  {
38  super.finalize();
39  destroy();
40  }
41 
42 }
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Xmipp -  v20.07 -
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MDLabel.java
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1 package xmipp.jni;
2 
3 public class MDLabel {
4  public static final int MDL_UNDEFINED = -1;
5  public static final int MDL_FIRST_LABEL = 0;
6  public static final int MDL_OBJID = MDL_FIRST_LABEL;
7  public static final int MDL_GATHER_ID = 1;
8  public static final int MDL_ANGLE_PSI = 2;
9  public static final int MDL_ANGLE_PSI2 = 3;
10  public static final int MDL_ANGLE_PSI3 = 4;
11  public static final int MDL_ANGLE_PSI_DIFF = 5;
12  public static final int MDL_ANGLE_ROT = 6;
13  public static final int MDL_ANGLE_ROT2 = 7;
14  public static final int MDL_ANGLE_ROT3 = 8;
15  public static final int MDL_ANGLE_ROT_DIFF = 9;
16  public static final int MDL_ANGLE_TILT = 10;
17  public static final int MDL_ANGLE_TILT2 = 11;
18  public static final int MDL_ANGLE_TILT3 = 12;
19  public static final int MDL_ANGLE_TILT_DIFF = 13;
20  public static final int MDL_ANGLE_DIFF0 = 14;
21  public static final int MDL_ANGLE_DIFF = 15;
22  public static final int MDL_ANGLE_DIFF2 = 16;
23  public static final int MDL_ANGLE_Y = 17;
24  public static final int MDL_ANGLE_Y2 = 18;
25  public static final int MDL_ANGLE_TEMPERATURE = 19;
26  public static final int MDL_APPLY_SHIFT = 20;
27  public static final int MDL_AVG = 21;
28  public static final int MDL_AVG_CHANGES_ORIENTATIONS = 22;
29  public static final int MDL_AVG_CHANGES_OFFSETS = 23;
30  public static final int MDL_AVG_CHANGES_CLASSES = 24;
31  public static final int MDL_AVGPMAX = 25;
32  public static final int MDL_BFACTOR = 26;
33  public static final int MDL_BGMEAN = 27;
34  public static final int MDL_BLOCK_NUMBER = 28;
35  public static final int MDL_CL2D_CHANGES = 29;
36  public static final int MDL_CL2D_SIMILARITY = 30;
37  public static final int MDL_CLASS_COUNT = 31;
38  public static final int MDL_CLASS_PERCENTAGE = 32;
39  public static final int MDL_CLASSIFICATION_DATA = 33;
40  public static final int MDL_CLASSIFICATION_DATA_SIZE = 34;
41  public static final int MDL_CLASSIFICATION_DPR_05 = 35;
42  public static final int MDL_CLASSIFICATION_INTRACLASS_DISTANCE = 36;
43  public static final int MDL_CLASSIFICATION_FRC_05 = 37;
44  public static final int MDL_COMMENT = 38;
45  public static final int MDL_COORD_CONSENSUS_SCORE = 39;
46  public static final int MDL_COST = 40;
47  public static final int MDL_COST_PERCENTILE = 41;
48  public static final int MDL_COUNT = 42;
49  public static final int MDL_COUNT2 = 43;
50  public static final int MDL_CORR_DENOISED_PROJECTION = 44;
51  public static final int MDL_CORR_DENOISED_NOISY = 45;
52  public static final int MDL_CLASS_INTERSECTION_SIZE_PVALUE = 46;
53  public static final int MDL_CLASS_INTERSECTION_RELATIVE_SIZE_PVALUE = 47;
54  public static final int MDL_CRYSTAL_CELLX = 48;
55  public static final int MDL_CRYSTAL_CELLY = 49;
56  public static final int MDL_CRYSTAL_LATTICE_A = 50;
57  public static final int MDL_CRYSTAL_LATTICE_B = 51;
58  public static final int MDL_CRYSTAL_DISAPPEAR_THRE = 52;
59  public static final int MDL_CRYSTAL_SHFILE = 53;
60  public static final int MDL_CRYSTAL_ORTHO_PRJ = 54;
61  public static final int MDL_CRYSTAL_PROJ = 55;
62  public static final int MDL_CRYSTAL_SHIFTX = 56;
63  public static final int MDL_CRYSTAL_SHIFTY = 57;
64  public static final int MDL_CRYSTAL_SHIFTZ = 58;
65  public static final int MDL_CRYSTAL_NOISE_SHIFT = 59;
66  public static final int MDL_CONTINUOUS_X = 60;
67  public static final int MDL_CONTINUOUS_Y = 61;
68  public static final int MDL_CONTINUOUS_FLIP = 62;
69  public static final int MDL_CONTINUOUS_GRAY_A = 63;
70  public static final int MDL_CONTINUOUS_GRAY_B = 64;
71  public static final int MDL_CONTINUOUS_SCALE_ANGLE = 65;
72  public static final int MDL_CONTINUOUS_SCALE_X = 66;
73  public static final int MDL_CONTINUOUS_SCALE_Y = 67;
74  public static final int MDL_CORRELATION_IDX = 68;
75  public static final int MDL_CORRELATION_MASK = 69;
76  public static final int MDL_CORRELATION_WEIGHT = 70;
77  public static final int MDL_CTF_DATA_PHASE_FLIPPED = 71; // Is the Data Phase-Flippled? ///
78  public static final int MDL_CTF_CORRECTED = 72; // Is the CTF corrected? ///
79  public static final int MDL_CTF_INPUTPARAMS = 73;
80  public static final int MDL_CTF_MODEL = 74;
81  public static final int MDL_CTF_MODEL2 = 75;
82  public static final int MDL_CTF_SAMPLING_RATE = 76;
83  public static final int MDL_CTF_SAMPLING_RATE_Z = 77;
84  public static final int MDL_CTF_VOLTAGE = 78;
85  public static final int MDL_CTF_DEFOCUSA = 79;
86  public static final int MDL_CTF_DEFOCUSU = 80;
87  public static final int MDL_CTF_DEFOCUSV = 81;
88  public static final int MDL_CTF_DEFOCUS_CHANGE = 82;
89  public static final int MDL_CTF_DEFOCUS_R2 = 83;
90  public static final int MDL_CTF_DEFOCUS_COEFS = 84;
91  public static final int MDL_CTF_DEFOCUS_RESIDUAL = 85;
92  public static final int MDL_CTF_X0 = 86;
93  public static final int MDL_CTF_Y0 = 87;
94  public static final int MDL_CTF_XF = 88;
95  public static final int MDL_CTF_YF = 89;
96  public static final int MDL_CTF_DEFOCUS_PLANEUA = 90;
97  public static final int MDL_CTF_DEFOCUS_PLANEUB = 91;
98  public static final int MDL_CTF_DEFOCUS_PLANEUC = 92;
99  public static final int MDL_CTF_DEFOCUS_PLANEVA = 93;
100  public static final int MDL_CTF_DEFOCUS_PLANEVB = 94;
101  public static final int MDL_CTF_DEFOCUS_PLANEVC = 95;
102  public static final int MDL_CTF_DEFOCUS_ANGLE = 96;
103  public static final int MDL_CTF_CS = 97;
104  public static final int MDL_CTF_CA = 98;
105  public static final int MDL_CTF_GROUP = 99;
106  public static final int MDL_CTF_ENERGY_LOSS = 100;
107  public static final int MDL_CTF_ENVELOPE = 101; //<Envelope function ///
108  public static final int MDL_CTF_ENVELOPE_PLOT = 102; //<Envelope function ///
109  public static final int MDL_CTF_LENS_STABILITY = 103;
110  public static final int MDL_CTF_CONVERGENCE_CONE = 104;
111  public static final int MDL_CTF_LONGITUDINAL_DISPLACEMENT = 105;
112  public static final int MDL_CTF_TRANSVERSAL_DISPLACEMENT = 106;
113  public static final int MDL_CTF_Q0 = 107;
114  public static final int MDL_CTF_K = 108;
115  public static final int MDL_CTF_ENV_R0 = 109;
116  public static final int MDL_CTF_ENV_R1 = 110;
117  public static final int MDL_CTF_ENV_R2 = 111;
118  public static final int MDL_CTF_BG_GAUSSIAN_K = 112;
119  public static final int MDL_CTF_BG_GAUSSIAN_SIGMAU = 113;
120  public static final int MDL_CTF_BG_GAUSSIAN_SIGMAV = 114;
121  public static final int MDL_CTF_BG_GAUSSIAN_CU = 115;
122  public static final int MDL_CTF_BG_GAUSSIAN_CV = 116;
123  public static final int MDL_CTF_BG_GAUSSIAN_ANGLE = 117;
124  public static final int MDL_CTF_BG_SQRT_K = 118;
125  public static final int MDL_CTF_BG_SQRT_U = 119;
126  public static final int MDL_CTF_BG_SQRT_V = 120;
127  public static final int MDL_CTF_BG_SQRT_ANGLE = 121;
128  public static final int MDL_CTF_BG_BASELINE = 122;
129  public static final int MDL_CTF_BG_GAUSSIAN2_K = 123;
130  public static final int MDL_CTF_BG_GAUSSIAN2_SIGMAU = 124;
131  public static final int MDL_CTF_BG_GAUSSIAN2_SIGMAV = 125;
132  public static final int MDL_CTF_BG_GAUSSIAN2_CU = 126;
133  public static final int MDL_CTF_BG_GAUSSIAN2_CV = 127;
134  public static final int MDL_CTF_BG_GAUSSIAN2_ANGLE = 128;
135  public static final int MDL_CTF_BG_R1 = 129;
136  public static final int MDL_CTF_BG_R2 = 130;
137  public static final int MDL_CTF_BG_R3 = 131;
138  public static final int MDL_CTF_CRIT_NONASTIGMATICVALIDITY = 132;
139  public static final int MDL_CTF_CRIT_PSDCORRELATION90 = 133;
140  public static final int MDL_CTF_CRIT_FIRSTZERORATIO = 134;
141  public static final int MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_RATIO = 135;
142  public static final int MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_DIFF_RATIO = 136;
143  public static final int MDL_CTF_CRIT_FIRSTZEROAVG = 137;
144  public static final int MDL_CTF_CRIT_FIRSTZERODISAGREEMENT = 138;
145  public static final int MDL_CTF_CRIT_MAXFREQ = 139;
146  public static final int MDL_CTF_CRIT_DAMPING = 140;
147  public static final int MDL_CTF_CRIT_PSDRADIALINTEGRAL = 141;
148  public static final int MDL_CTF_CRIT_FITTINGSCORE = 142;
149  public static final int MDL_CTF_CRIT_FITTINGCORR13 = 143;
150  public static final int MDL_CTF_CRIT_PSDVARIANCE = 144;
151  public static final int MDL_CTF_CRIT_PSDPCA1VARIANCE = 145;
152  public static final int MDL_CTF_CRIT_PSDPCARUNSTEST = 146;
153  public static final int MDL_CTF_CRIT_NORMALITY = 147;
154  public static final int MDL_CTF_CRIT_ICENESS = 148;
155  public static final int MDL_CTF_DOWNSAMPLE_PERFORMED = 149;
156  public static final int MDL_CTF_DIMENSIONS = 150; // Size in pixels of the 3D PSF to be created (Xdim = 150; Ydim = 150; Zdim) ///
157  public static final int MDL_CTF_LAMBDA = 151;
158  public static final int MDL_CTF_XRAY_LENS_TYPE = 152;
159  public static final int MDL_CTF_XRAY_OUTER_ZONE_WIDTH = 153;
160  public static final int MDL_CTF_XRAY_ZONES_NUMBER = 154; // Number of zones of the X-ray Fresnel lens ///
161  public static final int MDL_CTF_PHASE_SHIFT = 155; //Volta Phase Plate phase shift ///
162  public static final int MDL_CTF_VPP_RADIUS = 156; //Phase Plate radius ///
163  public static final int MDL_CUMULATIVE_SSNR = 157;
164  public static final int MDL_DATATYPE = 158;
165  public static final int MDL_DEFGROUP = 159;
166  public static final int MDL_DIMRED = 160;
167  public static final int MDL_DIRECTION = 161;
168  public static final int MDL_DM3_IDTAG = 162;
169  public static final int MDL_DM3_NODEID = 163;
170  public static final int MDL_DM3_NUMBER_TYPE = 164;
171  public static final int MDL_DM3_PARENTID = 165;
172  public static final int MDL_DM3_TAGCLASS = 166;
173  public static final int MDL_DM3_TAGNAME = 167;
174  public static final int MDL_DM3_SIZE = 168;
175  public static final int MDL_DM3_VALUE = 169;
176  public static final int MDL_DOSE = 170;
177  public static final int MDL_ENABLED = 171;
178  public static final int MDL_DATE = 172;// < timestamp (string) ///
179  public static final int MDL_TIME = 173;// < time in seconds (double) ///
180  public static final int MDL_FLIP = 174;
181  public static final int MDL_FOM = 175;
182  public static final int MDL_FRAME_ID = 176;
183  public static final int MDL_GRAPH_DISTANCE2MAX = 177;
184  public static final int MDL_GRAPH_DISTANCE2MAX_PREVIOUS = 178;
185  public static final int MDL_GRAPH_CC = 179;
186  public static final int MDL_GRAPH_CC_PREVIOUS = 180;
187  public static final int MDL_HALF1 = 181;
188  public static final int MDL_HALF2 = 182;
189  public static final int MDL_IDX = 183;
190  public static final int MDL_IMAGE = 184;
191  public static final int MDL_IMAGE_COVARIANCE = 185;
192  public static final int MDL_IMAGE_IDX = 186;
193  public static final int MDL_IMAGE_ORIGINAL = 187;
194  public static final int MDL_IMAGE_REF = 188;
195  public static final int MDL_IMAGE_RESIDUAL = 189;
196  public static final int MDL_IMAGE_TILTED = 190;
197  public static final int MDL_IMED = 191;
198  public static final int MDL_IMGMD = 192;
199  public static final int MDL_IMAGE1 = 193;
200  public static final int MDL_IMAGE2 = 194;
201  public static final int MDL_IMAGE3 = 195;
202  public static final int MDL_IMAGE4 = 196;
203  public static final int MDL_IMAGE5 = 197;
204  public static final int MDL_INTSCALE = 198;
205  public static final int MDL_ITEM_ID = 199;
206  public static final int MDL_ITER = 200;
207  public static final int MDL_KERDENSOM_FUNCTIONAL = 201;
208  public static final int MDL_KERDENSOM_REGULARIZATION = 202;
209  public static final int MDL_KERDENSOM_SIGMA = 203;
210  public static final int MDL_KEYWORDS = 204;
211  public static final int MDL_KMEANS2D_CENTROID = 205;
212  public static final int MDL_KSTEST = 206;
213  public static final int MDL_LL = 207;
214  public static final int MDL_LOCAL_ALIGNMENT_PATCHES = 208;
215  public static final int MDL_LOCAL_ALIGNMENT_COEFFS_X = 209;
216  public static final int MDL_LOCAL_ALIGNMENT_COEFFS_Y = 210;
217  public static final int MDL_LOCAL_ALIGNMENT_CONF_2_5_PERC = 211;
218  public static final int MDL_LOCAL_ALIGNMENT_CONF_97_5_PERC = 212;
219  public static final int MDL_LOCAL_ALIGNMENT_CONTROL_POINTS = 213;
220  public static final int MDL_MAGNIFICATION = 214;
221  public static final int MDL_MAPTOPOLOGY = 215;
222  public static final int MDL_MASK = 216;
223  public static final int MDL_MAXCC = 217;
224  public static final int MDL_MAXCC_PERCENTILE = 218;
225  public static final int MDL_MAX = 219;
226  public static final int MDL_MAXCC_PREVIOUS = 220;
227  public static final int MDL_MICROGRAPH = 221;
228  public static final int MDL_MICROGRAPH_ID = 222;
229  public static final int MDL_MICROGRAPH_MOVIE = 223;
230  public static final int MDL_MICROGRAPH_MOVIE_ID = 224;
231  public static final int MDL_MICROGRAPH_PARTICLES = 225;
232  public static final int MDL_MICROGRAPH_ORIGINAL = 226;
233  public static final int MDL_MICROGRAPH_TILTED = 227;
234  public static final int MDL_MICROGRAPH_TILTED_ORIGINAL = 228;
235  public static final int MDL_MIN = 229;
236  public static final int MDL_MIRRORFRAC = 230;
237  public static final int MDL_MISSINGREGION_NR = 231;
238  public static final int MDL_MISSINGREGION_TYPE = 232;
239  public static final int MDL_MISSINGREGION_THY0 = 233;
240  public static final int MDL_MISSINGREGION_THYF = 234;
241  public static final int MDL_MISSINGREGION_THX0 = 235;
242  public static final int MDL_MISSINGREGION_THXF = 236;
243  public static final int MDL_MLF_CTF = 237;
244  public static final int MDL_MLF_WIENER = 238;
245  public static final int MDL_MLF_SIGNAL = 239;
246  public static final int MDL_MLF_NOISE = 240;
247  public static final int MDL_MODELFRAC = 241;
248  public static final int MDL_NEIGHBORS = 242;
249  public static final int MDL_NEIGHBOR = 243;
250  public static final int MDL_NEIGHBORHOOD_RADIUS = 244;
251  public static final int MDL_NMA = 245;
252  public static final int MDL_NMA_COLLECTIVITY = 246;
253  public static final int MDL_NMA_ATOMSHIFT = 247;
254  public static final int MDL_NMA_ENERGY = 248;
255  public static final int MDL_NMA_MINRANGE = 249;
256  public static final int MDL_NMA_MAXRANGE = 250;
257  public static final int MDL_NMA_MODEFILE = 251;
258  public static final int MDL_NMA_SCORE = 252;
259  public static final int MDL_NMA_EIGENVAL = 253;
260  public static final int MDL_NOISE_ANGLES = 254;
261  public static final int MDL_NOISE_PARTICLE_COORD = 255;
262  public static final int MDL_NOISE_COORD = 256; //Use instead of MDL_NOISE_PARTICLE_COORD in future ///
263  public static final int MDL_NOISE_PIXEL_LEVEL = 257;
264  public static final int MDL_ORDER = 258;
265  public static final int MDL_ORIGIN_X = 259;
266  public static final int MDL_ORIGIN_Y = 260;
267  public static final int MDL_ORIGIN_Z = 261;
268  public static final int MDL_OPTICALFLOW_MEANX = 262;
269  public static final int MDL_OPTICALFLOW_MEANY = 263;
270  public static final int MDL_OPTICALFLOW_STDX = 264;
271  public static final int MDL_OPTICALFLOW_STDY = 265;
272  public static final int MDL_PARTICLE_ID = 266;
273  public static final int MDL_PHANTOM_BGDENSITY = 267;
274  public static final int MDL_PHANTOM_FEATURE_CENTER = 268;
275  public static final int MDL_PHANTOM_FEATURE_DENSITY = 269;
276  public static final int MDL_PHANTOM_FEATURE_OPERATION = 270;
277  public static final int MDL_PHANTOM_FEATURE_SPECIFIC = 271;
278  public static final int MDL_PHANTOM_FEATURE_TYPE = 272;
279  public static final int MDL_PHANTOM_SCALE = 273;
280  public static final int MDL_MACRO_CMD = 274; //ImageJ macro command on picker ///
281  public static final int MDL_MACRO_CMD_ARGS = 275; //ImageJ macro args on picker ///
282  public static final int MDL_COLOR = 276;
283  public static final int MDL_PICKING_TEMPLATES = 277;
284  public static final int MDL_PICKING_STATE = 278;
285  public static final int MDL_PICKING_MICROGRAPH_STATE = 279;
286  public static final int MDL_PICKING_AUTOPICKPERCENT = 280;
287  public static final int MDL_PICKING_PARTICLE_SIZE = 281;
288  public static final int MDL_PICKING_AUTOPARTICLES_SIZE = 282;
289  public static final int MDL_PICKING_MANUALPARTICLES_SIZE = 283;
290  public static final int MDL_PMAX = 284;
291  public static final int MDL_POINTSASYMETRICUNIT = 285;
292  public static final int MDL_PRJ_DIMENSIONS = 286; // X = 286;Y dimensions for the generated projections ///
293  public static final int MDL_PRJ_ANGFILE = 287;
294  public static final int MDL_PRJ_PSI_NOISE = 288;
295  public static final int MDL_PRJ_PSI_RANDSTR = 289;
296  public static final int MDL_PRJ_PSI_RANGE = 290;
297  public static final int MDL_PRJ_ROT_NOISE = 291;
298  public static final int MDL_PRJ_ROT_RANDSTR = 292;
299  public static final int MDL_PRJ_ROT_RANGE = 293;
300  public static final int MDL_PRJ_TILT_NOISE = 294;
301  public static final int MDL_PRJ_TILT_RANDSTR = 295;
302  public static final int MDL_PRJ_TILT_RANGE = 296; // Vector with the initial and final tilt angle values = 296; and step size ///
303  public static final int MDL_PRJ_VOL = 297; // Volume file name to generate projections from ///
304  public static final int MDL_PROGRAM = 298;// < program name ///
305  public static final int MDL_USER = 299;// < user name ///
306  public static final int MDL_DIMENSIONS_3D = 300; // X = 300;Y = 300;Z dimensions ///
307  public static final int MDL_DIMENSIONS_2D = 301; // X = 301;Y dimensions ///
308  public static final int MDL_PSD = 302;
309  public static final int MDL_PSD_ENHANCED = 303;
310  public static final int MDL_RANDOMSEED = 304;
311  public static final int MDL_REF3D = 305;
312  public static final int MDL_REF = 306;
313  public static final int MDL_REF2 = 307;
314  public static final int MDL_REFMD = 308;
315  public static final int MDL_ASSIGNED_DIR_REF_CC = 309;
316  public static final int MDL_RESIDUE = 310; //<residue of an atomic model (int) ///
317  public static final int MDL_RESOLUTION_ANISOTROPY = 311;
318  public static final int MDL_RESOLUTION_DPR = 312;
319  public static final int MDL_RESOLUTION_ERRORL2 = 313;
320  public static final int MDL_RESOLUTION_FRC = 314;
321  public static final int MDL_RESOLUTION_FRCRANDOMNOISE = 315;
322  public static final int MDL_RESOLUTION_FREQ = 316;
323  public static final int MDL_RESOLUTION_FREQ2 = 317;
324  public static final int MDL_RESOLUTION_FREQREAL = 318;
325  public static final int MDL_RESOLUTION_FSO = 319;
326  public static final int MDL_RESOLUTION_LOCAL_RESIDUE = 320;
327  public static final int MDL_RESOLUTION_LOG_STRUCTURE_FACTOR = 321;
328  public static final int MDL_RESOLUTION_SSNR = 322;
329  public static final int MDL_RESOLUTION_STRUCTURE_FACTOR = 323;
330  public static final int MDL_RESOLUTION_RFACTOR = 324;
331  public static final int MDL_SAMPLINGRATE = 325;
332  public static final int MDL_SAMPLINGRATE_ORIGINAL = 326;
333  public static final int MDL_SAMPLINGRATE_X = 327;
334  public static final int MDL_SAMPLINGRATE_Y = 328;
335  public static final int MDL_SAMPLINGRATE_Z = 329;
336  public static final int MDL_SCALE = 330;
337  public static final int MDL_SCORE_BY_PCA_RESIDUAL_PROJ = 331;
338  public static final int MDL_SCORE_BY_PCA_RESIDUAL_EXP = 332;
339  public static final int MDL_SCORE_BY_PCA_RESIDUAL = 333;
340  public static final int MDL_SCORE_BY_ALIGNABILITY = 334;
341  public static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION = 335;
342  public static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY = 336;
343  public static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXP = 337;
344  public static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION_REF = 338;
345  public static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXP = 339;
346  public static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REF = 340;
347  public static final int MDL_SCORE_BY_ALIGNABILITY_NOISE = 341;
348  public static final int MDL_SCORE_BY_EMPTINESS = 342;
349  public static final int MDL_SCORE_BY_ENTROPY = 343;
350  public static final int MDL_SCORE_BY_GRANULO = 344;
351  public static final int MDL_SCORE_BY_HISTDIST = 345;
352  public static final int MDL_SCORE_BY_LBP = 346;
353  public static final int MDL_SCORE_BY_MIRROR = 347;
354  public static final int MDL_SCORE_BY_RAMP = 348;
355  public static final int MDL_SCORE_BY_SCREENING = 349;
356  public static final int MDL_SCORE_BY_VARIANCE = 350;
357  public static final int MDL_SCORE_BY_VAR = 351;
358  public static final int MDL_SCORE_BY_GINI = 352;
359  public static final int MDL_SCORE_BY_ZERNIKE = 353;
360  public static final int MDL_SCORE_BY_ZSCORE = 354;
361  public static final int MDL_SELFILE = 355;
362  public static final int MDL_SERIE = 356;
363  public static final int MDL_SHIFT_X = 357;
364  public static final int MDL_SHIFT_X2 = 358;
365  public static final int MDL_SHIFT_X3 = 359;
366  public static final int MDL_SHIFT_X_DIFF = 360;
367  public static final int MDL_SHIFT_Y = 361;
368  public static final int MDL_SHIFT_Y2 = 362;
369  public static final int MDL_SHIFT_Y3 = 363;
370  public static final int MDL_SHIFT_Y_DIFF = 364;
371  public static final int MDL_SHIFT_Z = 365;
372  public static final int MDL_SHIFT_Z2 = 366;
373  public static final int MDL_SHIFT_Z3 = 367;
374  public static final int MDL_SHIFT_DIFF0 = 368;
375  public static final int MDL_SHIFT_DIFF = 369;
376  public static final int MDL_SHIFT_DIFF2 = 370;
377  public static final int MDL_SIGMANOISE = 371;
378  public static final int MDL_SIGMAOFFSET = 372;
379  public static final int MDL_SIGNALCHANGE = 373;
380  public static final int MDL_SPH_COEFFICIENTS = 374;
381  public static final int MDL_SPH_DEFORMATION = 375;
382  public static final int MDL_SPH_TSNE_COEFF1D = 376;
383  public static final int MDL_SPH_TSNE_COEFF2D = 377;
384  public static final int MDL_STDDEV = 378;
385  public static final int MDL_STAR_COMMENT = 379;
386  public static final int MDL_SUBTRACTION_R2 = 380;
387  public static final int MDL_SUBTRACTION_BETA0 = 381;
388  public static final int MDL_SUBTRACTION_BETA1 = 382;
389  public static final int MDL_SUM = 383;
390  public static final int MDL_SUMWEIGHT = 384;
391  public static final int MDL_SYMNO = 385;
392  public static final int MDL_TOMOGRAM_VOLUME = 386;
393  public static final int MDL_TOMOGRAMMD = 387;
394  public static final int MDL_TRANSFORM_MATRIX = 388;
395  public static final int MDL_TSID = 389;
396  public static final int MDL_TEST_SIZE = 390;// < number of test assigned to a program ///
397  public static final int MDL_TILT_ANALYSIS_MEAN = 391; // <Mean correlation between the PSD segments of a micrograph ///
398  public static final int MDL_TILT_ANALYSIS_STD = 392; // <STD correlation between the PSD segments of a micrograph ///
399  public static final int MDL_TILT_ANALYSIS_MIN = 393; // <Min correlation between the PSD segments of a micrograph ///
400  public static final int MDL_TILT_ANALYSIS_MAX = 394; // <Max correlation between the PSD segments of a micrograph ///
401  public static final int MDL_TILT_ANALYSIS_PSDs = 395; // <Image composed of the PSDs of each segment of a micrograph ///
402  public static final int MDL_VOLUME_SCORE_SUM = 396;
403  public static final int MDL_VOLUME_SCORE_SUM_TH = 397;
404  public static final int MDL_VOLUME_SCORE_MEAN = 398;
405  public static final int MDL_VOLUME_SCORE_MIN = 399;
406  public static final int MDL_VOLUME_SCORE1 = 400;
407  public static final int MDL_VOLUME_SCORE2 = 401;
408  public static final int MDL_VOLUME_SCORE3 = 402;
409  public static final int MDL_VOLUME_SCORE4 = 403;
410  public static final int MDL_WEIGHT = 404;
411  public static final int MDL_WEIGHT_P = 405;
412  public static final int MDL_WEIGHT_CONTINUOUS2 = 406;
413  public static final int MDL_WEIGHT_JUMPER0 = 407;
414  public static final int MDL_WEIGHT_JUMPER = 408;
415  public static final int MDL_WEIGHT_JUMPER2 = 409;
416  public static final int MDL_WEIGHT_REALCORR = 410;
417  public static final int MDL_WEIGHT_PHASECORR = 411;
418  public static final int MDL_WEIGHT_SIGNIFICANT = 412;
419  public static final int MDL_WEIGHT_SSNR = 413;
420  public static final int MDL_WEIGHT_PRECISION_ALIGNABILITY = 414;
421  public static final int MDL_WEIGHT_ALIGNABILITY = 415;
422  public static final int MDL_WEIGHT_ACCURACY_ALIGNABILITY = 416;
423  public static final int MDL_WEIGHT_PRECISION_MIRROR = 417;
424  public static final int MDL_WROBUST = 418;
425  public static final int MDL_X = 419;
426  public static final int MDL_XCOOR = 420;
427  public static final int MDL_XCOOR_TILT = 421;
428  public static final int MDL_XSIZE = 422;
429  public static final int MDL_Y = 423;
430  public static final int MDL_YCOOR = 424;
431  public static final int MDL_YCOOR_TILT = 425;
432  public static final int MDL_YSIZE = 426;
433  public static final int MDL_Z = 427;
434  public static final int MDL_ZCOOR = 428;
435  public static final int MDL_ZSCORE = 429;
436  public static final int MDL_ZSCORE_DEEPLEARNING1 = 430;
437  public static final int MDL_GOOD_REGION_SCORE = 431;
438  public static final int MDL_ZSCORE_HISTOGRAM = 432;
439  public static final int MDL_ZSCORE_RESMEAN = 433;
440  public static final int MDL_ZSCORE_RESVAR = 434;
441  public static final int MDL_ZSCORE_RESCOV = 435;
442  public static final int MDL_ZSCORE_SHAPE1 = 436;
443  public static final int MDL_ZSCORE_SHAPE2 = 437;
444  public static final int MDL_ZSCORE_SNR1 = 438;
445  public static final int MDL_ZSCORE_SNR2 = 439;
446  public static final int MDL_ZSIZE = 440;
447  public static final int RLN_AREA_ID = 441;
448  public static final int RLN_AREA_NAME = 442;
449  public static final int RLN_COMMENT = 443; // The RLN_COMMENT is handled specially as well ///
450  public static final int RLN_CTF_BFACTOR = 444;
451  public static final int RLN_CTF_SCALEFACTOR = 445;
452  public static final int RLN_CTF_SAMPLING_RATE = 446;
453  public static final int RLN_CTF_VOLTAGE = 447;
454  public static final int RLN_CTF_DEFOCUSU = 448;
455  public static final int RLN_CTF_DEFOCUSV = 449;
456  public static final int RLN_CTF_DEFOCUS_ANGLE = 450;
457  public static final int RLN_CTF_CS = 451;
458  public static final int RLN_CTF_CA = 452;
459  public static final int RLN_CTF_DETECTOR_PIXEL_SIZE = 453;
460  public static final int RLN_CTF_ENERGY_LOSS = 454;
461  public static final int RLN_CTF_FOM = 455;
462  public static final int RLN_CTF_IMAGE = 456;
463  public static final int RLN_CTF_LENS_STABILITY = 457;
464  public static final int RLN_CTF_MAGNIFICATION = 458;
465  public static final int RLN_CTF_MAXRES = 459;
466  public static final int RLN_CTF_CONVERGENCE_CONE = 460;
467  public static final int RLN_CTF_LONGITUDINAL_DISPLACEMENT = 461;
468  public static final int RLN_CTF_TRANSVERSAL_DISPLACEMENT = 462;
469  public static final int RLN_CTF_Q0 = 463;
470  public static final int RLN_CTF_K = 464;
471  public static final int RLN_CTF_VALUE = 465;
472  public static final int RLN_CTF_VALIDATIONSCORE = 466;
473  public static final int RLN_CTF_PHASESHIFT = 467;
474  public static final int RLN_IMAGE_NAME = 468;
475  public static final int RLN_IMAGE_RECONSTRUCT_NAME = 469;
476  public static final int RLN_IMAGE_ID = 470;
477  public static final int RLN_IMAGE_ENABLED = 471;
478  public static final int RLN_IMAGE_DATATYPE = 472;
479  public static final int RLN_IMAGE_DIMENSIONALITY = 473;
480  public static final int RLN_IMAGE_BEAMTILT_X = 474;
481  public static final int RLN_IMAGE_BEAMTILT_Y = 475;
482  public static final int RLN_IMAGE_BEAMTILT_GROUP = 476;
483  public static final int RLN_IMAGE_COORD_X = 477;
484  public static final int RLN_IMAGE_COORD_Y = 478;
485  public static final int RLN_IMAGE_COORD_Z = 479;
486  public static final int RLN_IMAGE_FRAME_NR = 480;
487  public static final int RLN_IMAGE_MAGNIFICATION_CORRECTION = 481;
488  public static final int RLN_IMAGE_NORM_CORRECTION = 482;
489  public static final int RLN_IMAGE_ORI_NAME = 483;
490  public static final int RLN_IMAGE_SAMPLINGRATE = 484;
491  public static final int RLN_IMAGE_SAMPLINGRATE_X = 485;
492  public static final int RLN_IMAGE_SAMPLINGRATE_Y = 486;
493  public static final int RLN_IMAGE_SAMPLINGRATE_Z = 487;
494  public static final int RLN_IMAGE_SIZE = 488;
495  public static final int RLN_IMAGE_SIZEX = 489;
496  public static final int RLN_IMAGE_SIZEY = 490;
497  public static final int RLN_IMAGE_SIZEZ = 491;
498  public static final int RLN_IMAGE_STATS_MIN = 492;
499  public static final int RLN_IMAGE_STATS_MAX = 493;
500  public static final int RLN_IMAGE_STATS_AVG = 494;
501  public static final int RLN_IMAGE_STATS_STDDEV = 495;
502  public static final int RLN_IMAGE_STATS_SKEW = 496;
503  public static final int RLN_IMAGE_STATS_KURT = 497;
504  public static final int RLN_IMAGE_WEIGHT = 498;
505  public static final int RLN_MASK_NAME = 499;
506  public static final int RLN_MATRIX_1_1 = 500;
507  public static final int RLN_MATRIX_1_2 = 501;
508  public static final int RLN_MATRIX_1_3 = 502;
509  public static final int RLN_MATRIX_2_1 = 503;
510  public static final int RLN_MATRIX_2_2 = 504;
511  public static final int RLN_MATRIX_2_3 = 505;
512  public static final int RLN_MATRIX_3_1 = 506;
513  public static final int RLN_MATRIX_3_2 = 507;
514  public static final int RLN_MATRIX_3_3 = 508;
515  public static final int RLN_MICROGRAPH_ID = 509;
516  public static final int RLN_MICROGRAPH_MOVIE_NAME = 510;
517  public static final int RLN_MICROGRAPH_NAME = 511;
518  public static final int RLN_MICROGRAPH_NAME_WODOSE = 512;
519  public static final int RLN_MICROGRAPH_TILT_ANGLE = 513;
520  public static final int RLN_MICROGRAPH_TILT_AXIS_DIRECTION = 514;
521  public static final int RLN_MICROGRAPH_TILT_AXIS_OUTOFPLANE = 515;
522  public static final int RLN_MLMODEL_ACCURACY_ROT = 516;
523  public static final int RLN_MLMODEL_ACCURACY_TRANS = 517;
524  public static final int RLN_MLMODEL_AVE_PMAX = 518;
525  public static final int RLN_MLMODEL_CURRENT_RESOLUTION = 519;
526  public static final int RLN_MLMODEL_CURRENT_SIZE = 520;
527  public static final int RLN_MLMODEL_DATA_VS_PRIOR_REF = 521;
528  public static final int RLN_MLMODEL_DIMENSIONALITY = 522;
529  public static final int RLN_MLMODEL_DIMENSIONALITY_DATA = 523;
530  public static final int RLN_MLMODEL_DIFF2_HALVES_REF = 524;
531  public static final int RLN_MLMODEL_ESTIM_RESOL_REF = 525;
532  public static final int RLN_MLMODEL_FOURIER_COVERAGE_REF = 526;
533  public static final int RLN_MLMODEL_FOURIER_COVERAGE_TOTAL_REF = 527;
534  public static final int RLN_MLMODEL_FSC_HALVES_REF = 528;
535  public static final int RLN_MLMODEL_GROUP_NAME = 529;
536  public static final int RLN_MLMODEL_GROUP_NO = 530;
537  public static final int RLN_MLMODEL_GROUP_NR_PARTICLES = 531;
538  public static final int RLN_MLMODEL_GROUP_SCALE_CORRECTION = 532;
539  public static final int RLN_MLMODEL_HELICAL_NR_ASU = 533;
540  public static final int RLN_MLMODEL_HELICAL_TWIST = 534;
541  public static final int RLN_MLMODEL_HELICAL_TWIST_MIN = 535;
542  public static final int RLN_MLMODEL_HELICAL_TWIST_MAX = 536;
543  public static final int RLN_MLMODEL_HELICAL_TWIST_INITIAL_STEP = 537;
544  public static final int RLN_MLMODEL_HELICAL_RISE = 538;
545  public static final int RLN_MLMODEL_HELICAL_RISE_MIN = 539;
546  public static final int RLN_MLMODEL_HELICAL_RISE_MAX = 540;
547  public static final int RLN_MLMODEL_HELICAL_RISE_INITIAL_STEP = 541;
548  public static final int RLN_MLMODEL_IS_HELIX = 542;
549  public static final int RLN_MLMODEL_INTERPOLATOR = 543;
550  public static final int RLN_MLMODEL_LL = 544;
551  public static final int RLN_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION = 545;
552  public static final int RLN_MLMODEL_NORM_CORRECTION_AVG = 546;
553  public static final int RLN_MLMODEL_NR_BODIES = 547;
554  public static final int RLN_MLMODEL_NR_CLASSES = 548;
555  public static final int RLN_MLMODEL_NR_GROUPS = 549;
556  public static final int RLN_MLMODEL_ORIGINAL_SIZE = 550;
557  public static final int RLN_MLMODEL_ORIENTABILITY_CONTRIBUTION = 551;
558  public static final int RLN_MLMODEL_PADDING_FACTOR = 552;
559  public static final int RLN_MLMODEL_PDF_CLASS = 553;
560  public static final int RLN_MLMODEL_PRIOR_OFFX_CLASS = 554;
561  public static final int RLN_MLMODEL_PRIOR_OFFY_CLASS = 555;
562  public static final int RLN_MLMODEL_PDF_ORIENT = 556;
563  public static final int RLN_MLMODEL_PIXEL_SIZE = 557;
564  public static final int RLN_MLMODEL_POWER_REF = 558;
565  public static final int RLN_MLMODEL_PRIOR_MODE = 559;
566  public static final int RLN_MLMODEL_SGD_GRADIENT_IMAGE = 560;
567  public static final int RLN_MLMODEL_SIGMA_OFFSET = 561;
568  public static final int RLN_MLMODEL_SIGMA_ROT = 562;
569  public static final int RLN_MLMODEL_SIGMA_TILT = 563;
570  public static final int RLN_MLMODEL_SIGMA_PSI = 564;
571  public static final int RLN_MLMODEL_REF_IMAGE = 565;
572  public static final int RLN_MLMODEL_SIGMA2_NOISE = 566;
573  public static final int RLN_MLMODEL_SIGMA2_REF = 567;
574  public static final int RLN_MLMODEL_SSNR_REF = 568;
575  public static final int RLN_MLMODEL_TAU2_FUDGE_FACTOR = 569;
576  public static final int RLN_MLMODEL_TAU2_REF = 570;
577  public static final int RLN_OPTIMISER_ACCURACY_ROT = 571;
578  public static final int RLN_OPTIMISER_ACCURACY_TRANS = 572;
579  public static final int RLN_OPTIMISER_ADAPTIVE_FRACTION = 573;
580  public static final int RLN_OPTIMISER_ADAPTIVE_OVERSAMPLING = 574;
581  public static final int RLN_OPTIMISER_AUTO_LOCAL_HP_ORDER = 575;
582  public static final int RLN_OPTIMISER_AVAILABLE_MEMORY = 576;
583  public static final int RLN_OPTIMISER_BEST_RESOL_THUS_FAR = 577;
584  public static final int RLN_OPTIMISER_CHANGES_OPTIMAL_OFFSETS = 578;
585  public static final int RLN_OPTIMISER_CHANGES_OPTIMAL_ORIENTS = 579;
586  public static final int RLN_OPTIMISER_CHANGES_OPTIMAL_CLASSES = 580;
587  public static final int RLN_OPTIMISER_COARSE_SIZE = 581;
588  public static final int RLN_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED = 582;
589  public static final int RLN_OPTIMISER_DATA_ARE_CTF_PREMULTIPLIED = 583;
590  public static final int RLN_OPTIMISER_DATA_STARFILE = 584;
591  public static final int RLN_OPTIMISER_DO_AUTO_REFINE = 585;
592  public static final int RLN_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES = 586;
593  public static final int RLN_OPTIMISER_DO_CORRECT_CTF = 587;
594  public static final int RLN_OPTIMISER_DO_CORRECT_MAGNIFICATION = 588;
595  public static final int RLN_OPTIMISER_DO_CORRECT_NORM = 589;
596  public static final int RLN_OPTIMISER_DO_CORRECT_SCALE = 590;
597  public static final int RLN_OPTIMISER_DO_HELICAL_REFINE = 591;
598  public static final int RLN_OPTIMISER_DO_REALIGN_MOVIES = 592;
599  public static final int RLN_OPTIMISER_DO_MAP = 593;
600  public static final int RLN_OPTIMISER_DO_SGD = 594;
601  public static final int RLN_OPTIMISER_DO_SOLVENT_FLATTEN = 595;
602  public static final int RLN_OPTIMISER_DO_SKIP_ALIGN = 596;
603  public static final int RLN_OPTIMISER_DO_SKIP_ROTATE = 597;
604  public static final int RLN_OPTIMISER_DO_SPLIT_RANDOM_HALVES = 598;
605  public static final int RLN_OPTIMISER_DO_ZERO_MASK = 599;
606  public static final int RLN_OPTIMISER_FIX_SIGMA_NOISE = 600;
607  public static final int RLN_OPTIMISER_FIX_SIGMA_OFFSET = 601;
608  public static final int RLN_OPTIMISER_FIX_TAU = 602;
609  public static final int RLN_OPTIMISER_HAS_CONVERGED = 603;
610  public static final int RLN_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT = 604;
611  public static final int RLN_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO = 605;
612  public static final int RLN_OPTIMISER_HELICAL_TWIST_INITIAL = 606;
613  public static final int RLN_OPTIMISER_HELICAL_RISE_INITIAL = 607;
614  public static final int RLN_OPTIMISER_HELICAL_Z_PERCENTAGE = 608;
615  public static final int RLN_OPTIMISER_HELICAL_TUBE_INNER_DIAMETER = 609;
616  public static final int RLN_OPTIMISER_HELICAL_TUBE_OUTER_DIAMETER = 610;
617  public static final int RLN_OPTIMISER_HELICAL_SYMMETRY_LOCAL_REFINEMENT = 611;
618  public static final int RLN_OPTIMISER_HELICAL_SIGMA_DISTANCE = 612;
619  public static final int RLN_OPTIMISER_HIGHRES_LIMIT_SGD = 613;
620  public static final int RLN_OPTIMISER_IGNORE_HELICAL_SYMMETRY = 614;
621  public static final int RLN_OPTIMISER_HELICAL_KEEP_TILT_PRIOR_FIXED = 615;
622  public static final int RLN_OPTIMISER_HIGHRES_LIMIT_EXP = 616;
623  public static final int RLN_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK = 617;
624  public static final int RLN_OPTIMISER_INCR_SIZE = 618;
625  public static final int RLN_OPTIMISER_ITERATION_NO = 619;
626  public static final int RLN_OPTIMISER_LOCAL_SYMMETRY_FILENAME = 620;
627  public static final int RLN_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES = 621;
628  public static final int RLN_OPTIMISER_MAGNIFICATION_RANGE = 622;
629  public static final int RLN_OPTIMISER_MAGNIFICATION_STEP = 623;
630  public static final int RLN_OPTIMISER_MAX_COARSE_SIZE = 624;
631  public static final int RLN_OPTIMISER_MAX_NR_POOL = 625;
632  public static final int RLN_OPTIMISER_MODEL_STARFILE = 626;
633  public static final int RLN_OPTIMISER_MODEL_STARFILE2 = 627;
634  public static final int RLN_OPTIMISER_NR_ITERATIONS = 628;
635  public static final int RLN_OPTIMISER_NR_ITER_WO_RESOL_GAIN = 629;
636  public static final int RLN_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES = 630;
637  public static final int RLN_OPTIMISER_OUTPUT_ROOTNAME = 631;
638  public static final int RLN_OPTIMISER_PARTICLE_DIAMETER = 632;
639  public static final int RLN_OPTIMISER_RADIUS_MASK_3D_MAP = 633;
640  public static final int RLN_OPTIMISER_RADIUS_MASK_EXP_PARTICLES = 634;
641  public static final int RLN_OPTIMISER_RANDOM_SEED = 635;
642  public static final int RLN_OPTIMISER_REFS_ARE_CTF_CORRECTED = 636;
643  public static final int RLN_OPTIMISER_SAMPLING_STARFILE = 637;
644  public static final int RLN_OPTIMISER_SGD_MU = 638;
645  public static final int RLN_OPTIMISER_SGD_SIGMA2FUDGE_INI = 639;
646  public static final int RLN_OPTIMISER_SGD_SIGMA2FUDGE_HALFLIFE = 640;
647  public static final int RLN_OPTIMISER_SGD_SUBSET_START = 641;
648  public static final int RLN_OPTIMISER_SGD_SUBSET_SIZE = 642;
649  public static final int RLN_OPTIMISER_SGD_WRITE_EVERY_SUBSET = 643;
650  public static final int RLN_OPTIMISER_SGD_MAX_SUBSETS = 644;
651  public static final int RLN_OPTIMISER_SGD_STEPSIZE = 645;
652  public static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES = 646;
653  public static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS = 647;
654  public static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS = 648;
655  public static final int RLN_OPTIMISER_SOLVENT_MASK_NAME = 649;
656  public static final int RLN_OPTIMISER_SOLVENT_MASK2_NAME = 650;
657  public static final int RLN_OPTIMISER_TAU_SPECTRUM_NAME = 651;
658  public static final int RLN_OPTIMISER_USE_TOO_COARSE_SAMPLING = 652;
659  public static final int RLN_OPTIMISER_WIDTH_MASK_EDGE = 653;
660  public static final int RLN_ORIENT_FLIP = 654;
661  public static final int RLN_ORIENT_ID = 655;
662  public static final int RLN_ORIENT_ORIGIN_X = 656;
663  public static final int RLN_ORIENT_ORIGIN_X_PRIOR = 657;
664  public static final int RLN_ORIENT_ORIGIN_Y = 658;
665  public static final int RLN_ORIENT_ORIGIN_Y_PRIOR = 659;
666  public static final int RLN_ORIENT_ORIGIN_Z = 660;
667  public static final int RLN_ORIENT_ORIGIN_Z_PRIOR = 661;
668  public static final int RLN_ORIENT_ROT = 662;
669  public static final int RLN_ORIENT_ROT_PRIOR = 663;
670  public static final int RLN_ORIENT_TILT = 664;
671  public static final int RLN_ORIENT_TILT_PRIOR = 665;
672  public static final int RLN_ORIENT_PSI = 666;
673  public static final int RLN_ORIENT_PSI_PRIOR = 667;
674  public static final int RLN_ORIENT_PSI_PRIOR_FLIP_RATIO = 668;
675  public static final int RLN_PARTICLE_AUTOPICK_FOM = 669;
676  public static final int RLN_PARTICLE_CLASS = 670;
677  public static final int RLN_PARTICLE_DLL = 671;
678  public static final int RLN_PARTICLE_ID = 672;
679  public static final int RLN_PARTICLE_FOM = 673;
680  public static final int RLN_PARTICLE_KL_DIVERGENCE = 674;
681  public static final int RLN_PARTICLE_MOVIE_RUNNING_AVG = 675;
682  public static final int RLN_PARTICLE_RANDOM_SUBSET = 676;
683  public static final int RLN_PARTICLE_NAME = 677;
684  public static final int RLN_PARTICLE_ORI_NAME = 678;
685  public static final int RLN_PARTICLE_NR_SIGNIFICANT_SAMPLES = 679;
686  public static final int RLN_PARTICLE_NR_FRAMES = 680;
687  public static final int RLN_PARTICLE_NR_FRAMES_AVG = 681;
688  public static final int RLN_PARTICLE_PMAX = 682;
689  public static final int RLN_PARTICLE_HELICAL_TUBE_ID = 683;
690  public static final int RLN_PARTICLE_HELICAL_TUBE_PITCH = 684;
691  public static final int RLN_PARTICLE_HELICAL_TRACK_LENGTH = 685;
692  public static final int RLN_PIPELINE_JOB_COUNTER = 686;
693  public static final int RLN_PIPELINE_NODE_NAME = 687;
694  public static final int RLN_PIPELINE_NODE_TYPE = 688;
695  public static final int RLN_PIPELINE_PROCESS_ALIAS = 689;
696  public static final int RLN_PIPELINE_PROCESS_NAME = 690;
697  public static final int RLN_PIPELINE_PROCESS_TYPE = 691;
698  public static final int RLN_PIPELINE_PROCESS_STATUS = 692;
699  public static final int RLN_PIPELINE_EDGE_FROM = 693;
700  public static final int RLN_PIPELINE_EDGE_TO = 694;
701  public static final int RLN_PIPELINE_EDGE_PROCESS = 695;
702  public static final int RLN_POSTPROCESS_AMPLCORR_MASKED = 696;
703  public static final int RLN_POSTPROCESS_AMPLCORR_UNMASKED = 697;
704  public static final int RLN_POSTPROCESS_BFACTOR = 698;
705  public static final int RLN_POSTPROCESS_DPR_MASKED = 699;
706  public static final int RLN_POSTPROCESS_DPR_UNMASKED = 700;
707  public static final int RLN_POSTPROCESS_FINAL_RESOLUTION = 701;
708  public static final int RLN_POSTPROCESS_FSC_GENERAL = 702;
709  public static final int RLN_POSTPROCESS_FSC_TRUE = 703;
710  public static final int RLN_POSTPROCESS_FSC_MASKED = 704;
711  public static final int RLN_POSTPROCESS_FSC_UNMASKED = 705;
712  public static final int RLN_POSTPROCESS_FSC_RANDOM_MASKED = 706;
713  public static final int RLN_POSTPROCESS_GUINIER_FIT_CORRELATION = 707;
714  public static final int RLN_POSTPROCESS_GUINIER_FIT_INTERCEPT = 708;
715  public static final int RLN_POSTPROCESS_GUINIER_FIT_SLOPE = 709;
716  public static final int RLN_POSTPROCESS_GUINIER_VALUE_IN = 710;
717  public static final int RLN_POSTPROCESS_GUINIER_VALUE_INVMTF = 711;
718  public static final int RLN_POSTPROCESS_GUINIER_VALUE_WEIGHTED = 712;
719  public static final int RLN_POSTPROCESS_GUINIER_VALUE_SHARPENED = 713;
720  public static final int RLN_POSTPROCESS_GUINIER_VALUE_INTERCEPT = 714;
721  public static final int RLN_POSTPROCESS_GUINIER_RESOL_SQUARED = 715;
722  public static final int RLN_POSTPROCESS_MTF_VALUE = 716;
723  public static final int RLN_SAMPLING_IS_3D = 717;
724  public static final int RLN_SAMPLING_IS_3D_TRANS = 718;
725  public static final int RLN_SAMPLING_HEALPIX_ORDER = 719;
726  public static final int RLN_SAMPLING_HELICAL_OFFSET_STEP = 720;
727  public static final int RLN_SAMPLING_LIMIT_TILT = 721;
728  public static final int RLN_SAMPLING_OFFSET_RANGE = 722;
729  public static final int RLN_SAMPLING_OFFSET_STEP = 723;
730  public static final int RLN_SAMPLING_PERTURB = 724;
731  public static final int RLN_SAMPLING_PERTURBATION_FACTOR = 725;
732  public static final int RLN_SAMPLING_PRIOR_MODE = 726;
733  public static final int RLN_SAMPLING_PSI_STEP = 727;
734  public static final int RLN_SAMPLING_SIGMA_ROT = 728;
735  public static final int RLN_SAMPLING_SIGMA_TILT = 729;
736  public static final int RLN_SAMPLING_SIGMA_PSI = 730;
737  public static final int RLN_SAMPLING_SYMMETRY = 731;
738  public static final int RLN_SELECTED = 732;
739  public static final int RLN_SELECT_PARTICLES_ZSCORE = 733;
740  public static final int RLN_SORTED_IDX = 734;
741  public static final int RLN_STARFILE_MOVIE_PARTICLES = 735;
742  public static final int RLN_PERFRAME_CUMULATIVE_WEIGHT = 736;
743  public static final int RLN_PERFRAME_RELATIVE_WEIGHT = 737;
744  public static final int RLN_RESOLUTION = 738;
745  public static final int RLN_RESOLUTION_ANGSTROM = 739;
746  public static final int RLN_RESOLUTION_INVPIXEL = 740;
747  public static final int RLN_SPECTRAL_IDX = 741;
748  public static final int MDL_LAST_LABEL = 742; // **** NOTE ****: Do keep this label always at the end;it is here for looping purposes ///
749 }
xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_TRUE
static final int RLN_POSTPROCESS_FSC_TRUE
Definition: MDLabel.java:709
-
xmipp.jni.MDLabel.MDL_SHIFT_X_DIFF
static final int MDL_SHIFT_X_DIFF
< Shift for the image in the X axis (double)
Definition: MDLabel.java:366
-
xmipp.jni.MDLabel.MDL_VOLUME_SCORE_SUM
static final int MDL_VOLUME_SCORE_SUM
Definition: MDLabel.java:402
-
xmipp.jni.MDLabel.RLN_MLMODEL_IS_HELIX
static final int RLN_MLMODEL_IS_HELIX
Definition: MDLabel.java:548
-
xmipp.jni.MDLabel.RLN_MLMODEL_GROUP_SCALE_CORRECTION
static final int RLN_MLMODEL_GROUP_SCALE_CORRECTION
Definition: MDLabel.java:538
-
xmipp.jni.MDLabel.MDL_SCORE_BY_SCREENING
static final int MDL_SCORE_BY_SCREENING
< Feature vectors used to classify particles (vector double)
Definition: MDLabel.java:355
-
xmipp.jni.MDLabel.MDL_RESOLUTION_ANISOTROPY
static final int MDL_RESOLUTION_ANISOTROPY
Definition: MDLabel.java:317
-
xmipp.jni.MDLabel.MDL_GRAPH_CC_PREVIOUS
static final int MDL_GRAPH_CC_PREVIOUS
< Correlation between assigned direction and graph filtered maximum
Definition: MDLabel.java:186
-
xmipp.jni.MDLabel.MDL_VOLUME_SCORE4
static final int MDL_VOLUME_SCORE4
< Score 3 for volumes
Definition: MDLabel.java:409
-
xmipp.jni.MDLabel.RLN_STARFILE_MOVIE_PARTICLES
static final int RLN_STARFILE_MOVIE_PARTICLES
Definition: MDLabel.java:741
-
xmipp.jni.MDLabel.MDL_MASK
static final int MDL_MASK
< Map topology (KerDenSOM, ...)
Definition: MDLabel.java:222
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEUB
static final int MDL_CTF_DEFOCUS_PLANEUB
< Defocus = A*x+B*y+C
Definition: MDLabel.java:97
-
xmipp.jni.MDLabel.RLN_SAMPLING_HELICAL_OFFSET_STEP
static final int RLN_SAMPLING_HELICAL_OFFSET_STEP
Definition: MDLabel.java:726
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REF
static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REF
< score by alignability experimental particles (double)
Definition: MDLabel.java:346
-
xmipp.jni.MDLabel.MDL_ANGLE_DIFF0
static final int MDL_ANGLE_DIFF0
< difference between tilt angles (double,degrees)
Definition: MDLabel.java:20
-
xmipp.jni.MDLabel.RLN_SAMPLING_PERTURBATION_FACTOR
static final int RLN_SAMPLING_PERTURBATION_FACTOR
Definition: MDLabel.java:731
-
xmipp.jni.MDLabel.MDL_CTF_XRAY_OUTER_ZONE_WIDTH
static final int MDL_CTF_XRAY_OUTER_ZONE_WIDTH
Algorithm used to generate Xray PSF.
Definition: MDLabel.java:159
-
xmipp.jni.MDLabel.RLN_MICROGRAPH_TILT_AXIS_DIRECTION
static final int RLN_MICROGRAPH_TILT_AXIS_DIRECTION
Definition: MDLabel.java:520
-
xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_MEAN
static final int MDL_TILT_ANALYSIS_MEAN
Definition: MDLabel.java:397
-
xmipp.jni.MDLabel.MDL_WEIGHT_CONTINUOUS2
static final int MDL_WEIGHT_CONTINUOUS2
< Weight assigned to the image accordint to its clusterability with a significance with respect noise...
Definition: MDLabel.java:412
-
xmipp.jni.MDLabel.MDL_SPH_TSNE_COEFF1D
static final int MDL_SPH_TSNE_COEFF1D
< Deformation in voxels
Definition: MDLabel.java:382
-
xmipp.jni.MDLabel.RLN_CTF_MAXRES
static final int RLN_CTF_MAXRES
< Magnification used for CTF-determination
Definition: MDLabel.java:465
-
xmipp.jni.MDLabel.MDL_SUBTRACTION_BETA0
static final int MDL_SUBTRACTION_BETA0
< R2 coefficient of subtracted particle
Definition: MDLabel.java:387
-
xmipp.jni.MDLabel.MDL_CTF_CA
static final int MDL_CTF_CA
< Spherical aberration
Definition: MDLabel.java:104
-
xmipp.jni.MDLabel.MDL_SHIFT_X2
static final int MDL_SHIFT_X2
< Shift for the image in the X axis (double)
Definition: MDLabel.java:364
-
xmipp.jni.MDLabel.RLN_CTF_VALIDATIONSCORE
static final int RLN_CTF_VALIDATIONSCORE
< CTF value
Definition: MDLabel.java:472
-
xmipp.jni.MDLabel.MDL_PRJ_TILT_NOISE
static final int MDL_PRJ_TILT_NOISE
Definition: MDLabel.java:300
-
xmipp.jni.MDLabel.MDL_IMAGE_REF
static final int MDL_IMAGE_REF
< Name of an image from which MDL_IMAGE is coming from
Definition: MDLabel.java:194
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_TWIST
static final int RLN_MLMODEL_HELICAL_TWIST
Definition: MDLabel.java:540
-
xmipp.jni.MDLabel.MDL_X
static final int MDL_X
< Weight of t-student distribution in robust Maximum likelihood
Definition: MDLabel.java:425
-
xmipp.jni.MDLabel.MDL_COUNT2
static final int MDL_COUNT2
< Number of elements of a type (int) [this is a genereic type do not use to transfer information to a...
Definition: MDLabel.java:49
-
xmipp.jni.MDLabel.RLN_PERFRAME_RELATIVE_WEIGHT
static final int RLN_PERFRAME_RELATIVE_WEIGHT
Definition: MDLabel.java:743
-
xmipp.jni.MDLabel.RLN_PARTICLE_RANDOM_SUBSET
static final int RLN_PARTICLE_RANDOM_SUBSET
Definition: MDLabel.java:682
-
xmipp.jni.MDLabel.RLN_MLMODEL_ACCURACY_TRANS
static final int RLN_MLMODEL_ACCURACY_TRANS
Definition: MDLabel.java:523
-
xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_COEFFS_X
static final int MDL_LOCAL_ALIGNMENT_COEFFS_X
< Two values representing number of patches used for local alignment (X, Y)
Definition: MDLabel.java:215
-
xmipp.jni.MDLabel.MDL_CTF_XRAY_LENS_TYPE
static final int MDL_CTF_XRAY_LENS_TYPE
Wavelength (nm)
Definition: MDLabel.java:158
-
xmipp.jni.MDLabel.RLN_AREA_NAME
static final int RLN_AREA_NAME
< ID for the area (or field of view). If one does not use (tilt) series, area would be the same as mi...
Definition: MDLabel.java:448
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_MTF_VALUE
static final int RLN_POSTPROCESS_MTF_VALUE
Definition: MDLabel.java:722
-
xmipp.jni.MDLabel.MDL_ANGLE_PSI
static final int MDL_ANGLE_PSI
Special label to be used when gathering MDs in MpiMetadataPrograms.
Definition: MDLabel.java:8
-
xmipp.jni.MDLabel.MDL_ANGLE_ROT3
static final int MDL_ANGLE_ROT3
< Rotation angle of an image (double,degrees)
Definition: MDLabel.java:14
-
xmipp.jni.MDLabel.MDL_RESOLUTION_LOCAL_RESIDUE
static final int MDL_RESOLUTION_LOCAL_RESIDUE
<Fourier shell occupancy (double)
Definition: MDLabel.java:326
-
xmipp.jni.MDLabel.RLN_OPTIMISER_MAX_COARSE_SIZE
static final int RLN_OPTIMISER_MAX_COARSE_SIZE
Definition: MDLabel.java:630
-
xmipp.jni.MDLabel.MDL_PRJ_ROT_NOISE
static final int MDL_PRJ_ROT_NOISE
< Psi angle range (vector double)
Definition: MDLabel.java:297
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT
static final int RLN_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT
Definition: MDLabel.java:610
-
xmipp.jni.MDLabel.MDL_IMAGE_RESIDUAL
static final int MDL_IMAGE_RESIDUAL
< Name of of the class image from which MDL_IMAGE is coming from
Definition: MDLabel.java:195
-
xmipp.jni.MDLabel.MDL_REFMD
static final int MDL_REFMD
< Store a second class (int)
Definition: MDLabel.java:314
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_AMPLCORR_MASKED
static final int RLN_POSTPROCESS_AMPLCORR_MASKED
Definition: MDLabel.java:702
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ZERNIKE
static final int MDL_SCORE_BY_ZERNIKE
< Micrographs Gini Coeff. (double)
Definition: MDLabel.java:359
-
xmipp.jni.MDLabel.MDL_SIGMAOFFSET
static final int MDL_SIGMAOFFSET
< Standard deviation of the noise in ML model
Definition: MDLabel.java:378
-
xmipp.jni.MDLabel.RLN_IMAGE_ORI_NAME
static final int RLN_IMAGE_ORI_NAME
Definition: MDLabel.java:489
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS
static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS
Definition: MDLabel.java:653
-
xmipp.jni.MDLabel.MDL_WEIGHT_JUMPER2
static final int MDL_WEIGHT_JUMPER2
< Weight due to angular jumping
Definition: MDLabel.java:415
-
xmipp.jni.MDLabel.MDL_DM3_NUMBER_TYPE
static final int MDL_DM3_NUMBER_TYPE
Definition: MDLabel.java:170
-
xmipp.jni.MDLabel.MDL_SCORE_BY_PCA_RESIDUAL
static final int MDL_SCORE_BY_PCA_RESIDUAL
Definition: MDLabel.java:339
-
xmipp.jni.MDLabel.RLN_SAMPLING_LIMIT_TILT
static final int RLN_SAMPLING_LIMIT_TILT
Definition: MDLabel.java:727
-
xmipp.jni.MDLabel.MDL_VOLUME_SCORE3
static final int MDL_VOLUME_SCORE3
< Score 2 for volumes
Definition: MDLabel.java:408
-
xmipp.jni.MDLabel.RLN_OPTIMISER_MODEL_STARFILE
static final int RLN_OPTIMISER_MODEL_STARFILE
Definition: MDLabel.java:632
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_ZERO_MASK
static final int RLN_OPTIMISER_DO_ZERO_MASK
Definition: MDLabel.java:605
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_TWIST_MIN
static final int RLN_MLMODEL_HELICAL_TWIST_MIN
Definition: MDLabel.java:541
-
xmipp.jni.MDLabel.RLN_OPTIMISER_CHANGES_OPTIMAL_OFFSETS
static final int RLN_OPTIMISER_CHANGES_OPTIMAL_OFFSETS
Definition: MDLabel.java:584
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_COEFS
static final int MDL_CTF_DEFOCUS_COEFS
< Defocus coefficient of determination
Definition: MDLabel.java:90
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_SIGMAV
static final int MDL_CTF_BG_GAUSSIAN2_SIGMAV
< CTF Background parameter
Definition: MDLabel.java:131
-
xmipp.jni.MDLabel.RLN_ORIENT_ID
static final int RLN_ORIENT_ID
Definition: MDLabel.java:661
-
xmipp.jni.MDLabel.MDL_SAMPLINGRATE_ORIGINAL
static final int MDL_SAMPLINGRATE_ORIGINAL
< sampling rate in A/pixel (double)
Definition: MDLabel.java:332
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDPCARUNSTEST
static final int MDL_CTF_CRIT_PSDPCARUNSTEST
< Variance in the first principal component of the PSDs
Definition: MDLabel.java:152
-
xmipp.jni.MDLabel.MDL_MAGNIFICATION
static final int MDL_MAGNIFICATION
< Three values representing number of control points used for local alignment (X, Y...
Definition: MDLabel.java:220
-
xmipp.jni.MDLabel.RLN_MLMODEL_FSC_HALVES_REF
static final int RLN_MLMODEL_FSC_HALVES_REF
Definition: MDLabel.java:534
-
xmipp.jni.MDLabel.MDL_MLF_CTF
static final int MDL_MLF_CTF
< Final tilt angle in X for missing region in subtomogram
Definition: MDLabel.java:243
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_MAP
static final int RLN_OPTIMISER_DO_MAP
Definition: MDLabel.java:599
-
xmipp.jni.MDLabel.RLN_OPTIMISER_ACCURACY_ROT
static final int RLN_OPTIMISER_ACCURACY_ROT
Definition: MDLabel.java:577
-
xmipp.jni.MDLabel.MDL_SHIFT_Z
static final int MDL_SHIFT_Z
< difference in Shift along Y axis (double)
Definition: MDLabel.java:371
-
xmipp.jni.MDLabel.RLN_SAMPLING_SIGMA_TILT
static final int RLN_SAMPLING_SIGMA_TILT
Definition: MDLabel.java:735
-
xmipp.jni.MDLabel.MDL_CTF_INPUTPARAMS
static final int MDL_CTF_INPUTPARAMS
Definition: MDLabel.java:79
-
xmipp.jni.MDLabel.RLN_SAMPLING_PERTURB
static final int RLN_SAMPLING_PERTURB
Definition: MDLabel.java:730
-
xmipp.jni.MDLabel.MDL_CLASS_INTERSECTION_SIZE_PVALUE
static final int MDL_CLASS_INTERSECTION_SIZE_PVALUE
<Correlation between the denoised image and the noisy version
Definition: MDLabel.java:52
-
xmipp.jni.MDLabel.RLN_IMAGE_SAMPLINGRATE_Y
static final int RLN_IMAGE_SAMPLINGRATE_Y
Definition: MDLabel.java:492
-
xmipp.jni.MDLabel.MDL_KSTEST
static final int MDL_KSTEST
< Centroid of a cluster for the KMEANS2D classification
Definition: MDLabel.java:212
-
xmipp.jni.MDLabel.RLN_CTF_CONVERGENCE_CONE
static final int RLN_CTF_CONVERGENCE_CONE
< Maximum resolution with Thon rings
Definition: MDLabel.java:466
-
xmipp.jni.MDLabel.MDL_NEIGHBORS
static final int MDL_NEIGHBORS
< Model fraction (alpha_k) for a Maximum Likelihood model
Definition: MDLabel.java:248
-
xmipp.jni.MDLabel.MDL_PRJ_VOL
static final int MDL_PRJ_VOL
Definition: MDLabel.java:303
-
xmipp.jni.MDLabel.MDL_TRANSFORM_MATRIX
static final int MDL_TRANSFORM_MATRIX
< Name for a Metadata file (std::string)
Definition: MDLabel.java:394
-
xmipp.jni.MDLabel.RLN_MATRIX_3_1
static final int RLN_MATRIX_3_1
Definition: MDLabel.java:512
-
xmipp.jni.MDLabel.MDL_CLASS_COUNT
static final int MDL_CLASS_COUNT
< Average cross-correlation for the image (double)
Definition: MDLabel.java:37
-
xmipp.jni.MDLabel.RLN_MLMODEL_INTERPOLATOR
static final int RLN_MLMODEL_INTERPOLATOR
Definition: MDLabel.java:549
-
xmipp.jni.MDLabel.RLN_IMAGE_NAME
static final int RLN_IMAGE_NAME
< Phase-shift from a phase-plate (in degrees)
Definition: MDLabel.java:474
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_RESIDUAL
static final int MDL_CTF_DEFOCUS_RESIDUAL
< Coefficients of the defocus adjustment plane
Definition: MDLabel.java:91
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_PRECISION_REF
static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION_REF
< score by alignability experimental particles (double)
Definition: MDLabel.java:344
-
xmipp.jni.MDLabel.MDL_CTF_LONGITUDINAL_DISPLACEMENT
static final int MDL_CTF_LONGITUDINAL_DISPLACEMENT
< Convergence cone
Definition: MDLabel.java:111
-
xmipp.jni.MDLabel.RLN_CTF_SCALEFACTOR
static final int RLN_CTF_SCALEFACTOR
< B-factor
Definition: MDLabel.java:451
-
xmipp.jni.MDLabel.MDL_ZSCORE_RESVAR
static final int MDL_ZSCORE_RESVAR
< Z Score of the mean of the residuals (double)
Definition: MDLabel.java:440
-
xmipp.jni.MDLabel.MDL_DIMENSIONS_3D
static final int MDL_DIMENSIONS_3D
Definition: MDLabel.java:306
-
xmipp.jni.MDLabel.RLN_OPTIMISER_MAGNIFICATION_STEP
static final int RLN_OPTIMISER_MAGNIFICATION_STEP
Definition: MDLabel.java:629
-
xmipp.jni.MDLabel.MDL_CRYSTAL_CELLX
static final int MDL_CRYSTAL_CELLX
< P-value (1-percentile) of the relative class size (size/max(original_classes)) compared to a random...
Definition: MDLabel.java:54
-
xmipp.jni.MDLabel.MDL_NMA_COLLECTIVITY
static final int MDL_NMA_COLLECTIVITY
< Normal mode displacements (vector double)
Definition: MDLabel.java:252
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_R2
static final int MDL_CTF_DEFOCUS_R2
< Defocus change with respect to previous defoucs (Angstroms)
Definition: MDLabel.java:89
-
xmipp.jni.MDLabel.RLN_MLMODEL_GROUP_NAME
static final int RLN_MLMODEL_GROUP_NAME
Definition: MDLabel.java:535
-
xmipp.jni.MDLabel.MDL_PRJ_PSI_NOISE
static final int MDL_PRJ_PSI_NOISE
< File for generated angles
Definition: MDLabel.java:294
-
xmipp.jni.MDLabel.MDL_ANGLE_Y
static final int MDL_ANGLE_Y
< difference between two angles (double,degrees)
Definition: MDLabel.java:23
-
xmipp.jni.MDLabel.MDL_CRYSTAL_SHIFTX
static final int MDL_CRYSTAL_SHIFTX
< Have a crystal projection (bool)
Definition: MDLabel.java:62
-
xmipp.jni.MDLabel.MDL_VOLUME_SCORE_MIN
static final int MDL_VOLUME_SCORE_MIN
< Score corresponding to the mean of cc with cc>threshold
Definition: MDLabel.java:405
-
xmipp.jni.MDLabel.RLN_MATRIX_1_1
static final int RLN_MATRIX_1_1
Definition: MDLabel.java:506
-
xmipp.jni.MDLabel.RLN_PARTICLE_DLL
static final int RLN_PARTICLE_DLL
Definition: MDLabel.java:677
-
xmipp.jni.MDLabel.MDL_NMA
static final int MDL_NMA
< Radius of the neighborhood (radians)
Definition: MDLabel.java:251
-
xmipp.jni.MDLabel.RLN_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK
static final int RLN_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK
Definition: MDLabel.java:623
-
xmipp.jni.MDLabel.RLN_OPTIMISER_RANDOM_SEED
static final int RLN_OPTIMISER_RANDOM_SEED
Definition: MDLabel.java:641
-
xmipp.jni.MDLabel.MDL_MACRO_CMD
static final int MDL_MACRO_CMD
< Number which will multiply all features (double)
Definition: MDLabel.java:280
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DATA_STARFILE
static final int RLN_OPTIMISER_DATA_STARFILE
Definition: MDLabel.java:590
-
xmipp.jni.MDLabel.MDL_NOISE_COORD
static final int MDL_NOISE_COORD
< Noise description for particle&#39;s center coordenates (when projecting)
Definition: MDLabel.java:262
-
xmipp.jni.MDLabel.MDL_SCORE_BY_HISTDIST
static final int MDL_SCORE_BY_HISTDIST
< Feature vectors used to classify particles (vector double)
Definition: MDLabel.java:351
-
xmipp.jni.MDLabel.MDL_AVG_CHANGES_OFFSETS
static final int MDL_AVG_CHANGES_OFFSETS
Average change in angular orientation (double degrees)
Definition: MDLabel.java:29
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_RISE_INITIAL_STEP
static final int RLN_MLMODEL_HELICAL_RISE_INITIAL_STEP
Definition: MDLabel.java:547
-
xmipp.jni.MDLabel.RLN_OPTIMISER_NR_ITERATIONS
static final int RLN_OPTIMISER_NR_ITERATIONS
Definition: MDLabel.java:634
-
xmipp.jni.MDLabel.RLN_PARTICLE_HELICAL_TRACK_LENGTH
static final int RLN_PARTICLE_HELICAL_TRACK_LENGTH
Definition: MDLabel.java:691
-
xmipp.jni.MDLabel.MDL_SCORE_BY_GRANULO
static final int MDL_SCORE_BY_GRANULO
< Feature vectors used to classify particles (vector double)
Definition: MDLabel.java:350
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_RATIO
static final int MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_RATIO
< First zero ratio
Definition: MDLabel.java:141
-
xmipp.jni.MDLabel.RLN_AREA_ID
static final int RLN_AREA_ID
< Z size (int)
Definition: MDLabel.java:447
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_SIGMAU
static final int MDL_CTF_BG_GAUSSIAN_SIGMAU
< CTF Background parameter
Definition: MDLabel.java:119
-
xmipp.jni.MDLabel.MDL_OPTICALFLOW_MEANY
static final int MDL_OPTICALFLOW_MEANY
<Mean of="" the="" movement="" in="" x="" direction="" of="" the="" motion="" map>=""> (double) ...
Definition: MDLabel.java:269
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_NORMALITY
static final int MDL_CTF_CRIT_NORMALITY
< Runs test on the projection of the PSD on the first principal component
Definition: MDLabel.java:153
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SKIP_ALIGN
static final int RLN_OPTIMISER_DO_SKIP_ALIGN
Definition: MDLabel.java:602
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_AMPLCORR_UNMASKED
static final int RLN_POSTPROCESS_AMPLCORR_UNMASKED
Definition: MDLabel.java:703
-
xmipp.jni.MDLabel.MDL_RESOLUTION_DPR
static final int MDL_RESOLUTION_DPR
<Resolution anisotropy used to store the significance of the Bingham Test (double) ...
Definition: MDLabel.java:318
-
xmipp.jni.MDLabel.RLN_IMAGE_SIZEZ
static final int RLN_IMAGE_SIZEZ
Definition: MDLabel.java:497
-
xmipp.jni.MDLabel.MDL_MODELFRAC
static final int MDL_MODELFRAC
< MLF Wiener filter (double)
Definition: MDLabel.java:247
-
xmipp.jni.MDLabel.RLN_OPTIMISER_COARSE_SIZE
static final int RLN_OPTIMISER_COARSE_SIZE
Definition: MDLabel.java:587
-
xmipp.jni.MDLabel.MDL_SHIFT_Y2
static final int MDL_SHIFT_Y2
< Shift for the image in the Y axis (double)
Definition: MDLabel.java:368
-
xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_COEFFS_Y
static final int MDL_LOCAL_ALIGNMENT_COEFFS_Y
< BSpline coefficient in X dim
Definition: MDLabel.java:216
-
xmipp.jni.MDLabel.MDL_CTF_BG_BASELINE
static final int MDL_CTF_BG_BASELINE
< CTF Background parameter
Definition: MDLabel.java:128
-
xmipp.jni.MDLabel.RLN_MLMODEL_TAU2_FUDGE_FACTOR
static final int RLN_MLMODEL_TAU2_FUDGE_FACTOR
Definition: MDLabel.java:575
-
xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_CONF_97_5_PERC
static final int MDL_LOCAL_ALIGNMENT_CONF_97_5_PERC
< A shift amount at confidence level of 2.5%
Definition: MDLabel.java:218
-
xmipp.jni.MDLabel.MDL_NMA_MAXRANGE
static final int MDL_NMA_MAXRANGE
< Minimum value observed for a given NMA mode
Definition: MDLabel.java:256
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEVC
static final int MDL_CTF_DEFOCUS_PLANEVC
< Defocus = A*x+B*y+C
Definition: MDLabel.java:101
-
xmipp.jni.MDLabel.MDL_COUNT
static final int MDL_COUNT
< Cost percentile for the image (double)
Definition: MDLabel.java:48
-
xmipp.jni.MDLabel.MDL_IMED
static final int MDL_IMED
< Name of the tilted images associated to MDL_IMAGE
Definition: MDLabel.java:197
-
xmipp.jni.MDLabel.MDL_IMAGE_TILTED
static final int MDL_IMAGE_TILTED
< Name of a residual image associated to this image
Definition: MDLabel.java:196
-
xmipp.jni.MDLabel.MDL_KMEANS2D_CENTROID
static final int MDL_KMEANS2D_CENTROID
< Keywords associated to this line, should be a single string block (do not use spaces as separators)...
Definition: MDLabel.java:211
-
xmipp.jni.MDLabel.MDL_NMA_ATOMSHIFT
static final int MDL_NMA_ATOMSHIFT
< NMA Collectivity of a given mode
Definition: MDLabel.java:253
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_RISE_MIN
static final int RLN_MLMODEL_HELICAL_RISE_MIN
Definition: MDLabel.java:545
-
xmipp.jni.MDLabel.MDL_SHIFT_DIFF
static final int MDL_SHIFT_DIFF
< shift difference (double)
Definition: MDLabel.java:375
-
xmipp.jni.MDLabel.MDL_DM3_TAGCLASS
static final int MDL_DM3_TAGCLASS
Definition: MDLabel.java:172
-
xmipp.jni.MDLabel.MDL_PICKING_AUTOPICKPERCENT
static final int MDL_PICKING_AUTOPICKPERCENT
< Micrograph state for particle picking
Definition: MDLabel.java:286
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_SIGMAV
static final int MDL_CTF_BG_GAUSSIAN_SIGMAV
< CTF Background parameter
Definition: MDLabel.java:120
-
xmipp.jni.MDLabel.MDL_ITEM_ID
static final int MDL_ITEM_ID
< Intensity scale for an image
Definition: MDLabel.java:205
-
xmipp.jni.MDLabel.RLN_PIPELINE_PROCESS_TYPE
static final int RLN_PIPELINE_PROCESS_TYPE
Definition: MDLabel.java:697
-
xmipp.jni.MDLabel.MDL_PICKING_MICROGRAPH_STATE
static final int MDL_PICKING_MICROGRAPH_STATE
< State for particle picking
Definition: MDLabel.java:285
-
xmipp.jni.MDLabel.MDL_RESOLUTION_FREQ2
static final int MDL_RESOLUTION_FREQ2
<Frequency in 1/A (double)
Definition: MDLabel.java:323
-
xmipp.jni.MDLabel.RLN_CTF_Q0
static final int RLN_CTF_Q0
< Transversal displacemente
Definition: MDLabel.java:469
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUSU
static final int MDL_CTF_DEFOCUSU
< average defocus (Angtroms)
Definition: MDLabel.java:86
-
xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_CONF_2_5_PERC
static final int MDL_LOCAL_ALIGNMENT_CONF_2_5_PERC
< BSpline coefficient in Y dim
Definition: MDLabel.java:217
-
xmipp.jni.MDLabel.RLN_MLMODEL_PDF_CLASS
static final int RLN_MLMODEL_PDF_CLASS
Definition: MDLabel.java:559
-
xmipp.jni.MDLabel.MDL_WEIGHT_PRECISION_MIRROR
static final int MDL_WEIGHT_PRECISION_MIRROR
< Weight due to Alignability Accuracy
Definition: MDLabel.java:423
-
xmipp.jni.MDLabel.MDL_SAMPLINGRATE
static final int MDL_SAMPLINGRATE
rfactor
Definition: MDLabel.java:331
-
xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_OPERATION
static final int MDL_PHANTOM_FEATURE_OPERATION
< The density of the feature (double)
Definition: MDLabel.java:276
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES
static final int RLN_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES
Definition: MDLabel.java:592
-
xmipp.jni.MDLabel.RLN_MATRIX_2_3
static final int RLN_MATRIX_2_3
Definition: MDLabel.java:511
-
xmipp.jni.MDLabel.RLN_OPTIMISER_AUTO_LOCAL_HP_ORDER
static final int RLN_OPTIMISER_AUTO_LOCAL_HP_ORDER
Definition: MDLabel.java:581
-
xmipp.jni.MDLabel.MDL_MLF_SIGNAL
static final int MDL_MLF_SIGNAL
< MLF Wiener filter (double)
Definition: MDLabel.java:245
-
xmipp.jni.MDLabel.RLN_PARTICLE_NAME
static final int RLN_PARTICLE_NAME
Definition: MDLabel.java:683
-
xmipp.jni.MDLabel.RLN_PIPELINE_PROCESS_NAME
static final int RLN_PIPELINE_PROCESS_NAME
Definition: MDLabel.java:696
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_DIFF_RATIO
static final int MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_DIFF_RATIO
< Ratio sigma(firstMinimum)/sigma(firstZero)
Definition: MDLabel.java:142
-
xmipp.jni.MDLabel.MDL_RESOLUTION_FRC
static final int MDL_RESOLUTION_FRC
<Error in l2 (double)
Definition: MDLabel.java:320
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDVARIANCE
static final int MDL_CTF_CRIT_PSDVARIANCE
< Correlation between the 1st and 3rd ring of the CTF
Definition: MDLabel.java:150
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_CORRECT_NORM
static final int RLN_OPTIMISER_DO_CORRECT_NORM
Definition: MDLabel.java:595
-
xmipp.jni.MDLabel.MDL_CONTINUOUS_SCALE_X
static final int MDL_CONTINUOUS_SCALE_X
< scale angle of continuous assignment
Definition: MDLabel.java:72
-
xmipp.jni.MDLabel.MDL_PRJ_DIMENSIONS
static final int MDL_PRJ_DIMENSIONS
< Number of non-redundant projections directions (size_t)
Definition: MDLabel.java:292
-
xmipp.jni.MDLabel.MDL_WEIGHT_SSNR
static final int MDL_WEIGHT_SSNR
< Weight due to Angular significance
Definition: MDLabel.java:419
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_RISE_MAX
static final int RLN_MLMODEL_HELICAL_RISE_MAX
Definition: MDLabel.java:546
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY
static final int MDL_SCORE_BY_ALIGNABILITY
Definition: MDLabel.java:340
-
xmipp.jni.MDLabel.MDL_RESOLUTION_RFACTOR
static final int MDL_RESOLUTION_RFACTOR
<Structure factor
Definition: MDLabel.java:330
-
xmipp.jni.MDLabel.MDL_MAXCC
static final int MDL_MAXCC
< Name of a mask associated to image
Definition: MDLabel.java:223
-
xmipp.jni.MDLabel.MDL_BLOCK_NUMBER
static final int MDL_BLOCK_NUMBER
< Mean background value for an image
Definition: MDLabel.java:34
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEVA
static final int MDL_CTF_DEFOCUS_PLANEVA
< Defocus = A*x+B*y+C
Definition: MDLabel.java:99
-
xmipp.jni.MDLabel.RLN_ORIENT_TILT
static final int RLN_ORIENT_TILT
Definition: MDLabel.java:670
-
xmipp.jni.MDLabel.MDL_NOISE_ANGLES
static final int MDL_NOISE_ANGLES
< NMA Eigenvalue of a given mode
Definition: MDLabel.java:260
-
xmipp.jni.MDLabel.MDL_ANGLE_TILT3
static final int MDL_ANGLE_TILT3
< Tilting angle of an image (double,degrees)
Definition: MDLabel.java:18
-
xmipp.jni.MDLabel.RLN_MLMODEL_ESTIM_RESOL_REF
static final int RLN_MLMODEL_ESTIM_RESOL_REF
Definition: MDLabel.java:531
-
xmipp.jni.MDLabel.MDL_XSIZE
static final int MDL_XSIZE
< X component in tilted micrograph (int)
Definition: MDLabel.java:428
-
xmipp.jni.MDLabel.MDL_SUM
static final int MDL_SUM
< Beta 1 coefficient of adjusted model for subtract particle
Definition: MDLabel.java:389
-
xmipp.jni.MDLabel.MDL_CTF_ENERGY_LOSS
static final int MDL_CTF_ENERGY_LOSS
< group images by defocus
Definition: MDLabel.java:106
-
xmipp.jni.MDLabel.MDL_KERDENSOM_REGULARIZATION
static final int MDL_KERDENSOM_REGULARIZATION
< Functional value (double)
Definition: MDLabel.java:208
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_REALIGN_MOVIES
static final int RLN_OPTIMISER_DO_REALIGN_MOVIES
Definition: MDLabel.java:598
-
xmipp.jni.MDLabel.RLN_OPTIMISER_RADIUS_MASK_3D_MAP
static final int RLN_OPTIMISER_RADIUS_MASK_3D_MAP
Definition: MDLabel.java:639
-
xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_DENSITY
static final int MDL_PHANTOM_FEATURE_DENSITY
< Center of the feature (vector double)
Definition: MDLabel.java:275
-
xmipp.jni.MDLabel.MDL_APPLY_SHIFT
static final int MDL_APPLY_SHIFT
< Angular temperature (double,degrees)
Definition: MDLabel.java:26
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_RISE
static final int RLN_MLMODEL_HELICAL_RISE
Definition: MDLabel.java:544
-
xmipp.jni.MDLabel.RLN_PARTICLE_HELICAL_TUBE_PITCH
static final int RLN_PARTICLE_HELICAL_TUBE_PITCH
Definition: MDLabel.java:690
-
xmipp.jni.MDLabel.RLN_PIPELINE_EDGE_TO
static final int RLN_PIPELINE_EDGE_TO
Definition: MDLabel.java:700
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_RISE_INITIAL
static final int RLN_OPTIMISER_HELICAL_RISE_INITIAL
Definition: MDLabel.java:613
-
xmipp.jni.MDLabel.RLN_IMAGE_STATS_STDDEV
static final int RLN_IMAGE_STATS_STDDEV
Definition: MDLabel.java:501
-
xmipp.jni.MDLabel.MDL_ZSIZE
static final int MDL_ZSIZE
< Z Score (double)
Definition: MDLabel.java:446
-
xmipp.jni.MDLabel.RLN_IMAGE_SIZEY
static final int RLN_IMAGE_SIZEY
Definition: MDLabel.java:496
-
xmipp.jni.MDLabel.RLN_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES
static final int RLN_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES
Definition: MDLabel.java:636
-
xmipp.jni.MDLabel.RLN_OPTIMISER_MAX_NR_POOL
static final int RLN_OPTIMISER_MAX_NR_POOL
Definition: MDLabel.java:631
-
xmipp.jni.MDLabel.MDL_MISSINGREGION_TYPE
static final int MDL_MISSINGREGION_TYPE
< Number of missing region in subtomogram
Definition: MDLabel.java:238
-
xmipp.jni.MDLabel.MDL_COMMENT
static final int MDL_COMMENT
< Digital frequency at which the FRC drops below 0.5 (double)
Definition: MDLabel.java:44
-
xmipp.jni.MDLabel.RLN_MLMODEL_LL
static final int RLN_MLMODEL_LL
Definition: MDLabel.java:550
-
xmipp.jni.MDLabel.RLN_RESOLUTION_ANGSTROM
static final int RLN_RESOLUTION_ANGSTROM
Definition: MDLabel.java:745
-
xmipp.jni.MDLabel.MDL_CTF_CONVERGENCE_CONE
static final int MDL_CTF_CONVERGENCE_CONE
< Lens stability
Definition: MDLabel.java:110
-
xmipp.jni.MDLabel.RLN_PARTICLE_ORI_NAME
static final int RLN_PARTICLE_ORI_NAME
Definition: MDLabel.java:684
-
xmipp.jni.MDLabel.MDL_CTF_ENV_R0
static final int MDL_CTF_ENV_R0
< CTF gain
Definition: MDLabel.java:115
-
xmipp.jni.MDLabel.RLN_OPTIMISER_FIX_SIGMA_NOISE
static final int RLN_OPTIMISER_FIX_SIGMA_NOISE
Definition: MDLabel.java:606
-
xmipp.jni.MDLabel.MDL_CTF_BG_SQRT_K
static final int MDL_CTF_BG_SQRT_K
< CTF Background parameter
Definition: MDLabel.java:124
-
xmipp.jni.MDLabel.MDL_RANDOMSEED
static final int MDL_RANDOMSEED
< A enhanced Power Spectrum Density file name (std::string)
Definition: MDLabel.java:310
-
xmipp.jni.MDLabel.MDL_CRYSTAL_SHIFTZ
static final int MDL_CRYSTAL_SHIFTZ
< Shift for the image in the Y axis (double) for crystals
Definition: MDLabel.java:64
-
xmipp.jni.MDLabel.RLN_IMAGE_DIMENSIONALITY
static final int RLN_IMAGE_DIMENSIONALITY
Definition: MDLabel.java:479
-
xmipp.jni.MDLabel.RLN_OPTIMISER_AVAILABLE_MEMORY
static final int RLN_OPTIMISER_AVAILABLE_MEMORY
Definition: MDLabel.java:582
-
xmipp.jni.MDLabel.RLN_MLMODEL_DIFF2_HALVES_REF
static final int RLN_MLMODEL_DIFF2_HALVES_REF
Definition: MDLabel.java:530
-
xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
-
xmipp.jni.MDLabel.MDL_SHIFT_Y
static final int MDL_SHIFT_Y
< difference in Shift along X axis (double)
Definition: MDLabel.java:367
-
xmipp.jni.MDLabel.RLN_PARTICLE_PMAX
static final int RLN_PARTICLE_PMAX
Definition: MDLabel.java:688
-
xmipp.jni.MDLabel.MDL_VOLUME_SCORE2
static final int MDL_VOLUME_SCORE2
< Score 1 for volumes
Definition: MDLabel.java:407
-
xmipp.jni.MDLabel.MDL_MAPTOPOLOGY
static final int MDL_MAPTOPOLOGY
Magnification of microscope.
Definition: MDLabel.java:221
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SKIP_ROTATE
static final int RLN_OPTIMISER_DO_SKIP_ROTATE
Definition: MDLabel.java:603
-
xmipp.jni.MDLabel.MDL_DIMENSIONS_2D
static final int MDL_DIMENSIONS_2D
Definition: MDLabel.java:307
-
xmipp.jni.MDLabel.RLN_ORIENT_TILT_PRIOR
static final int RLN_ORIENT_TILT_PRIOR
Definition: MDLabel.java:671
-
xmipp.jni.MDLabel.MDL_CTF_LAMBDA
static final int MDL_CTF_LAMBDA
Definition: MDLabel.java:157
-
xmipp.jni.MDLabel.RLN_MLMODEL_ORIGINAL_SIZE
static final int RLN_MLMODEL_ORIGINAL_SIZE
Definition: MDLabel.java:556
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_ANGLE
static final int MDL_CTF_BG_GAUSSIAN2_ANGLE
< CTF Background parameter
Definition: MDLabel.java:134
-
xmipp.jni.MDLabel.MDL_CTF_X0
static final int MDL_CTF_X0
< Difference between the observed defocus value and the estimated defocus value
Definition: MDLabel.java:92
-
xmipp.jni.MDLabel.RLN_PARTICLE_NR_FRAMES_AVG
static final int RLN_PARTICLE_NR_FRAMES_AVG
Definition: MDLabel.java:687
-
xmipp.jni.MDLabel.RLN_CTF_K
static final int RLN_CTF_K
< Amplitude contrast
Definition: MDLabel.java:470
-
xmipp.jni.MDLabel.MDL_MLF_NOISE
static final int MDL_MLF_NOISE
< MLF signal (double)
Definition: MDLabel.java:246
-
xmipp.jni.MDLabel.MDL_ANGLE_ROT2
static final int MDL_ANGLE_ROT2
< Rotation angle of an image (double,degrees)
Definition: MDLabel.java:13
-
xmipp.jni.MDLabel.RLN_ORIENT_ROT
static final int RLN_ORIENT_ROT
Definition: MDLabel.java:668
-
xmipp.jni.MDLabel.MDL_SCORE_BY_PCA_RESIDUAL_PROJ
static final int MDL_SCORE_BY_PCA_RESIDUAL_PROJ
< scaling factor for an image or volume (double)
Definition: MDLabel.java:337
-
xmipp.jni.MDLabel.MDL_ORIGIN_Y
static final int MDL_ORIGIN_Y
< Origin for the image in the X axis (double)
Definition: MDLabel.java:266
-
xmipp.jni.MDLabel.MDL_COST
static final int MDL_COST
< Store a score for the coords. consensus (it will change the behavoir of the viewer) ...
Definition: MDLabel.java:46
-
xmipp.jni.MDLabel.MDL_MICROGRAPH_TILTED
static final int MDL_MICROGRAPH_TILTED
< Name of the original micrograph, MDL_MICROGRAPH is probably a downsampled version of this one (std:...
Definition: MDLabel.java:233
-
xmipp.jni.MDLabel.MDL_NEIGHBOR
static final int MDL_NEIGHBOR
< Vector of indexes to points some "neighbors"
Definition: MDLabel.java:249
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXP
static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXP
< score by alignability references (double)
Definition: MDLabel.java:345
-
xmipp.jni.MDLabel.MDL_ANGLE_ROT
static final int MDL_ANGLE_ROT
< difference between psi angles (double,degrees)
Definition: MDLabel.java:12
-
xmipp.jni.MDLabel.MDL_SCORE_BY_VAR
static final int MDL_SCORE_BY_VAR
< Feature vectors used to classify particles (vector double)
Definition: MDLabel.java:357
-
xmipp.jni.MDLabel.MDL_SPH_DEFORMATION
static final int MDL_SPH_DEFORMATION
< Deformation coefficients
Definition: MDLabel.java:381
-
xmipp.jni.MDLabel.MDL_ZSCORE_SNR1
static final int MDL_ZSCORE_SNR1
< Z Score (double)
Definition: MDLabel.java:444
-
xmipp.jni.MDLabel.RLN_OPTIMISER_USE_TOO_COARSE_SAMPLING
static final int RLN_OPTIMISER_USE_TOO_COARSE_SAMPLING
Definition: MDLabel.java:658
-
xmipp.jni.MDLabel.MDL_NMA_MINRANGE
static final int MDL_NMA_MINRANGE
< NMA energy contained in the NMA displacement vector
Definition: MDLabel.java:255
-
xmipp.jni.MDLabel.RLN_MATRIX_3_2
static final int RLN_MATRIX_3_2
Definition: MDLabel.java:513
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_TUBE_INNER_DIAMETER
static final int RLN_OPTIMISER_HELICAL_TUBE_INNER_DIAMETER
Definition: MDLabel.java:615
-
xmipp.jni.MDLabel.MDL_IMAGE4
static final int MDL_IMAGE4
< Image associated to this object (std::string)
Definition: MDLabel.java:202
-
xmipp.jni.MDLabel.MDL_FIRST_LABEL
static final int MDL_FIRST_LABEL
Definition: MDLabel.java:5
-
xmipp.jni.MDLabel.RLN_PARTICLE_AUTOPICK_FOM
static final int RLN_PARTICLE_AUTOPICK_FOM
Definition: MDLabel.java:675
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_MASKED
static final int RLN_POSTPROCESS_FSC_MASKED
Definition: MDLabel.java:710
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDRADIALINTEGRAL
static final int MDL_CTF_CRIT_PSDRADIALINTEGRAL
< Minimum damping at border
Definition: MDLabel.java:147
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_ICENESS
static final int MDL_CTF_CRIT_ICENESS
< Normality test between histogram of micrography and gaussian distribution
Definition: MDLabel.java:154
-
xmipp.jni.MDLabel.MDL_SIGMANOISE
static final int MDL_SIGMANOISE
< shift difference (double)
Definition: MDLabel.java:377
-
xmipp.jni.MDLabel.MDL_SHIFT_Y3
static final int MDL_SHIFT_Y3
< Shift for the image in the Y axis (double)
Definition: MDLabel.java:369
-
xmipp.jni.MDLabel.MDL_CRYSTAL_LATTICE_A
static final int MDL_CRYSTAL_LATTICE_A
< Cell location for crystals
Definition: MDLabel.java:56
-
xmipp.jni.MDLabel.MDL_CTF_ENVELOPE
static final int MDL_CTF_ENVELOPE
< Energy loss
Definition: MDLabel.java:107
-
xmipp.jni.MDLabel.MDL_CTF_MODEL
static final int MDL_CTF_MODEL
< Parameters file for the CTF Model (std::string)
Definition: MDLabel.java:80
-
xmipp.jni.MDLabel.RLN_CTF_DEFOCUSV
static final int RLN_CTF_DEFOCUSV
< Defocus U (Angstroms)
Definition: MDLabel.java:455
-
xmipp.jni.MDLabel.MDL_CONTINUOUS_GRAY_B
static final int MDL_CONTINUOUS_GRAY_B
< a value of continuous assignment
Definition: MDLabel.java:70
-
xmipp.jni.MDLabel.MDL_SCALE
static final int MDL_SCALE
< sampling rate in A/pixel (double)
Definition: MDLabel.java:336
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SOLVENT_MASK2_NAME
static final int RLN_OPTIMISER_SOLVENT_MASK2_NAME
Definition: MDLabel.java:656
-
xmipp.jni.MDLabel.MDL_PICKING_TEMPLATES
static final int MDL_PICKING_TEMPLATES
< Color for particle picking
Definition: MDLabel.java:283
-
xmipp.jni.MDLabel.MDL_MACRO_CMD_ARGS
static final int MDL_MACRO_CMD_ARGS
Definition: MDLabel.java:281
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HAS_CONVERGED
static final int RLN_OPTIMISER_HAS_CONVERGED
Definition: MDLabel.java:609
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_FIT_SLOPE
static final int RLN_POSTPROCESS_GUINIER_FIT_SLOPE
Definition: MDLabel.java:715
-
xmipp.jni.MDLabel.RLN_OPTIMISER_ITERATION_NO
static final int RLN_OPTIMISER_ITERATION_NO
Definition: MDLabel.java:625
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_SHARPENED
static final int RLN_POSTPROCESS_GUINIER_VALUE_SHARPENED
Definition: MDLabel.java:719
-
xmipp.jni.MDLabel.RLN_MLMODEL_NORM_CORRECTION_AVG
static final int RLN_MLMODEL_NORM_CORRECTION_AVG
Definition: MDLabel.java:552
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_CV
static final int MDL_CTF_BG_GAUSSIAN2_CV
< CTF Background parameter
Definition: MDLabel.java:133
-
xmipp.jni.MDLabel.RLN_MATRIX_2_2
static final int RLN_MATRIX_2_2
Definition: MDLabel.java:510
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_K
static final int MDL_CTF_BG_GAUSSIAN2_K
< CTF Background parameter
Definition: MDLabel.java:129
-
xmipp.jni.MDLabel.MDL_DOSE
static final int MDL_DOSE
Definition: MDLabel.java:176
-
xmipp.jni.MDLabel.MDL_OPTICALFLOW_STDX
static final int MDL_OPTICALFLOW_STDX
<Mean of="" the="" movement="" in="" y="" direction="" of="" the="" motion="" map>=""> (double) ...
Definition: MDLabel.java:270
-
xmipp.jni.MDLabel.MDL_IMAGE5
static final int MDL_IMAGE5
< Image associated to this object (std::string)
Definition: MDLabel.java:203
-
xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA_PSI
static final int RLN_MLMODEL_SIGMA_PSI
Definition: MDLabel.java:570
-
xmipp.jni.MDLabel.RLN_SAMPLING_PRIOR_MODE
static final int RLN_SAMPLING_PRIOR_MODE
Definition: MDLabel.java:732
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SAMPLING_STARFILE
static final int RLN_OPTIMISER_SAMPLING_STARFILE
Definition: MDLabel.java:643
-
xmipp.jni.MDLabel.MDL_MICROGRAPH_TILTED_ORIGINAL
static final int MDL_MICROGRAPH_TILTED_ORIGINAL
< Name of the corresponding tilted micrograph (std::string)
Definition: MDLabel.java:234
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_DPR_MASKED
static final int RLN_POSTPROCESS_DPR_MASKED
Definition: MDLabel.java:705
-
xmipp.jni.MDLabel.MDL_MAX
static final int MDL_MAX
< Percentile of the maximum cross-correlation for the image (double)
Definition: MDLabel.java:225
-
xmipp.jni.MDLabel.MDL_DM3_SIZE
static final int MDL_DM3_SIZE
Definition: MDLabel.java:174
-
xmipp.jni.MDLabel.MDL_SPH_TSNE_COEFF2D
static final int MDL_SPH_TSNE_COEFF2D
tsne coefficicient in 1D
Definition: MDLabel.java:383
-
xmipp.jni.MDLabel.RLN_ORIENT_PSI_PRIOR
static final int RLN_ORIENT_PSI_PRIOR
Definition: MDLabel.java:673
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_SUBSET_SIZE
static final int RLN_OPTIMISER_SGD_SUBSET_SIZE
Definition: MDLabel.java:648
-
xmipp.jni.MDLabel.RLN_OPTIMISER_MODEL_STARFILE2
static final int RLN_OPTIMISER_MODEL_STARFILE2
Definition: MDLabel.java:633
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_MU
static final int RLN_OPTIMISER_SGD_MU
Definition: MDLabel.java:644
-
xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_X
static final int RLN_ORIENT_ORIGIN_X
Definition: MDLabel.java:662
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS
static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS
Definition: MDLabel.java:654
-
xmipp.jni.MDLabel.MDL_PRJ_PSI_RANDSTR
static final int MDL_PRJ_PSI_RANDSTR
< Psi angle dev and mean noise (vector double)
Definition: MDLabel.java:295
-
xmipp.jni.MDLabel.MDL_CLASSIFICATION_DPR_05
static final int MDL_CLASSIFICATION_DPR_05
< Size of data vectors for classification (int)
Definition: MDLabel.java:41
-
xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_TYPE
static final int MDL_PHANTOM_FEATURE_TYPE
< Specific parameters for a feature (vector double)
Definition: MDLabel.java:278
-
xmipp.jni.MDLabel.MDL_PHANTOM_SCALE
static final int MDL_PHANTOM_SCALE
< Type of the feature (Sphere, Blob, ...) (std::string)
Definition: MDLabel.java:279
-
xmipp.jni.MDLabel.MDL_WEIGHT_REALCORR
static final int MDL_WEIGHT_REALCORR
< Weight due to angular jumping
Definition: MDLabel.java:416
-
xmipp.jni.MDLabel.RLN_OPTIMISER_IGNORE_HELICAL_SYMMETRY
static final int RLN_OPTIMISER_IGNORE_HELICAL_SYMMETRY
Definition: MDLabel.java:620
-
xmipp.jni.MDLabel.RLN_SELECTED
static final int RLN_SELECTED
Definition: MDLabel.java:738
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_NONASTIGMATICVALIDITY
static final int MDL_CTF_CRIT_NONASTIGMATICVALIDITY
< CTF Background polynomial parameter
Definition: MDLabel.java:138
-
xmipp.jni.MDLabel.MDL_CONTINUOUS_Y
static final int MDL_CONTINUOUS_Y
< X shift of continuous assignment
Definition: MDLabel.java:67
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SOLVENT_FLATTEN
static final int RLN_OPTIMISER_DO_SOLVENT_FLATTEN
Definition: MDLabel.java:601
-
xmipp.jni.MDLabel.MDL_XCOOR_TILT
static final int MDL_XCOOR_TILT
< X component (int)
Definition: MDLabel.java:427
-
xmipp.jni.MDLabel.MDL_ZSCORE_DEEPLEARNING1
static final int MDL_ZSCORE_DEEPLEARNING1
< Global Z Score (double)
Definition: MDLabel.java:436
-
xmipp.jni.MDLabel.MDL_CRYSTAL_LATTICE_B
static final int MDL_CRYSTAL_LATTICE_B
< Lattice vector for projection (vector double)
Definition: MDLabel.java:57
-
xmipp.jni.MDLabel.RLN_PARTICLE_KL_DIVERGENCE
static final int RLN_PARTICLE_KL_DIVERGENCE
Definition: MDLabel.java:680
-
xmipp.jni.MDLabel.MDL_ORIGIN_X
static final int MDL_ORIGIN_X
auxiliary label to be used as an index (long)
Definition: MDLabel.java:265
-
xmipp.jni.MDLabel.MDL_NMA_ENERGY
static final int MDL_NMA_ENERGY
< NMA Atom shift in Angstroms
Definition: MDLabel.java:254
-
xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Y
static final int RLN_ORIENT_ORIGIN_Y
Definition: MDLabel.java:664
-
xmipp.jni.MDLabel.RLN_OPTIMISER_FIX_TAU
static final int RLN_OPTIMISER_FIX_TAU
Definition: MDLabel.java:608
-
xmipp.jni.MDLabel.RLN_MLMODEL_NR_BODIES
static final int RLN_MLMODEL_NR_BODIES
Definition: MDLabel.java:553
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTZERODISAGREEMENT
static final int MDL_CTF_CRIT_FIRSTZERODISAGREEMENT
< First zero average (in Angstroms)
Definition: MDLabel.java:144
-
xmipp.jni.MDLabel.MDL_CTF_PHASE_SHIFT
static final int MDL_CTF_PHASE_SHIFT
Definition: MDLabel.java:161
-
xmipp.jni.MDLabel.MDL_NEIGHBORHOOD_RADIUS
static final int MDL_NEIGHBORHOOD_RADIUS
< Particular neighbor (pointed myNEIGHBORS)
Definition: MDLabel.java:250
-
xmipp.jni.MDLabel.MDL_CTF_CORRECTED
static final int MDL_CTF_CORRECTED
Definition: MDLabel.java:78
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_STEPSIZE
static final int RLN_OPTIMISER_SGD_STEPSIZE
Definition: MDLabel.java:651
-
xmipp.jni.MDLabel.MDL_SCORE_BY_EMPTINESS
static final int MDL_SCORE_BY_EMPTINESS
< score by alignability noise (double)
Definition: MDLabel.java:348
-
xmipp.jni.MDLabel.RLN_PARTICLE_NR_FRAMES
static final int RLN_PARTICLE_NR_FRAMES
Definition: MDLabel.java:686
-
xmipp.jni.MDLabel.MDL_INTSCALE
static final int MDL_INTSCALE
< Image associated to this object (std::string)
Definition: MDLabel.java:204
-
xmipp.jni.MDLabel.RLN_MICROGRAPH_TILT_AXIS_OUTOFPLANE
static final int RLN_MICROGRAPH_TILT_AXIS_OUTOFPLANE
Definition: MDLabel.java:521
-
xmipp.jni.MDLabel.MDL_PRJ_TILT_RANGE
static final int MDL_PRJ_TILT_RANGE
< Type of randomness for Tilt (std::string)
Definition: MDLabel.java:302
-
xmipp.jni.MDLabel.MDL_SUBTRACTION_R2
static final int MDL_SUBTRACTION_R2
< A comment for this object /*** NOTE THIS IS A SPECIAL CASE AND SO IS TREATED ***/ ...
Definition: MDLabel.java:386
-
xmipp.jni.MDLabel.MDL_CTF_ENVELOPE_PLOT
static final int MDL_CTF_ENVELOPE_PLOT
Definition: MDLabel.java:108
-
xmipp.jni.MDLabel.MDL_CRYSTAL_SHIFTY
static final int MDL_CRYSTAL_SHIFTY
< Shift for the image in the X axis (double) for crystals
Definition: MDLabel.java:63
-
xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE1
static final int MDL_ZSCORE_SHAPE1
< Z Score of the covariance matrix of the residuals (double)
Definition: MDLabel.java:442
-
xmipp.jni.MDLabel.RLN_PERFRAME_CUMULATIVE_WEIGHT
static final int RLN_PERFRAME_CUMULATIVE_WEIGHT
Definition: MDLabel.java:742
-
xmipp.jni.MDLabel.RLN_MLMODEL_DIMENSIONALITY_DATA
static final int RLN_MLMODEL_DIMENSIONALITY_DATA
Definition: MDLabel.java:529
-
xmipp.jni.MDLabel.MDL_MISSINGREGION_THXF
static final int MDL_MISSINGREGION_THXF
< Initial tilt angle in X for missing region in subtomogram
Definition: MDLabel.java:242
-
xmipp.jni.MDLabel.MDL_POINTSASYMETRICUNIT
static final int MDL_POINTSASYMETRICUNIT
< Maximum value of normalized probability function (now called "Pmax/sumP") (double) ...
Definition: MDLabel.java:291
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_FIT_INTERCEPT
static final int RLN_POSTPROCESS_GUINIER_FIT_INTERCEPT
Definition: MDLabel.java:714
-
xmipp.jni.MDLabel.RLN_MLMODEL_PRIOR_OFFX_CLASS
static final int RLN_MLMODEL_PRIOR_OFFX_CLASS
Definition: MDLabel.java:560
-
xmipp.jni.MDLabel.MDL_MISSINGREGION_THYF
static final int MDL_MISSINGREGION_THYF
< Initial tilt angle in Y for missing region in subtomogram
Definition: MDLabel.java:240
-
xmipp.jni.MDLabel.RLN_CTF_CA
static final int RLN_CTF_CA
< Spherical aberration
Definition: MDLabel.java:458
-
xmipp.jni.MDLabel.MDL_SHIFT_Z2
static final int MDL_SHIFT_Z2
< Shift for the image in the Z axis (double)
Definition: MDLabel.java:372
-
xmipp.jni.MDLabel.RLN_IMAGE_SIZEX
static final int RLN_IMAGE_SIZEX
Definition: MDLabel.java:495
-
xmipp.jni.MDLabel.MDL_PHANTOM_BGDENSITY
static final int MDL_PHANTOM_BGDENSITY
< Particle unique identifier for reference. (The MDL_ITEM_ID should be used when particle list) ...
Definition: MDLabel.java:273
-
xmipp.jni.MDLabel.MDL_SCORE_BY_VARIANCE
static final int MDL_SCORE_BY_VARIANCE
< Feature vectors used to classify particles (vector double)
Definition: MDLabel.java:356
-
xmipp.jni.MDLabel.MDL_OBJID
static final int MDL_OBJID
< The label MDL_OBJID is special and should not be used
Definition: MDLabel.java:6
-
xmipp.jni.MDLabel.RLN_PARTICLE_NR_SIGNIFICANT_SAMPLES
static final int RLN_PARTICLE_NR_SIGNIFICANT_SAMPLES
Definition: MDLabel.java:685
-
xmipp.jni.MDLabel.RLN_CTF_DEFOCUSU
static final int RLN_CTF_DEFOCUSU
< Microscope voltage (kV)
Definition: MDLabel.java:454
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_WRITE_EVERY_SUBSET
static final int RLN_OPTIMISER_SGD_WRITE_EVERY_SUBSET
Definition: MDLabel.java:649
-
xmipp.jni.MDLabel.MDL_SCORE_BY_MIRROR
static final int MDL_SCORE_BY_MIRROR
< Feature vectors used to classify particles (vector double)
Definition: MDLabel.java:353
-
xmipp.jni.MDLabel.MDL_PSD_ENHANCED
static final int MDL_PSD_ENHANCED
< A Power Spectrum Density file name (std::string)
Definition: MDLabel.java:309
-
xmipp.jni.MDLabel.RLN_MICROGRAPH_NAME
static final int RLN_MICROGRAPH_NAME
Definition: MDLabel.java:517
-
xmipp.jni.MDLabel.RLN_COMMENT
static final int RLN_COMMENT
< Name for the area (or field of view). If one does not use (tilt) series, area would be the same as ...
Definition: MDLabel.java:449
-
xmipp.jni.MDLabel.MDL_CRYSTAL_NOISE_SHIFT
static final int MDL_CRYSTAL_NOISE_SHIFT
< Shift for the image in the Z axis (double) for crystals
Definition: MDLabel.java:65
-
xmipp.jni.MDLabel.MDL_CRYSTAL_CELLY
static final int MDL_CRYSTAL_CELLY
< Cell location for crystals
Definition: MDLabel.java:55
-
xmipp.jni.MDLabel.RLN_CTF_LONGITUDINAL_DISPLACEMENT
static final int RLN_CTF_LONGITUDINAL_DISPLACEMENT
< Convergence cone
Definition: MDLabel.java:467
-
xmipp.jni.MDLabel.MDL_IMAGE_ORIGINAL
static final int MDL_IMAGE_ORIGINAL
< Index of an image within a list (size_t)
Definition: MDLabel.java:193
-
xmipp.jni.MDLabel.MDL_AVG
static final int MDL_AVG
<Apply shift when project the volume ,
Definition: MDLabel.java:27
-
xmipp.jni.MDLabel.MDL_ORIGIN_Z
static final int MDL_ORIGIN_Z
< Origin for the image in the Y axis (double)
Definition: MDLabel.java:267
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_NOISE
static final int MDL_SCORE_BY_ALIGNABILITY_NOISE
< score by alignability references (double)
Definition: MDLabel.java:347
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDCORRELATION90
static final int MDL_CTF_CRIT_PSDCORRELATION90
< Maximum frequency (in Angstroms) at which non-astigmatic CTF correction is valid ...
Definition: MDLabel.java:139
-
xmipp.jni.MDLabel.RLN_OPTIMISER_MAGNIFICATION_RANGE
static final int RLN_OPTIMISER_MAGNIFICATION_RANGE
Definition: MDLabel.java:628
-
xmipp.jni.MDLabel.RLN_MLMODEL_PDF_ORIENT
static final int RLN_MLMODEL_PDF_ORIENT
Definition: MDLabel.java:562
-
xmipp.jni.MDLabel.MDL_MAXCC_PERCENTILE
static final int MDL_MAXCC_PERCENTILE
< Maximum cross-correlation for the image (double)
Definition: MDLabel.java:224
-
xmipp.jni.MDLabel.RLN_SAMPLING_SIGMA_PSI
static final int RLN_SAMPLING_SIGMA_PSI
Definition: MDLabel.java:736
-
xmipp.jni.MDLabel.MDL_YCOOR_TILT
static final int MDL_YCOOR_TILT
< Y component (int)
Definition: MDLabel.java:431
-
xmipp.jni.MDLabel.MDL_CONTINUOUS_SCALE_Y
static final int MDL_CONTINUOUS_SCALE_Y
< scale x of continuous assignment
Definition: MDLabel.java:73
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_CV
static final int MDL_CTF_BG_GAUSSIAN_CV
<CTF_ CTF Background parameter
Definition: MDLabel.java:122
-
xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE2
static final int MDL_ZSCORE_SHAPE2
< Z Score (double)
Definition: MDLabel.java:443
-
xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
-
xmipp.jni.MDLabel.RLN_MLMODEL_GROUP_NO
static final int RLN_MLMODEL_GROUP_NO
Definition: MDLabel.java:536
-
xmipp.jni.MDLabel.MDL_CTF_Y0
static final int MDL_CTF_Y0
< The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates
Definition: MDLabel.java:93
-
xmipp.jni.MDLabel.MDL_VOLUME_SCORE_MEAN
static final int MDL_VOLUME_SCORE_MEAN
< Score corresponding to the sum of cc-threshold with cc>threshold
Definition: MDLabel.java:404
-
xmipp.jni.MDLabel.MDL_ZSCORE_SNR2
static final int MDL_ZSCORE_SNR2
< Z Score (double)
Definition: MDLabel.java:445
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HIGHRES_LIMIT_SGD
static final int RLN_OPTIMISER_HIGHRES_LIMIT_SGD
Definition: MDLabel.java:619
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUSV
static final int MDL_CTF_DEFOCUSV
< Defocus U (Angstroms)
Definition: MDLabel.java:87
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ENTROPY
static final int MDL_SCORE_BY_ENTROPY
< Small values represent worse particles. Much larger than 1 for good particles
Definition: MDLabel.java:349
-
xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA_TILT
static final int RLN_MLMODEL_SIGMA_TILT
Definition: MDLabel.java:569
-
xmipp.jni.MDLabel.MDL_KERDENSOM_FUNCTIONAL
static final int MDL_KERDENSOM_FUNCTIONAL
< Current iteration number (int)
Definition: MDLabel.java:207
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_KEEP_TILT_PRIOR_FIXED
static final int RLN_OPTIMISER_HELICAL_KEEP_TILT_PRIOR_FIXED
Definition: MDLabel.java:621
-
xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_MAX
static final int MDL_TILT_ANALYSIS_MAX
Definition: MDLabel.java:400
-
xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_PATCHES
static final int MDL_LOCAL_ALIGNMENT_PATCHES
< contribution of an image to log-likelihood value
Definition: MDLabel.java:214
-
xmipp.jni.MDLabel.MDL_IMAGE_IDX
static final int MDL_IMAGE_IDX
< Name of the covariance imagee associated to this image
Definition: MDLabel.java:192
-
xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
-
xmipp.jni.MDLabel.MDL_SHIFT_Y_DIFF
static final int MDL_SHIFT_Y_DIFF
< Shift for the image in the Y axis (double)
Definition: MDLabel.java:370
-
xmipp.jni.MDLabel.MDL_MICROGRAPH_PARTICLES
static final int MDL_MICROGRAPH_PARTICLES
< Unique identifier of a movie.
Definition: MDLabel.java:231
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_TWIST_INITIAL_STEP
static final int RLN_MLMODEL_HELICAL_TWIST_INITIAL_STEP
Definition: MDLabel.java:543
-
xmipp.jni.MDLabel.RLN_PIPELINE_NODE_TYPE
static final int RLN_PIPELINE_NODE_TYPE
Definition: MDLabel.java:694
-
xmipp.jni.MDLabel.RLN_IMAGE_ID
static final int RLN_IMAGE_ID
Definition: MDLabel.java:476
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_CHANGE
static final int MDL_CTF_DEFOCUS_CHANGE
< Defocus V (Angstroms)
Definition: MDLabel.java:88
-
xmipp.jni.MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED
static final int MDL_CTF_DOWNSAMPLE_PERFORMED
< Iceness of the micrograph
Definition: MDLabel.java:155
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXP
static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXP
< score by alignability (double)
Definition: MDLabel.java:343
-
xmipp.jni.MDLabel.RLN_IMAGE_DATATYPE
static final int RLN_IMAGE_DATATYPE
Definition: MDLabel.java:478
-
xmipp.jni.MDLabel.MDL_ZSCORE_HISTOGRAM
static final int MDL_ZSCORE_HISTOGRAM
< Z Score (double)
Definition: MDLabel.java:438
-
xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_MIN
static final int MDL_TILT_ANALYSIS_MIN
Definition: MDLabel.java:399
-
xmipp.jni.MDLabel.MDL_CTF_DIMENSIONS
static final int MDL_CTF_DIMENSIONS
< Downsampling performed to estimate the CTF
Definition: MDLabel.java:156
-
xmipp.jni.MDLabel.RLN_IMAGE_COORD_X
static final int RLN_IMAGE_COORD_X
Definition: MDLabel.java:483
-
xmipp.jni.MDLabel.RLN_SAMPLING_OFFSET_RANGE
static final int RLN_SAMPLING_OFFSET_RANGE
Definition: MDLabel.java:728
-
xmipp.jni.MDLabel.MDL_MIRRORFRAC
static final int MDL_MIRRORFRAC
< Minimum value (double)
Definition: MDLabel.java:236
-
xmipp.jni.MDLabel.MDL_ANGLE_TILT2
static final int MDL_ANGLE_TILT2
< Tilting angle of an image (double,degrees)
Definition: MDLabel.java:17
-
xmipp.jni.MDLabel.RLN_CTF_FOM
static final int RLN_CTF_FOM
< Energy loss
Definition: MDLabel.java:461
-
xmipp.jni.MDLabel.MDL_SAMPLINGRATE_X
static final int MDL_SAMPLINGRATE_X
< original sampling rate in A/pixel (double)
Definition: MDLabel.java:333
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_FITTINGSCORE
static final int MDL_CTF_CRIT_FITTINGSCORE
< Integral of the radial PSD
Definition: MDLabel.java:148
-
xmipp.jni.MDLabel.MDL_GRAPH_CC
static final int MDL_GRAPH_CC
< when previous assignment validation
Definition: MDLabel.java:185
-
xmipp.jni.MDLabel.MDL_GRAPH_DISTANCE2MAX_PREVIOUS
static final int MDL_GRAPH_DISTANCE2MAX_PREVIOUS
< Distance to graph filtered max
Definition: MDLabel.java:184
-
xmipp.jni.MDLabel.MDL_MLF_WIENER
static final int MDL_MLF_WIENER
< MLF CTF estimated value (double)
Definition: MDLabel.java:244
-
xmipp.jni.MDLabel.MDL_CRYSTAL_PROJ
static final int MDL_CRYSTAL_PROJ
<Orthogonal projection or not (bool)
Definition: MDLabel.java:61
-
xmipp.jni.MDLabel.MDL_CTF_XF
static final int MDL_CTF_XF
< The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates
Definition: MDLabel.java:94
-
xmipp.jni.MDLabel.MDL_RESOLUTION_SSNR
static final int MDL_RESOLUTION_SSNR
<Logarithm of the structure factor
Definition: MDLabel.java:328
-
xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Z_PRIOR
static final int RLN_ORIENT_ORIGIN_Z_PRIOR
Definition: MDLabel.java:667
-
xmipp.jni.MDLabel.MDL_ZSCORE
static final int MDL_ZSCORE
< Z component (int)
Definition: MDLabel.java:435
-
xmipp.jni.MDLabel.MDL_CTF_GROUP
static final int MDL_CTF_GROUP
< Chromatic aberration
Definition: MDLabel.java:105
-
xmipp.jni.MDLabel.RLN_MICROGRAPH_TILT_ANGLE
static final int RLN_MICROGRAPH_TILT_ANGLE
Definition: MDLabel.java:519
-
xmipp.jni.MDLabel.MDL_REF2
static final int MDL_REF2
< Class to which the image belongs (int)
Definition: MDLabel.java:313
-
xmipp.jni.MDLabel.RLN_IMAGE_SAMPLINGRATE
static final int RLN_IMAGE_SAMPLINGRATE
Definition: MDLabel.java:490
-
xmipp.jni.MDLabel.RLN_MICROGRAPH_MOVIE_NAME
static final int RLN_MICROGRAPH_MOVIE_NAME
Definition: MDLabel.java:516
-
xmipp.jni.MDLabel.MDL_CORRELATION_IDX
static final int MDL_CORRELATION_IDX
< scale y of continuous assignment
Definition: MDLabel.java:74
-
xmipp.jni.MDLabel.MDL_GRAPH_DISTANCE2MAX
static final int MDL_GRAPH_DISTANCE2MAX
< Unique id of frame inside a Movie
Definition: MDLabel.java:183
-
xmipp.jni.MDLabel.MDL_SCORE_BY_GINI
static final int MDL_SCORE_BY_GINI
< Particle variance (double)
Definition: MDLabel.java:358
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HIGHRES_LIMIT_EXP
static final int RLN_OPTIMISER_HIGHRES_LIMIT_EXP
Definition: MDLabel.java:622
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_K
static final int MDL_CTF_BG_GAUSSIAN_K
< CTF Envelope polynomial parameter
Definition: MDLabel.java:118
-
xmipp.jni.MDLabel.MDL_USER
static final int MDL_USER
Definition: MDLabel.java:305
-
xmipp.jni.MDLabel.MDL_NMA_SCORE
static final int MDL_NMA_SCORE
< File with an NMA mode
Definition: MDLabel.java:258
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_SIGMA_DISTANCE
static final int RLN_OPTIMISER_HELICAL_SIGMA_DISTANCE
Definition: MDLabel.java:618
-
xmipp.jni.MDLabel.RLN_MASK_NAME
static final int RLN_MASK_NAME
Definition: MDLabel.java:505
-
xmipp.jni.MDLabel.MDL_IMAGE3
static final int MDL_IMAGE3
< Image associated to this object (std::string)
Definition: MDLabel.java:201
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_BFACTOR
static final int RLN_POSTPROCESS_BFACTOR
Definition: MDLabel.java:704
-
xmipp.jni.MDLabel.RLN_MLMODEL_REF_IMAGE
static final int RLN_MLMODEL_REF_IMAGE
Definition: MDLabel.java:571
-
xmipp.jni.MDLabel.MDL_WEIGHT_JUMPER0
static final int MDL_WEIGHT_JUMPER0
< Weight due to angular continuous assignment
Definition: MDLabel.java:413
-
xmipp.jni.MDLabel.MDL_CTF_BG_SQRT_V
static final int MDL_CTF_BG_SQRT_V
< CTF Background parameter
Definition: MDLabel.java:126
-
xmipp.jni.MDLabel.RLN_CTF_LENS_STABILITY
static final int RLN_CTF_LENS_STABILITY
< name of an image describing the CTF model
Definition: MDLabel.java:463
-
xmipp.jni.MDLabel.MDL_WROBUST
static final int MDL_WROBUST
< Weight due to Mirror Precision
Definition: MDLabel.java:424
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SPLIT_RANDOM_HALVES
static final int RLN_OPTIMISER_DO_SPLIT_RANDOM_HALVES
Definition: MDLabel.java:604
-
xmipp.jni.MDLabel.RLN_MLMODEL_NR_GROUPS
static final int RLN_MLMODEL_NR_GROUPS
Definition: MDLabel.java:555
-
xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_CENTER
static final int MDL_PHANTOM_FEATURE_CENTER
< Phantom background density (double)
Definition: MDLabel.java:274
-
xmipp.jni.MDLabel.MDL_CTF_VOLTAGE
static final int MDL_CTF_VOLTAGE
< Sampling rate in Z direction
Definition: MDLabel.java:84
-
xmipp.jni.MDLabel.MDL_NOISE_PIXEL_LEVEL
static final int MDL_NOISE_PIXEL_LEVEL
Definition: MDLabel.java:263
-
xmipp.jni.MDLabel.RLN_OPTIMISER_CHANGES_OPTIMAL_CLASSES
static final int RLN_OPTIMISER_CHANGES_OPTIMAL_CLASSES
Definition: MDLabel.java:586
-
xmipp.jni.MDLabel.MDL_PRJ_PSI_RANGE
static final int MDL_PRJ_PSI_RANGE
< Type of randomness for Psi (std::string)
Definition: MDLabel.java:296
-
xmipp.jni.MDLabel.MDL_MAXCC_PREVIOUS
static final int MDL_MAXCC_PREVIOUS
< Maximum value (double)
Definition: MDLabel.java:226
-
xmipp.jni.MDLabel.RLN_IMAGE_SAMPLINGRATE_Z
static final int RLN_IMAGE_SAMPLINGRATE_Z
Definition: MDLabel.java:493
-
xmipp.jni.MDLabel.MDL_NOISE_PARTICLE_COORD
static final int MDL_NOISE_PARTICLE_COORD
< Noise description for projected angles
Definition: MDLabel.java:261
-
xmipp.jni.MDLabel.RLN_MLMODEL_TAU2_REF
static final int RLN_MLMODEL_TAU2_REF
Definition: MDLabel.java:576
-
xmipp.jni.MDLabel.MDL_AVG_CHANGES_ORIENTATIONS
static final int MDL_AVG_CHANGES_ORIENTATIONS
< average value (double)
Definition: MDLabel.java:28
-
xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA2_REF
static final int RLN_MLMODEL_SIGMA2_REF
Definition: MDLabel.java:573
-
xmipp.jni.MDLabel.MDL_STDDEV
static final int MDL_STDDEV
tsne coefficients in 2D
Definition: MDLabel.java:384
-
xmipp.jni.MDLabel.MDL_CTF_BG_R3
static final int MDL_CTF_BG_R3
< CTF Background polynomial parameter
Definition: MDLabel.java:137
-
xmipp.jni.MDLabel.RLN_OPTIMISER_INCR_SIZE
static final int RLN_OPTIMISER_INCR_SIZE
Definition: MDLabel.java:624
-
xmipp.jni.MDLabel.RLN_CTF_MAGNIFICATION
static final int RLN_CTF_MAGNIFICATION
< Lens stability
Definition: MDLabel.java:464
-
xmipp.jni.MDLabel.MDL_MICROGRAPH_MOVIE_ID
static final int MDL_MICROGRAPH_MOVIE_ID
< Name of a movie (std::string)
Definition: MDLabel.java:230
-
xmipp.jni.MDLabel.MDL_DATATYPE
static final int MDL_DATATYPE
<Cumulative SSNR (double)
Definition: MDLabel.java:164
-
xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA_ROT
static final int RLN_MLMODEL_SIGMA_ROT
Definition: MDLabel.java:568
-
xmipp.jni.MDLabel.RLN_CTF_SAMPLING_RATE
static final int RLN_CTF_SAMPLING_RATE
< linear scale-factor
Definition: MDLabel.java:452
-
xmipp.jni.MDLabel.MDL_AVGPMAX
static final int MDL_AVGPMAX
Average change in class assignment(double dimensionaless)
Definition: MDLabel.java:31
-
xmipp.jni.MDLabel.RLN_IMAGE_RECONSTRUCT_NAME
static final int RLN_IMAGE_RECONSTRUCT_NAME
Definition: MDLabel.java:475
-
xmipp.jni.MDLabel.MDL_SIGNALCHANGE
static final int MDL_SIGNALCHANGE
< Standard deviation of the offsets in ML model
Definition: MDLabel.java:379
-
xmipp.jni.MDLabel.MDL_DIMRED
static final int MDL_DIMRED
< Defocus group
Definition: MDLabel.java:166
-
xmipp.jni.MDLabel.MDL_CUMULATIVE_SSNR
static final int MDL_CUMULATIVE_SSNR
Definition: MDLabel.java:163
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_IN
static final int RLN_POSTPROCESS_GUINIER_VALUE_IN
Definition: MDLabel.java:716
-
xmipp.jni.MDLabel.RLN_CTF_TRANSVERSAL_DISPLACEMENT
static final int RLN_CTF_TRANSVERSAL_DISPLACEMENT
< Longitudinal displacement
Definition: MDLabel.java:468
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_CORRECT_CTF
static final int RLN_OPTIMISER_DO_CORRECT_CTF
Definition: MDLabel.java:593
-
xmipp.jni.MDLabel.MDL_SHIFT_Z3
static final int MDL_SHIFT_Z3
< Shift for the image in the Z axis (double)
Definition: MDLabel.java:373
-
xmipp.jni.MDLabel.MDL_WEIGHT_SIGNIFICANT
static final int MDL_WEIGHT_SIGNIFICANT
< Weight due phase correlation between two images/subtomos
Definition: MDLabel.java:418
-
xmipp.jni.MDLabel.MDL_ANGLE_PSI2
static final int MDL_ANGLE_PSI2
< Psi angle of an image (double,degrees)
Definition: MDLabel.java:9
- -
xmipp.jni.MDLabel.RLN_MLMODEL_PRIOR_OFFY_CLASS
static final int RLN_MLMODEL_PRIOR_OFFY_CLASS
Definition: MDLabel.java:561
-
xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_CONTROL_POINTS
static final int MDL_LOCAL_ALIGNMENT_CONTROL_POINTS
< A shift amount at confidence level of 95.5%
Definition: MDLabel.java:219
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_FINAL_RESOLUTION
static final int RLN_POSTPROCESS_FINAL_RESOLUTION
Definition: MDLabel.java:707
-
xmipp.jni.MDLabel.RLN_IMAGE_SIZE
static final int RLN_IMAGE_SIZE
Definition: MDLabel.java:494
-
xmipp.jni.MDLabel.RLN_CTF_DEFOCUS_ANGLE
static final int RLN_CTF_DEFOCUS_ANGLE
< Defocus V (Angstroms)
Definition: MDLabel.java:456
-
xmipp.jni.MDLabel.MDL_SUMWEIGHT
static final int MDL_SUMWEIGHT
< Sum of elements of a given type (double) [this is a genereic type do not use to transfer informatio...
Definition: MDLabel.java:390
-
xmipp.jni.MDLabel.MDL_UNDEFINED
static final int MDL_UNDEFINED
Definition: MDLabel.java:4
-
xmipp.jni.MDLabel.RLN_MLMODEL_PIXEL_SIZE
static final int RLN_MLMODEL_PIXEL_SIZE
Definition: MDLabel.java:563
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_Z_PERCENTAGE
static final int RLN_OPTIMISER_HELICAL_Z_PERCENTAGE
Definition: MDLabel.java:614
-
xmipp.jni.MDLabel.MDL_IMAGE_COVARIANCE
static final int MDL_IMAGE_COVARIANCE
< Name of an image (std::string)
Definition: MDLabel.java:191
-
xmipp.jni.MDLabel.RLN_CTF_ENERGY_LOSS
static final int RLN_CTF_ENERGY_LOSS
< Pixel size for detector as used in CTF-determination
Definition: MDLabel.java:460
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SGD
static final int RLN_OPTIMISER_DO_SGD
Definition: MDLabel.java:600
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_UNMASKED
static final int RLN_POSTPROCESS_FSC_UNMASKED
Definition: MDLabel.java:711
-
xmipp.jni.MDLabel.MDL_SHIFT_X
static final int MDL_SHIFT_X
< A collection of micrographs, e.g. a tilt serie (std::string)
Definition: MDLabel.java:363
-
xmipp.jni.MDLabel.RLN_MATRIX_1_2
static final int RLN_MATRIX_1_2
Definition: MDLabel.java:507
-
xmipp.jni.MDLabel.MDL_PRJ_ROT_RANGE
static final int MDL_PRJ_ROT_RANGE
< Type of randomness for Rotational (std::string)
Definition: MDLabel.java:299
-
xmipp.jni.MDLabel.RLN_PIPELINE_PROCESS_STATUS
static final int RLN_PIPELINE_PROCESS_STATUS
Definition: MDLabel.java:698
-
xmipp.jni.MDLabel.RLN_MLMODEL_GROUP_NR_PARTICLES
static final int RLN_MLMODEL_GROUP_NR_PARTICLES
Definition: MDLabel.java:537
-
xmipp.jni.MDLabel.MDL_KERDENSOM_SIGMA
static final int MDL_KERDENSOM_SIGMA
< Regularization value (double)
Definition: MDLabel.java:209
-
xmipp.jni.MDLabel.RLN_IMAGE_STATS_MIN
static final int RLN_IMAGE_STATS_MIN
Definition: MDLabel.java:498
-
xmipp.jni.MDLabel.RLN_IMAGE_FRAME_NR
static final int RLN_IMAGE_FRAME_NR
Definition: MDLabel.java:486
-
xmipp.jni.MDLabel.MDL_MISSINGREGION_THX0
static final int MDL_MISSINGREGION_THX0
< Final tilt angle in Y for missing region in subtomogram
Definition: MDLabel.java:241
-
xmipp.jni.MDLabel.MDL_CORR_DENOISED_PROJECTION
static final int MDL_CORR_DENOISED_PROJECTION
< Number of elements of a type (int) [this is a genereic type do not use to transfer information to a...
Definition: MDLabel.java:50
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_TUBE_OUTER_DIAMETER
static final int RLN_OPTIMISER_HELICAL_TUBE_OUTER_DIAMETER
Definition: MDLabel.java:616
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_ANGLE
static final int MDL_CTF_BG_GAUSSIAN_ANGLE
< CTF Background parameter
Definition: MDLabel.java:123
-
xmipp.jni.MDLabel.MDL_CTF_BG_R1
static final int MDL_CTF_BG_R1
< CTF Background parameter
Definition: MDLabel.java:135
-
xmipp.jni.MDLabel.RLN_MLMODEL_ACCURACY_ROT
static final int RLN_MLMODEL_ACCURACY_ROT
Definition: MDLabel.java:522
-
xmipp.jni.MDLabel.RLN_IMAGE_COORD_Z
static final int RLN_IMAGE_COORD_Z
Definition: MDLabel.java:485
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DATA_ARE_CTF_PREMULTIPLIED
static final int RLN_OPTIMISER_DATA_ARE_CTF_PREMULTIPLIED
Definition: MDLabel.java:589
-
xmipp.jni.MDLabel.RLN_OPTIMISER_CHANGES_OPTIMAL_ORIENTS
static final int RLN_OPTIMISER_CHANGES_OPTIMAL_ORIENTS
Definition: MDLabel.java:585
-
xmipp.jni.MDLabel.MDL_DATE
static final int MDL_DATE
< Is this image enabled? (int [-1 or 1])
Definition: MDLabel.java:178
-
xmipp.jni.MDLabel.MDL_IMAGE1
static final int MDL_IMAGE1
< Name of Metadata file for all images (string)
Definition: MDLabel.java:199
-
xmipp.jni.MDLabel.MDL_CORRELATION_WEIGHT
static final int MDL_CORRELATION_WEIGHT
< masked correlation value between a particle and its assigned projection inside the region with pixe...
Definition: MDLabel.java:76
-
xmipp.jni.MDLabel.MDL_CTF_ENV_R2
static final int MDL_CTF_ENV_R2
< CTF Envelope polynomial parameter
Definition: MDLabel.java:117
-
xmipp.jni.MDLabel.RLN_MICROGRAPH_ID
static final int RLN_MICROGRAPH_ID
Definition: MDLabel.java:515
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEVB
static final int MDL_CTF_DEFOCUS_PLANEVB
< Defocus = A*x+B*y+C
Definition: MDLabel.java:100
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED
static final int RLN_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED
Definition: MDLabel.java:588
-
xmipp.jni.MDLabel.MDL_PSD
static final int MDL_PSD
Definition: MDLabel.java:308
-
xmipp.jni.MDLabel.MDL_ASSIGNED_DIR_REF_CC
static final int MDL_ASSIGNED_DIR_REF_CC
< Name of Metadata file for all references(string)
Definition: MDLabel.java:315
-
xmipp.jni.MDLabel.RLN_CTF_DETECTOR_PIXEL_SIZE
static final int RLN_CTF_DETECTOR_PIXEL_SIZE
< Chromatic aberration
Definition: MDLabel.java:459
-
xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_STD
static final int MDL_TILT_ANALYSIS_STD
Definition: MDLabel.java:398
-
xmipp.jni.MDLabel.RLN_PARTICLE_CLASS
static final int RLN_PARTICLE_CLASS
Definition: MDLabel.java:676
-
xmipp.jni.MDLabel.MDL_CLASS_INTERSECTION_RELATIVE_SIZE_PVALUE
static final int MDL_CLASS_INTERSECTION_RELATIVE_SIZE_PVALUE
< P-value (1-percentile) of the class size compared to a random distribution (double in [0...
Definition: MDLabel.java:53
-
xmipp.jni.MDLabel.MDL_ANGLE_PSI_DIFF
static final int MDL_ANGLE_PSI_DIFF
< Psi angle of an image (double,degrees)
Definition: MDLabel.java:11
-
xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_X_PRIOR
static final int RLN_ORIENT_ORIGIN_X_PRIOR
Definition: MDLabel.java:663
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_RANDOM_MASKED
static final int RLN_POSTPROCESS_FSC_RANDOM_MASKED
Definition: MDLabel.java:712
-
xmipp.jni.MDLabel.RLN_OPTIMISER_ADAPTIVE_FRACTION
static final int RLN_OPTIMISER_ADAPTIVE_FRACTION
Definition: MDLabel.java:579
-
xmipp.jni.MDLabel.RLN_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION
static final int RLN_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION
Definition: MDLabel.java:551
-
xmipp.jni.MDLabel.RLN_MLMODEL_FOURIER_COVERAGE_REF
static final int RLN_MLMODEL_FOURIER_COVERAGE_REF
Definition: MDLabel.java:532
-
xmipp.jni.MDLabel.MDL_DM3_VALUE
static final int MDL_DM3_VALUE
Definition: MDLabel.java:175
-
xmipp.jni.MDLabel.MDL_CLASSIFICATION_DATA_SIZE
static final int MDL_CLASSIFICATION_DATA_SIZE
< Data vector for classification (vector double)
Definition: MDLabel.java:40
-
xmipp.jni.MDLabel.MDL_IMAGE
static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
-
xmipp.jni.MDLabel.MDL_COST_PERCENTILE
static final int MDL_COST_PERCENTILE
< Cost for the image (double)
Definition: MDLabel.java:47
-
xmipp.jni.MDLabel.RLN_MATRIX_2_1
static final int RLN_MATRIX_2_1
Definition: MDLabel.java:509
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_TWIST_MAX
static final int RLN_MLMODEL_HELICAL_TWIST_MAX
Definition: MDLabel.java:542
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_PRECISION
static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION
< score by alignability (double)
Definition: MDLabel.java:341
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_MAXFREQ
static final int MDL_CTF_CRIT_MAXFREQ
< First zero disagreement with second model (in Angstroms)
Definition: MDLabel.java:145
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTZEROAVG
static final int MDL_CTF_CRIT_FIRSTZEROAVG
< Ratio sigma(firstMinimum-firstZero)/sigma(firstZero)
Definition: MDLabel.java:143
-
xmipp.jni.MDLabel.RLN_IMAGE_COORD_Y
static final int RLN_IMAGE_COORD_Y
Definition: MDLabel.java:484
-
xmipp.jni.MDLabel.MDL_WEIGHT_ACCURACY_ALIGNABILITY
static final int MDL_WEIGHT_ACCURACY_ALIGNABILITY
< Weight due to Alignability Precision and Accuracy
Definition: MDLabel.java:422
-
xmipp.jni.MDLabel.RLN_SAMPLING_IS_3D
static final int RLN_SAMPLING_IS_3D
< Detector MTF value
Definition: MDLabel.java:723
-
xmipp.jni.MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE
static final int MDL_PICKING_AUTOPARTICLES_SIZE
< Particle size for particle picking
Definition: MDLabel.java:288
-
xmipp.jni.MDLabel.MDL_DEFGROUP
static final int MDL_DEFGROUP
< if read from file original image datatype, this is an struct defined in image
Definition: MDLabel.java:165
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_INVMTF
static final int RLN_POSTPROCESS_GUINIER_VALUE_INVMTF
Definition: MDLabel.java:717
-
xmipp.jni.MDLabel.RLN_SAMPLING_SYMMETRY
static final int RLN_SAMPLING_SYMMETRY
Definition: MDLabel.java:737
-
xmipp.jni.MDLabel.RLN_SAMPLING_OFFSET_STEP
static final int RLN_SAMPLING_OFFSET_STEP
Definition: MDLabel.java:729
-
xmipp.jni.MDLabel.MDL_TOMOGRAMMD
static final int MDL_TOMOGRAMMD
< Name for the reconstructed tomogram volume (std::string)
Definition: MDLabel.java:393
-
xmipp.jni.MDLabel.RLN_OPTIMISER_PARTICLE_DIAMETER
static final int RLN_OPTIMISER_PARTICLE_DIAMETER
Definition: MDLabel.java:638
-
xmipp.jni.MDLabel.MDL_TSID
static final int MDL_TSID
< transformation matrix in numpy string format or space separated (std::string)
Definition: MDLabel.java:395
-
xmipp.jni.MDLabel.MDL_DM3_NODEID
static final int MDL_DM3_NODEID
Definition: MDLabel.java:169
-
xmipp.jni.MDLabel.MDL_IMGMD
static final int MDL_IMGMD
< imed value between a particle and its assigned projection
Definition: MDLabel.java:198
-
xmipp.jni.MDLabel.MDL_YSIZE
static final int MDL_YSIZE
< Y component in tilted micrograph (int)
Definition: MDLabel.java:432
-
xmipp.jni.MDLabel.MDL_RESOLUTION_STRUCTURE_FACTOR
static final int MDL_RESOLUTION_STRUCTURE_FACTOR
<Fourier shell correlation (double)
Definition: MDLabel.java:329
-
xmipp.jni.MDLabel.MDL_RESOLUTION_FRCRANDOMNOISE
static final int MDL_RESOLUTION_FRCRANDOMNOISE
<Fourier shell correlation (double)
Definition: MDLabel.java:321
-
xmipp.jni.MDLabel.MDL_SCORE_BY_RAMP
static final int MDL_SCORE_BY_RAMP
< score by mirror (double)
Definition: MDLabel.java:354
-
xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA2_NOISE
static final int RLN_MLMODEL_SIGMA2_NOISE
Definition: MDLabel.java:572
-
xmipp.jni.MDLabel.RLN_CTF_PHASESHIFT
static final int RLN_CTF_PHASESHIFT
< Gctf-based validation score for CTF fit
Definition: MDLabel.java:473
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_ANGLE
static final int MDL_CTF_DEFOCUS_ANGLE
< Defocus = A*x+B*y+C
Definition: MDLabel.java:102
-
xmipp.jni.MDLabel.MDL_NMA_MODEFILE
static final int MDL_NMA_MODEFILE
< Maximum value observed for a given NMA mode
Definition: MDLabel.java:257
-
xmipp.jni.MDLabel.RLN_ORIENT_PSI_PRIOR_FLIP_RATIO
static final int RLN_ORIENT_PSI_PRIOR_FLIP_RATIO
Definition: MDLabel.java:674
-
xmipp.jni.MDLabel.RLN_MATRIX_1_3
static final int RLN_MATRIX_1_3
Definition: MDLabel.java:508
-
xmipp.jni.MDLabel.RLN_OPTIMISER_WIDTH_MASK_EDGE
static final int RLN_OPTIMISER_WIDTH_MASK_EDGE
Definition: MDLabel.java:659
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES
static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES
Definition: MDLabel.java:652
-
xmipp.jni.MDLabel.RLN_PIPELINE_NODE_NAME
static final int RLN_PIPELINE_NODE_NAME
Definition: MDLabel.java:693
-
xmipp.jni.MDLabel.MDL_RESOLUTION_LOG_STRUCTURE_FACTOR
static final int MDL_RESOLUTION_LOG_STRUCTURE_FACTOR
< Frequency in A of the local resolution of a residue (double)
Definition: MDLabel.java:327
-
xmipp.jni.MDLabel.MDL_CRYSTAL_DISAPPEAR_THRE
static final int MDL_CRYSTAL_DISAPPEAR_THRE
< Lattice vector for projection (vector double)
Definition: MDLabel.java:58
-
xmipp.jni.MDLabel.RLN_PIPELINE_PROCESS_ALIAS
static final int RLN_PIPELINE_PROCESS_ALIAS
Definition: MDLabel.java:695
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_WEIGHTED
static final int RLN_POSTPROCESS_GUINIER_VALUE_WEIGHTED
Definition: MDLabel.java:718
-
xmipp.jni.MDLabel.RLN_OPTIMISER_ACCURACY_TRANS
static final int RLN_OPTIMISER_ACCURACY_TRANS
Definition: MDLabel.java:578
-
xmipp.jni.MDLabel.MDL_CTF_VPP_RADIUS
static final int MDL_CTF_VPP_RADIUS
Definition: MDLabel.java:162
-
xmipp.jni.MDLabel.MDL_VOLUME_SCORE_SUM_TH
static final int MDL_VOLUME_SCORE_SUM_TH
< Score corresponding to the sum of cc with cc>threshold
Definition: MDLabel.java:403
-
xmipp.jni.MDLabel.MDL_CORR_DENOISED_NOISY
static final int MDL_CORR_DENOISED_NOISY
<Correlation between the denoised image and the projection proposed
Definition: MDLabel.java:51
-
xmipp.jni.MDLabel.RLN_MLMODEL_POWER_REF
static final int RLN_MLMODEL_POWER_REF
Definition: MDLabel.java:564
-
xmipp.jni.MDLabel.MDL_TIME
static final int MDL_TIME
Definition: MDLabel.java:179
-
xmipp.jni.MDLabel.RLN_CTF_IMAGE
static final int RLN_CTF_IMAGE
< ctffind3 FOM (CC) for quality of CTF-fit
Definition: MDLabel.java:462
-
xmipp.jni.MDLabel.RLN_MLMODEL_ORIENTABILITY_CONTRIBUTION
static final int RLN_MLMODEL_ORIENTABILITY_CONTRIBUTION
Definition: MDLabel.java:557
-
xmipp.jni.MDLabel.RLN_IMAGE_STATS_SKEW
static final int RLN_IMAGE_STATS_SKEW
Definition: MDLabel.java:502
-
xmipp.jni.MDLabel.MDL_LAST_LABEL
static final int MDL_LAST_LABEL
Definition: MDLabel.java:748
-
xmipp.jni.MDLabel.RLN_RESOLUTION_INVPIXEL
static final int RLN_RESOLUTION_INVPIXEL
Definition: MDLabel.java:746
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_RESOL_SQUARED
static final int RLN_POSTPROCESS_GUINIER_RESOL_SQUARED
Definition: MDLabel.java:721
-
xmipp.jni.MDLabel.MDL_CTF_CS
static final int MDL_CTF_CS
< Defocus angle (degrees)
Definition: MDLabel.java:103
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_ACCURACY
static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY
< score by alignability (double)
Definition: MDLabel.java:342
-
xmipp.jni.MDLabel.RLN_CTF_VOLTAGE
static final int RLN_CTF_VOLTAGE
< Sampling rate
Definition: MDLabel.java:453
-
xmipp.jni.MDLabel.RLN_SELECT_PARTICLES_ZSCORE
static final int RLN_SELECT_PARTICLES_ZSCORE
Definition: MDLabel.java:739
-
xmipp.jni.MDLabel.MDL_WEIGHT_PRECISION_ALIGNABILITY
static final int MDL_WEIGHT_PRECISION_ALIGNABILITY
< Weight due to SSNR
Definition: MDLabel.java:420
-
xmipp.jni.MDLabel.MDL_MISSINGREGION_NR
static final int MDL_MISSINGREGION_NR
< Mirror fraction for a Maximum Likelihood model
Definition: MDLabel.java:237
-
xmipp.jni.MDLabel.MDL_CRYSTAL_SHFILE
static final int MDL_CRYSTAL_SHFILE
< Disappearing threshold (double)
Definition: MDLabel.java:59
-
xmipp.jni.MDLabel.RLN_CTF_VALUE
static final int RLN_CTF_VALUE
< CTF gain
Definition: MDLabel.java:471
-
xmipp.jni.MDLabel.RLN_MLMODEL_SSNR_REF
static final int RLN_MLMODEL_SSNR_REF
Definition: MDLabel.java:574
-
xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Z
static final int RLN_ORIENT_ORIGIN_Z
Definition: MDLabel.java:666
-
xmipp.jni.MDLabel.MDL_CL2D_SIMILARITY
static final int MDL_CL2D_SIMILARITY
< Number of changes between iterations
Definition: MDLabel.java:36
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_SUBSET_START
static final int RLN_OPTIMISER_SGD_SUBSET_START
Definition: MDLabel.java:647
-
xmipp.jni.MDLabel.MDL_SHIFT_X3
static final int MDL_SHIFT_X3
< Shift for the image in the X axis (double)
Definition: MDLabel.java:365
-
xmipp.jni.MDLabel.MDL_RESOLUTION_FSO
static final int MDL_RESOLUTION_FSO
< Frequency in A (double)
Definition: MDLabel.java:325
-
xmipp.jni.MDLabel.RLN_SAMPLING_HEALPIX_ORDER
static final int RLN_SAMPLING_HEALPIX_ORDER
Definition: MDLabel.java:725
-
xmipp.jni.MDLabel.MDL_MIN
static final int MDL_MIN
< Name of the corresponding original, tilted micrograph (std::string)
Definition: MDLabel.java:235
-
xmipp.jni.MDLabel.RLN_MLMODEL_PRIOR_MODE
static final int RLN_MLMODEL_PRIOR_MODE
Definition: MDLabel.java:565
-
xmipp.jni.MDLabel.MDL_SAMPLINGRATE_Y
static final int MDL_SAMPLINGRATE_Y
< sampling rate in A/pixel (double)
Definition: MDLabel.java:334
-
xmipp.jni.MDLabel.MDL_CTF_YF
static final int MDL_CTF_YF
< The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates
Definition: MDLabel.java:95
-
xmipp.jni.MDLabel.RLN_CTF_CS
static final int RLN_CTF_CS
< Defocus angle (degrees)
Definition: MDLabel.java:457
-
xmipp.jni.MDLabel.MDL_PICKING_STATE
static final int MDL_PICKING_STATE
< Number of templates
Definition: MDLabel.java:284
-
xmipp.jni.MDLabel.MDL_GATHER_ID
static final int MDL_GATHER_ID
< object id (int), NOTE: This label is special and shouldn&#39;t be used
Definition: MDLabel.java:7
-
xmipp.jni.MDLabel.MDL_WEIGHT_P
static final int MDL_WEIGHT_P
< Weight assigned to the image (double)
Definition: MDLabel.java:411
-
xmipp.jni.MDLabel.MDL_AVG_CHANGES_CLASSES
static final int MDL_AVG_CHANGES_CLASSES
Average change in offset (double pixels)
Definition: MDLabel.java:30
-
xmipp.jni.MDLabel.MDL_CTF_XRAY_ZONES_NUMBER
static final int MDL_CTF_XRAY_ZONES_NUMBER
Outermost zone width of the X-ray Fresnel lens (nm)
Definition: MDLabel.java:160
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_SIGMAU
static final int MDL_CTF_BG_GAUSSIAN2_SIGMAU
< CTF Background parameter
Definition: MDLabel.java:130
-
xmipp.jni.MDLabel.MDL_FLIP
static final int MDL_FLIP
Definition: MDLabel.java:180
-
xmipp.jni.MDLabel.RLN_IMAGE_BEAMTILT_X
static final int RLN_IMAGE_BEAMTILT_X
Definition: MDLabel.java:480
-
xmipp.jni.MDLabel.MDL_Y
static final int MDL_Y
< X size (int)
Definition: MDLabel.java:429
-
xmipp.jni.MDLabel.MDL_SELFILE
static final int MDL_SELFILE
Definition: MDLabel.java:361
-
xmipp.jni.MDLabel.MDL_DIRECTION
static final int MDL_DIRECTION
< Projection onto a reduced manifold (vector double)
Definition: MDLabel.java:167
-
xmipp.jni.MDLabel.MDL_COLOR
static final int MDL_COLOR
Definition: MDLabel.java:282
-
xmipp.jni.MDLabel.RLN_MLMODEL_FOURIER_COVERAGE_TOTAL_REF
static final int RLN_MLMODEL_FOURIER_COVERAGE_TOTAL_REF
Definition: MDLabel.java:533
-
xmipp.jni.MDLabel.MDL_CTF_SAMPLING_RATE_Z
static final int MDL_CTF_SAMPLING_RATE_Z
< Sampling rate
Definition: MDLabel.java:83
-
xmipp.jni.MDLabel.MDL_REF
static final int MDL_REF
< 3D Class to which the image belongs (int)
Definition: MDLabel.java:312
-
xmipp.jni.MDLabel.MDL_CTF_Q0
static final int MDL_CTF_Q0
< Transversal displacemente
Definition: MDLabel.java:113
-
xmipp.jni.MDLabel.MDL_ANGLE_PSI3
static final int MDL_ANGLE_PSI3
< Psi angle of an image (double,degrees)
Definition: MDLabel.java:10
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_CORRECT_SCALE
static final int RLN_OPTIMISER_DO_CORRECT_SCALE
Definition: MDLabel.java:596
-
xmipp.jni.MDLabel.MDL_IDX
static final int MDL_IDX
< Half map/image file name (string)
Definition: MDLabel.java:189
-
xmipp.jni.MDLabel.RLN_IMAGE_STATS_KURT
static final int RLN_IMAGE_STATS_KURT
Definition: MDLabel.java:503
-
xmipp.jni.MDLabel.MDL_ANGLE_DIFF2
static final int MDL_ANGLE_DIFF2
< difference between two angles (double,degrees)
Definition: MDLabel.java:22
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTZERORATIO
static final int MDL_CTF_CRIT_FIRSTZERORATIO
< PSD correlation at 90 degrees
Definition: MDLabel.java:140
-
xmipp.jni.MDLabel.MDL_TOMOGRAM_VOLUME
static final int MDL_TOMOGRAM_VOLUME
< Symmetry number for a projection (used in ART)
Definition: MDLabel.java:392
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDPCA1VARIANCE
static final int MDL_CTF_CRIT_PSDPCA1VARIANCE
< PSD variance
Definition: MDLabel.java:151
-
xmipp.jni.MDLabel.MDL_PARTICLE_ID
static final int MDL_PARTICLE_ID
<Standard deviation="" of="" the="" movement="" in="" y="" direction="" of="" the="" motion="" map>="...
Definition: MDLabel.java:272
-
xmipp.jni.MDLabel.RLN_ORIENT_PSI
static final int RLN_ORIENT_PSI
Definition: MDLabel.java:672
-
xmipp.jni.MDLabel.MDL_ANGLE_DIFF
static final int MDL_ANGLE_DIFF
< difference between two angles (double,degrees)
Definition: MDLabel.java:21
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUSA
static final int MDL_CTF_DEFOCUSA
< Microscope voltage (kV)
Definition: MDLabel.java:85
-
xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Y_PRIOR
static final int RLN_ORIENT_ORIGIN_Y_PRIOR
Definition: MDLabel.java:665
-
xmipp.jni.MDLabel.MDL_PRJ_ANGFILE
static final int MDL_PRJ_ANGFILE
Definition: MDLabel.java:293
-
xmipp.jni.MDLabel.RLN_MATRIX_3_3
static final int RLN_MATRIX_3_3
Definition: MDLabel.java:514
-
xmipp.jni.MDLabel.MDL_CLASSIFICATION_DATA
static final int MDL_CLASSIFICATION_DATA
< Percentage of images assigned to the same class as this image
Definition: MDLabel.java:39
-
xmipp.jni.MDLabel.MDL_MICROGRAPH_MOVIE
static final int MDL_MICROGRAPH_MOVIE
< Micrograph unique id for reference (MDL_ITEM_ID should be used for Micrographs list) ...
Definition: MDLabel.java:229
-
xmipp.jni.MDLabel.MDL_DM3_IDTAG
static final int MDL_DM3_IDTAG
< Direction in 3D
Definition: MDLabel.java:168
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_CORRECT_MAGNIFICATION
static final int RLN_OPTIMISER_DO_CORRECT_MAGNIFICATION
Definition: MDLabel.java:594
-
xmipp.jni.MDLabel.MDL_CONTINUOUS_FLIP
static final int MDL_CONTINUOUS_FLIP
< Y shift of continuous assignment
Definition: MDLabel.java:68
-
xmipp.jni.MDLabel.RLN_OPTIMISER_FIX_SIGMA_OFFSET
static final int RLN_OPTIMISER_FIX_SIGMA_OFFSET
Definition: MDLabel.java:607
-
xmipp.jni.MDLabel.RLN_PARTICLE_FOM
static final int RLN_PARTICLE_FOM
Definition: MDLabel.java:679
-
xmipp.jni.MDLabel.MDL_SCORE_BY_ZSCORE
static final int MDL_SCORE_BY_ZSCORE
< Feature vectors used to classify particles (vector double)
Definition: MDLabel.java:360
-
xmipp.jni.MDLabel.RLN_ORIENT_ROT_PRIOR
static final int RLN_ORIENT_ROT_PRIOR
Definition: MDLabel.java:669
-
xmipp.jni.MDLabel.MDL_CTF_BG_SQRT_U
static final int MDL_CTF_BG_SQRT_U
< CTF Background parameter
Definition: MDLabel.java:125
-
xmipp.jni.MDLabel.MDL_SHIFT_DIFF2
static final int MDL_SHIFT_DIFF2
< shift difference (double)
Definition: MDLabel.java:376
-
xmipp.jni.MDLabel.MDL_CTF_DATA_PHASE_FLIPPED
static final int MDL_CTF_DATA_PHASE_FLIPPED
< weighted correlation value between a particle and its assigned projection taking into the differenc...
Definition: MDLabel.java:77
-
xmipp.jni.MDLabel.MDL_CLASSIFICATION_INTRACLASS_DISTANCE
static final int MDL_CLASSIFICATION_INTRACLASS_DISTANCE
< Differential Phase Residual evaluated at FRC=0.5
Definition: MDLabel.java:42
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_HELICAL_REFINE
static final int RLN_OPTIMISER_DO_HELICAL_REFINE
Definition: MDLabel.java:597
-
xmipp.jni.MDLabel.RLN_OPTIMISER_ADAPTIVE_OVERSAMPLING
static final int RLN_OPTIMISER_ADAPTIVE_OVERSAMPLING
Definition: MDLabel.java:580
-
xmipp.jni.MDLabel.RLN_MLMODEL_CURRENT_RESOLUTION
static final int RLN_MLMODEL_CURRENT_RESOLUTION
Definition: MDLabel.java:525
-
xmipp.jni.MDLabel.RLN_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES
static final int RLN_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES
Definition: MDLabel.java:627
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_SIGMA2FUDGE_INI
static final int RLN_OPTIMISER_SGD_SIGMA2FUDGE_INI
Definition: MDLabel.java:645
-
xmipp.jni.MDLabel.RLN_MLMODEL_NR_CLASSES
static final int RLN_MLMODEL_NR_CLASSES
Definition: MDLabel.java:554
-
xmipp.jni.MDLabel.RLN_OPTIMISER_REFS_ARE_CTF_CORRECTED
static final int RLN_OPTIMISER_REFS_ARE_CTF_CORRECTED
Definition: MDLabel.java:642
-
xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_NR_ASU
static final int RLN_MLMODEL_HELICAL_NR_ASU
Definition: MDLabel.java:539
-
xmipp.jni.MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE
static final int MDL_PICKING_MANUALPARTICLES_SIZE
< Number of automatic particles picked
Definition: MDLabel.java:289
-
xmipp.jni.MDLabel.RLN_PIPELINE_EDGE_PROCESS
static final int RLN_PIPELINE_EDGE_PROCESS
Definition: MDLabel.java:701
-
xmipp.jni.MDLabel.MDL_CTF_BG_SQRT_ANGLE
static final int MDL_CTF_BG_SQRT_ANGLE
< CTF Background parameter
Definition: MDLabel.java:127
-
xmipp.jni.MDLabel.MDL_IMAGE2
static final int MDL_IMAGE2
< Image associated to this object (std::string)
Definition: MDLabel.java:200
-
xmipp.jni.MDLabel.MDL_RESIDUE
static final int MDL_RESIDUE
< correlation of references assigned by two methods
Definition: MDLabel.java:316
-
xmipp.jni.MDLabel.RLN_IMAGE_STATS_AVG
static final int RLN_IMAGE_STATS_AVG
Definition: MDLabel.java:500
-
xmipp.jni.MDLabel.RLN_CTF_BFACTOR
static final int RLN_CTF_BFACTOR
Definition: MDLabel.java:450
-
xmipp.jni.MDLabel.RLN_PIPELINE_EDGE_FROM
static final int RLN_PIPELINE_EDGE_FROM
Definition: MDLabel.java:699
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_FIT_CORRELATION
static final int RLN_POSTPROCESS_GUINIER_FIT_CORRELATION
Definition: MDLabel.java:713
-
xmipp.jni.MDLabel.MDL_TEST_SIZE
static final int MDL_TEST_SIZE
<Tilt series id (std::string)
Definition: MDLabel.java:396
-
xmipp.jni.MDLabel.MDL_ORDER
static final int MDL_ORDER
< Noise description for pixels&#39; gray level (when projecting)
Definition: MDLabel.java:264
-
xmipp.jni.MDLabel.MDL_RESOLUTION_FREQREAL
static final int MDL_RESOLUTION_FREQREAL
< Frequency in 1/A squared (double)
Definition: MDLabel.java:324
-
xmipp.jni.MDLabel.RLN_SPECTRAL_IDX
static final int RLN_SPECTRAL_IDX
Definition: MDLabel.java:747
-
xmipp.jni.MDLabel.MDL_ANGLE_TILT
static final int MDL_ANGLE_TILT
< difference between rot angles (double,degrees)
Definition: MDLabel.java:16
-
xmipp.jni.MDLabel.MDL_RESOLUTION_ERRORL2
static final int MDL_RESOLUTION_ERRORL2
<differential phase residual (double)
Definition: MDLabel.java:319
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SOLVENT_MASK_NAME
static final int RLN_OPTIMISER_SOLVENT_MASK_NAME
Definition: MDLabel.java:655
-
xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_PSDs
static final int MDL_TILT_ANALYSIS_PSDs
Definition: MDLabel.java:401
-
xmipp.jni.MDLabel.MDL_OPTICALFLOW_STDY
static final int MDL_OPTICALFLOW_STDY
<Standatd deviation="" of="" the="" movement="" in="" x="" direction="" of="" the="" motion="" map>="...
Definition: MDLabel.java:271
-
xmipp.jni.MDLabel.MDL_CTF_BG_R2
static final int MDL_CTF_BG_R2
< CTF Background polynomial parameter
Definition: MDLabel.java:136
-
xmipp.jni.MDLabel.MDL_CTF_ENV_R1
static final int MDL_CTF_ENV_R1
< CTF Envelope polynomial parameter
Definition: MDLabel.java:116
-
xmipp.jni.MDLabel.RLN_SAMPLING_PSI_STEP
static final int RLN_SAMPLING_PSI_STEP
Definition: MDLabel.java:733
-
xmipp.jni.MDLabel.RLN_IMAGE_SAMPLINGRATE_X
static final int RLN_IMAGE_SAMPLINGRATE_X
Definition: MDLabel.java:491
-
xmipp.jni.MDLabel.MDL_VOLUME_SCORE1
static final int MDL_VOLUME_SCORE1
< Score corresponding to the min of cc with cc>threshold
Definition: MDLabel.java:406
-
xmipp.jni.MDLabel.MDL_LL
static final int MDL_LL
<KS-test statistics
Definition: MDLabel.java:213
-
xmipp.jni.MDLabel.RLN_RESOLUTION
static final int RLN_RESOLUTION
Definition: MDLabel.java:744
-
xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA_OFFSET
static final int RLN_MLMODEL_SIGMA_OFFSET
Definition: MDLabel.java:567
-
xmipp.jni.MDLabel.MDL_CTF_LENS_STABILITY
static final int MDL_CTF_LENS_STABILITY
Definition: MDLabel.java:109
-
xmipp.jni.MDLabel.MDL_ZSCORE_RESMEAN
static final int MDL_ZSCORE_RESMEAN
< Z Score (double)
Definition: MDLabel.java:439
-
xmipp.jni.MDLabel.MDL_SHIFT_DIFF0
static final int MDL_SHIFT_DIFF0
< Shift for the image in the Z axis (double)
Definition: MDLabel.java:374
-
xmipp.jni.MDLabel.MDL_FOM
static final int MDL_FOM
< Flip the image? (bool)
Definition: MDLabel.java:181
-
xmipp.jni.MDLabel.RLN_OPTIMISER_NR_ITER_WO_RESOL_GAIN
static final int RLN_OPTIMISER_NR_ITER_WO_RESOL_GAIN
Definition: MDLabel.java:635
-
xmipp.jni.MDLabel.RLN_MLMODEL_CURRENT_SIZE
static final int RLN_MLMODEL_CURRENT_SIZE
Definition: MDLabel.java:526
-
xmipp.jni.MDLabel.MDL_NMA_EIGENVAL
static final int MDL_NMA_EIGENVAL
< NMA Score of a given mode
Definition: MDLabel.java:259
-
xmipp.jni.MDLabel.MDL_ANGLE_TEMPERATURE
static final int MDL_ANGLE_TEMPERATURE
< Angle between y-axis and tilt-axis (double, degrees) for tilted micrographs
Definition: MDLabel.java:25
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEUC
static final int MDL_CTF_DEFOCUS_PLANEUC
< Defocus = A*x+B*y+C
Definition: MDLabel.java:98
-
xmipp.jni.MDLabel.MDL_ANGLE_Y2
static final int MDL_ANGLE_Y2
< Angle between y-axis and tilt-axis (double, degrees) for untilted micrographs
Definition: MDLabel.java:24
-
xmipp.jni.MDLabel.MDL_WEIGHT_ALIGNABILITY
static final int MDL_WEIGHT_ALIGNABILITY
< Weight due to Alignability Precision
Definition: MDLabel.java:421
-
xmipp.jni.MDLabel.MDL_WEIGHT_JUMPER
static final int MDL_WEIGHT_JUMPER
< Weight due to angular jumping
Definition: MDLabel.java:414
-
xmipp.jni.MDLabel.RLN_PARTICLE_HELICAL_TUBE_ID
static final int RLN_PARTICLE_HELICAL_TUBE_ID
Definition: MDLabel.java:689
-
xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_SPECIFIC
static final int MDL_PHANTOM_FEATURE_SPECIFIC
< Operation in case of overlapping features (+,-)
Definition: MDLabel.java:277
-
xmipp.jni.MDLabel.MDL_RESOLUTION_FREQ
static final int MDL_RESOLUTION_FREQ
<Fourier shell correlation noise (double)
Definition: MDLabel.java:322
-
xmipp.jni.MDLabel.MDL_HALF1
static final int MDL_HALF1
< when previous assignment validation
Definition: MDLabel.java:187
-
xmipp.jni.MDLabel.MDL_BFACTOR
static final int MDL_BFACTOR
< Average (per class) of the maximum value of normalized probability function) (double) ...
Definition: MDLabel.java:32
-
xmipp.jni.MDLabel.RLN_IMAGE_STATS_MAX
static final int RLN_IMAGE_STATS_MAX
Definition: MDLabel.java:499
-
xmipp.jni.MDLabel.MDL_SERIE
static final int MDL_SERIE
< Name of an image (std::string)
Definition: MDLabel.java:362
-
xmipp.jni.MDLabel.MDL_DM3_TAGNAME
static final int MDL_DM3_TAGNAME
Definition: MDLabel.java:173
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_INTERCEPT
static final int RLN_POSTPROCESS_GUINIER_VALUE_INTERCEPT
Definition: MDLabel.java:720
-
xmipp.jni.MDLabel.MDL_WEIGHT
static final int MDL_WEIGHT
< Score 4 for volumes
Definition: MDLabel.java:410
-
xmipp.jni.MDLabel.RLN_MLMODEL_SGD_GRADIENT_IMAGE
static final int RLN_MLMODEL_SGD_GRADIENT_IMAGE
Definition: MDLabel.java:566
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_SIGMA2FUDGE_HALFLIFE
static final int RLN_OPTIMISER_SGD_SIGMA2FUDGE_HALFLIFE
Definition: MDLabel.java:646
-
xmipp.jni.MDLabel.RLN_SORTED_IDX
static final int RLN_SORTED_IDX
Definition: MDLabel.java:740
-
xmipp.jni.MDLabel.MDL_CONTINUOUS_X
static final int MDL_CONTINUOUS_X
< noise if center of unit cell (vector double)
Definition: MDLabel.java:66
-
xmipp.jni.MDLabel.MDL_SYMNO
static final int MDL_SYMNO
< Sum of all weights in ML model
Definition: MDLabel.java:391
-
xmipp.jni.MDLabel.MDL_CONTINUOUS_GRAY_A
static final int MDL_CONTINUOUS_GRAY_A
< Flip of continuous assignment
Definition: MDLabel.java:69
-
xmipp.jni.MDLabel.MDL_WEIGHT_PHASECORR
static final int MDL_WEIGHT_PHASECORR
< Weight due correlation between two images/subtomos
Definition: MDLabel.java:417
-
xmipp.jni.MDLabel.MDL_PRJ_TILT_RANDSTR
static final int MDL_PRJ_TILT_RANDSTR
< Tilt angle dev and mean noise (vector double)
Definition: MDLabel.java:301
-
xmipp.jni.MDLabel.RLN_MLMODEL_AVE_PMAX
static final int RLN_MLMODEL_AVE_PMAX
Definition: MDLabel.java:524
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_TWIST_INITIAL
static final int RLN_OPTIMISER_HELICAL_TWIST_INITIAL
Definition: MDLabel.java:612
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_FITTINGCORR13
static final int MDL_CTF_CRIT_FITTINGCORR13
< Score of the fitting
Definition: MDLabel.java:149
-
xmipp.jni.MDLabel.MDL_MICROGRAPH_ORIGINAL
static final int MDL_MICROGRAPH_ORIGINAL
< Name of a position file (std::string)
Definition: MDLabel.java:232
-
xmipp.jni.MDLabel.RLN_IMAGE_BEAMTILT_Y
static final int RLN_IMAGE_BEAMTILT_Y
Definition: MDLabel.java:481
-
xmipp.jni.MDLabel.MDL_MICROGRAPH_ID
static final int MDL_MICROGRAPH_ID
< Name of a micrograph (std::string)
Definition: MDLabel.java:228
-
xmipp.jni.MDLabel.MDL_PMAX
static final int MDL_PMAX
< Number of manual particles picked
Definition: MDLabel.java:290
-
xmipp.jni.MDLabel.RLN_OPTIMISER_BEST_RESOL_THUS_FAR
static final int RLN_OPTIMISER_BEST_RESOL_THUS_FAR
Definition: MDLabel.java:583
-
xmipp.jni.MDLabel.MDL_SPH_COEFFICIENTS
static final int MDL_SPH_COEFFICIENTS
< Signal change for an image
Definition: MDLabel.java:380
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_GENERAL
static final int RLN_POSTPROCESS_FSC_GENERAL
Definition: MDLabel.java:708
-
xmipp.jni.MDLabel.MDL_PRJ_ROT_RANDSTR
static final int MDL_PRJ_ROT_RANDSTR
< Rotational angle dev and mean noise (vector double)
Definition: MDLabel.java:298
-
xmipp.jni.MDLabel.MDL_KEYWORDS
static final int MDL_KEYWORDS
< Sigma value (double)
Definition: MDLabel.java:210
-
xmipp.jni.MDLabel.RLN_OPTIMISER_RADIUS_MASK_EXP_PARTICLES
static final int RLN_OPTIMISER_RADIUS_MASK_EXP_PARTICLES
Definition: MDLabel.java:640
-
xmipp.jni.MDLabel.RLN_IMAGE_BEAMTILT_GROUP
static final int RLN_IMAGE_BEAMTILT_GROUP
Definition: MDLabel.java:482
-
xmipp.jni.MDLabel.MDL_ANGLE_ROT_DIFF
static final int MDL_ANGLE_ROT_DIFF
< Rotation angle of an image (double,degrees)
Definition: MDLabel.java:15
-
xmipp.jni.MDLabel.RLN_PARTICLE_ID
static final int RLN_PARTICLE_ID
Definition: MDLabel.java:678
-
xmipp.jni.MDLabel.MDL_ITER
static final int MDL_ITER
< Unique identifier for items inside a list or set (std::size_t)
Definition: MDLabel.java:206
-
xmipp.jni.MDLabel.MDL_FRAME_ID
static final int MDL_FRAME_ID
< Figure of Merit in 0-1 range (double)
Definition: MDLabel.java:182
-
xmipp.jni.MDLabel.MDL_ZSCORE_RESCOV
static final int MDL_ZSCORE_RESCOV
< Z Score of the stddev of the residuals (double)
Definition: MDLabel.java:441
-
xmipp.jni.MDLabel.MDL_SAMPLINGRATE_Z
static final int MDL_SAMPLINGRATE_Z
< sampling rate in A/pixel (double)
Definition: MDLabel.java:335
-
xmipp.jni.MDLabel.MDL_PICKING_PARTICLE_SIZE
static final int MDL_PICKING_PARTICLE_SIZE
Definition: MDLabel.java:287
-
xmipp.jni.MDLabel.MDL_CTF_K
static final int MDL_CTF_K
< Inelastic absorption
Definition: MDLabel.java:114
-
xmipp.jni.MDLabel.MDL_REF3D
static final int MDL_REF3D
< Seed for random number generator
Definition: MDLabel.java:311
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEUA
static final int MDL_CTF_DEFOCUS_PLANEUA
< The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates
Definition: MDLabel.java:96
-
xmipp.jni.MDLabel.RLN_SAMPLING_IS_3D_TRANS
static final int RLN_SAMPLING_IS_3D_TRANS
Definition: MDLabel.java:724
-
xmipp.jni.MDLabel.MDL_BGMEAN
static final int MDL_BGMEAN
<Bfactor of a map, or even a local bfactor
Definition: MDLabel.java:33
-
xmipp.jni.MDLabel.RLN_PARTICLE_MOVIE_RUNNING_AVG
static final int RLN_PARTICLE_MOVIE_RUNNING_AVG
Definition: MDLabel.java:681
-
xmipp.jni.MDLabel.MDL_MISSINGREGION_THY0
static final int MDL_MISSINGREGION_THY0
< Type of missing region in subtomogram
Definition: MDLabel.java:239
-
xmipp.jni.MDLabel.MDL_CRYSTAL_ORTHO_PRJ
static final int MDL_CRYSTAL_ORTHO_PRJ
< Shift file for crystal projection
Definition: MDLabel.java:60
-
xmipp.jni.MDLabel.MDL_SCORE_BY_LBP
static final int MDL_SCORE_BY_LBP
< Feature vectors used to classify particles (vector double)
Definition: MDLabel.java:352
-
xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
-
xmipp.jni.MDLabel.MDL_OPTICALFLOW_MEANX
static final int MDL_OPTICALFLOW_MEANX
< Origin for the image in the Z axis (double)
Definition: MDLabel.java:268
-
xmipp.jni.MDLabel.MDL_CORRELATION_MASK
static final int MDL_CORRELATION_MASK
< correlation value between a particle and its assigned projection
Definition: MDLabel.java:75
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_CU
static final int MDL_CTF_BG_GAUSSIAN2_CU
< CTF Background parameter
Definition: MDLabel.java:132
-
xmipp.jni.MDLabel.MDL_ZCOOR
static final int MDL_ZCOOR
< Z component (double)
Definition: MDLabel.java:434
-
xmipp.jni.MDLabel.MDL_CLASSIFICATION_FRC_05
static final int MDL_CLASSIFICATION_FRC_05
< Average intraclass distance (double)
Definition: MDLabel.java:43
-
xmipp.jni.MDLabel.MDL_CONTINUOUS_SCALE_ANGLE
static final int MDL_CONTINUOUS_SCALE_ANGLE
< b value of continuous assignment
Definition: MDLabel.java:71
-
xmipp.jni.MDLabel.MDL_COORD_CONSENSUS_SCORE
static final int MDL_COORD_CONSENSUS_SCORE
< Serve to make annotations on the metadata row
Definition: MDLabel.java:45
-
xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_MAX_SUBSETS
static final int RLN_OPTIMISER_SGD_MAX_SUBSETS
Definition: MDLabel.java:650
-
xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_CU
static final int MDL_CTF_BG_GAUSSIAN_CU
< CTF Background parameter
Definition: MDLabel.java:121
-
xmipp.jni.MDLabel.RLN_MLMODEL_DIMENSIONALITY
static final int RLN_MLMODEL_DIMENSIONALITY
Definition: MDLabel.java:528
-
xmipp.jni.MDLabel.MDL_CTF_MODEL2
static final int MDL_CTF_MODEL2
< Name for the CTF Model (std::string)
Definition: MDLabel.java:81
-
xmipp.jni.MDLabel.MDL_Z
static final int MDL_Z
< Y size (int)
Definition: MDLabel.java:433
-
xmipp.jni.MDLabel.MDL_CTF_CRIT_DAMPING
static final int MDL_CTF_CRIT_DAMPING
< Maximum frequency at which the envelope drops below 0.1 (in Angstroms)
Definition: MDLabel.java:146
-
xmipp.jni.MDLabel.MDL_ANGLE_TILT_DIFF
static final int MDL_ANGLE_TILT_DIFF
< Tilting angle of an image (double,degrees)
Definition: MDLabel.java:19
-
xmipp.jni.MDLabel.RLN_SAMPLING_SIGMA_ROT
static final int RLN_SAMPLING_SIGMA_ROT
Definition: MDLabel.java:734
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_SYMMETRY_LOCAL_REFINEMENT
static final int RLN_OPTIMISER_HELICAL_SYMMETRY_LOCAL_REFINEMENT
Definition: MDLabel.java:617
-
xmipp.jni.MDLabel.MDL_CTF_SAMPLING_RATE
static final int MDL_CTF_SAMPLING_RATE
< Name for another CTF model (std::string)
Definition: MDLabel.java:82
-
xmipp.jni.MDLabel.RLN_IMAGE_WEIGHT
static final int RLN_IMAGE_WEIGHT
Definition: MDLabel.java:504
-
xmipp.jni.MDLabel.MDL_STAR_COMMENT
static final int MDL_STAR_COMMENT
<stdandard deviation value (double)
Definition: MDLabel.java:385
-
xmipp.jni.MDLabel.RLN_MLMODEL_DATA_VS_PRIOR_REF
static final int RLN_MLMODEL_DATA_VS_PRIOR_REF
Definition: MDLabel.java:527
-
xmipp.jni.MDLabel.RLN_OPTIMISER_TAU_SPECTRUM_NAME
static final int RLN_OPTIMISER_TAU_SPECTRUM_NAME
Definition: MDLabel.java:657
-
xmipp.jni.MDLabel.RLN_MLMODEL_PADDING_FACTOR
static final int RLN_MLMODEL_PADDING_FACTOR
Definition: MDLabel.java:558
-
xmipp.jni.MDLabel.MDL_SCORE_BY_PCA_RESIDUAL_EXP
static final int MDL_SCORE_BY_PCA_RESIDUAL_EXP
Definition: MDLabel.java:338
-
xmipp.jni.MDLabel.MDL_GOOD_REGION_SCORE
static final int MDL_GOOD_REGION_SCORE
< Z Score (double)
Definition: MDLabel.java:437
-
xmipp.jni.MDLabel.RLN_OPTIMISER_OUTPUT_ROOTNAME
static final int RLN_OPTIMISER_OUTPUT_ROOTNAME
Definition: MDLabel.java:637
-
xmipp.jni.MDLabel.RLN_IMAGE_ENABLED
static final int RLN_IMAGE_ENABLED
Definition: MDLabel.java:477
-
xmipp.jni.MDLabel.RLN_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO
static final int RLN_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO
Definition: MDLabel.java:611
-
xmipp.jni.MDLabel.RLN_MICROGRAPH_NAME_WODOSE
static final int RLN_MICROGRAPH_NAME_WODOSE
Definition: MDLabel.java:518
-
xmipp.jni.MDLabel.MDL_CLASS_PERCENTAGE
static final int MDL_CLASS_PERCENTAGE
< Number of images assigned to the same class as this image
Definition: MDLabel.java:38
-
xmipp.jni.MDLabel.MDL_CTF_TRANSVERSAL_DISPLACEMENT
static final int MDL_CTF_TRANSVERSAL_DISPLACEMENT
< Longitudinal displacement
Definition: MDLabel.java:112
-
xmipp.jni.MDLabel.RLN_OPTIMISER_DO_AUTO_REFINE
static final int RLN_OPTIMISER_DO_AUTO_REFINE
Definition: MDLabel.java:591
-
xmipp.jni.MDLabel.MDL_DM3_PARENTID
static final int MDL_DM3_PARENTID
Definition: MDLabel.java:171
-
xmipp.jni.MDLabel.MDL_PROGRAM
static final int MDL_PROGRAM
Definition: MDLabel.java:304
-
xmipp.jni.MDLabel.RLN_IMAGE_NORM_CORRECTION
static final int RLN_IMAGE_NORM_CORRECTION
Definition: MDLabel.java:488
-
xmipp.jni.MDLabel.RLN_PIPELINE_JOB_COUNTER
static final int RLN_PIPELINE_JOB_COUNTER
Definition: MDLabel.java:692
-
xmipp.jni.MDLabel.MDL_SUBTRACTION_BETA1
static final int MDL_SUBTRACTION_BETA1
< Beta 0 coefficient of adjusted model for subtract particle
Definition: MDLabel.java:388
-
xmipp.jni.MDLabel.RLN_ORIENT_FLIP
static final int RLN_ORIENT_FLIP
Definition: MDLabel.java:660
-
xmipp.jni.MDLabel.MDL_HALF2
static final int MDL_HALF2
< Half map/image 1 file name (string)
Definition: MDLabel.java:188
-
xmipp.jni.MDLabel.RLN_IMAGE_MAGNIFICATION_CORRECTION
static final int RLN_IMAGE_MAGNIFICATION_CORRECTION
Definition: MDLabel.java:487
-
xmipp.jni.MDLabel.RLN_POSTPROCESS_DPR_UNMASKED
static final int RLN_POSTPROCESS_DPR_UNMASKED
Definition: MDLabel.java:706
-
xmipp.jni.MDLabel.RLN_OPTIMISER_LOCAL_SYMMETRY_FILENAME
static final int RLN_OPTIMISER_LOCAL_SYMMETRY_FILENAME
Definition: MDLabel.java:626
-
xmipp.jni.MDLabel.MDL_CL2D_CHANGES
static final int MDL_CL2D_CHANGES
< Current block number (for incremental EM)
Definition: MDLabel.java:35
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.jni;
27 
31 public class MDRow {
32  // hold pointer to Image class in C++ space
33  private long peer;
34 
35  static {
36  System.loadLibrary("XmippJNI");
37  // storeIds();
38  }
39 
40  // caching some ids
41  // private static native void storeIds();
42  // functions to create images
43  private native void create();
44  private native void createRef(long id);
45 
46 
47  // destructor
48  public synchronized native void destroy();
49 
50  // clear metadata
51  public native void clear();
52 
53  public native int size();
54 
55  public native boolean containsLabel(int label);
56 
57  public native boolean removeLabel(int label);
58 
59  // get values from metadata
60  public native int getValueInt(int label);
61 
62  public native long getValueLong(int label);
63 
64  public native double getValueDouble(int label);
65 
67  public native String getValueString(int label);
68 
69 
70  // set functions connection with MDRow class in C++
71  public boolean setEnabled(boolean value) {
72  return setValueInt(MDLabel.MDL_ENABLED, value ? 1 : -1);
73  }
74 
75  public boolean getEnabled(long objId) {
76  return getValueInt(MDLabel.MDL_ENABLED) > 0;
77  }
78 
79  public native boolean setValueInt(int label, int value);
80 
81  public native boolean setValueLong(int label, long value);
82 
83  public native boolean setValueDouble(int label, double value);
84 
85  public native boolean setValueString(int label, String value);
86 
87  public native boolean setValueBoolean(int label, boolean value);
88 
89  public native void addLabel(int label);
90 
91  /*********** Non-native functions ********************/
93  public MDRow() {
94  create();
95  }
96 
97  public MDRow(long peer) {
98  createRef(peer);
99 
100  }
101 
106  @Override
107  protected void finalize() throws Throwable {
108  super.finalize();
109  destroy();
110  }
111 
112 }
xmipp.jni.MDRow.setValueLong
native boolean setValueLong(int label, long value)
-
xmipp.jni.MDRow.setValueString
native boolean setValueString(int label, String value)
-
xmipp.jni.MDRow.addLabel
native void addLabel(int label)
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xmipp.jni.MDRow.getValueDouble
native double getValueDouble(int label)
-
xmipp.jni.MDRow.setEnabled
boolean setEnabled(boolean value)
Definition: MDRow.java:71
-
xmipp.jni.MDRow.setValueInt
native boolean setValueInt(int label, int value)
-
xmipp.jni.MDRow.size
native int size()
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xmipp.jni.MDRow.destroy
synchronized native void destroy()
-
xmipp.jni.MDRow.clear
native void clear()
-
xmipp.jni.MDRow.getEnabled
boolean getEnabled(long objId)
Definition: MDRow.java:75
-
xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
-
xmipp.jni.MDRow.setValueBoolean
native boolean setValueBoolean(int label, boolean value)
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xmipp.jni.MDRow.getValueInt
native int getValueInt(int label)
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xmipp.jni.MDRow.getValueLong
native long getValueLong(int label)
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xmipp.jni.MDRow.containsLabel
native boolean containsLabel(int label)
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xmipp.jni.MDRow.finalize
void finalize()
Definition: MDRow.java:107
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xmipp.jni.MDRow.MDRow
MDRow(long peer)
Definition: MDRow.java:97
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xmipp.jni.MDRow.removeLabel
native boolean removeLabel(int label)
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import java.awt.Component;
29 import java.awt.GridBagConstraints;
30 import java.awt.GridBagLayout;
31 import java.awt.Insets;
32 import java.awt.event.ActionEvent;
33 import java.util.List;
34 import javax.swing.BorderFactory;
35 import javax.swing.ButtonGroup;
36 import javax.swing.JButton;
37 import javax.swing.JCheckBox;
38 import javax.swing.JComboBox;
39 import javax.swing.JFrame;
40 import javax.swing.JLabel;
41 import javax.swing.JPanel;
42 import javax.swing.JRadioButton;
43 import javax.swing.JTable;
44 import javax.swing.JTextField;
45 import xmipp.jni.MetaData;
46 import xmipp.utils.XmippDialog;
47 import xmipp.utils.XmippResource;
48 import xmipp.utils.XmippWindowUtil;
49 import xmipp.viewer.models.ColumnInfo;
50 import xmipp.viewer.models.GalleryData;
51 import xmipp.viewer.models.MetadataTableModel;
52 
53 
54 
55 /* This class will serve for find and replace values
56  * in a MetadataGallery
57  */
58 public class MDSearchJDialog extends XmippDialog {
59  private static final long serialVersionUID = 1L;
60  protected GalleryJFrame parent;
61  protected GalleryData data;
62  protected JTable table;
63  protected long[] ids;
64  protected int selected_index = -1;
65  protected ColumnInfo label;
66  protected List<ColumnInfo> labels;
67 
68  protected GridBagConstraints gbc = new GridBagConstraints();
69  protected JPanel mainPanel;
70  protected JComboBox jcbLabel, jcbFillMode;
71 
72  private JTextField jtFind;
73  private JTextField jtReplace;
74  private JButton btnReplace;
75  private JButton btnFind;
76  private JButton btnReplaceFind;
77  private JButton btnReplaceAll;
78  private JRadioButton jrbForward;
79  private JCheckBox jchCase;
80  private int column;
81 
86  public MDSearchJDialog(JFrame parent, JTable table, GalleryData data) {
87  super(parent, "Find and Replace", false);
88 
89  this.parent = (GalleryJFrame) parent;
90  this.data = data;
91  this.table = table;
92  this.ids = data.getIds();
93  this.labels = data.getColumns();
94  this.label = labels.get(0);
95  btnOkText = "Close";
96  btnCancelDisplay = false;
97  initComponents();
98  }// constructor MDSearchJDialog
99 
104  protected void addPair(JPanel panel, String text, Component c, int col,
105  int row) {
106  JLabel label = new JLabel(text);
107  gbc.anchor = GridBagConstraints.EAST;
108  panel.add(label, XmippWindowUtil.getConstraints(gbc, col, row));
109  gbc.anchor = GridBagConstraints.WEST;
110  panel.add(c, XmippWindowUtil.getConstraints(gbc, col + 1, row));
111  }
112 
113  @Override
114  protected void createContent(JPanel panel) {
115  setResizable(false);
116  mainPanel = new JPanel(new GridBagLayout());
117  gbc.insets = new Insets(5, 5, 0, 0);
118 
119  jtFind = new JTextField(15);
120  jtReplace = new JTextField(15);
121 
122  int row = 0;
123  addPair(mainPanel, "Find", jtFind, 0, row++);
124  addPair(mainPanel, "Replace", jtReplace, 0, row++);
125 
126  jtFind.addActionListener(this);
127 
128  // setPreferredSize(new Dimension(350, 180));
129  setIconImage(XmippResource.getIcon("search.gif").getImage());
130 
131  JPanel optPanel = new JPanel(new GridBagLayout());
132  mainPanel.add(optPanel,
133  XmippWindowUtil.getConstraints(gbc, 0, row++, 2));
134  optPanel.setBorder(BorderFactory.createTitledBorder("Options"));
135 
136  // Create labels combo
137  jcbLabel = new JComboBox();
138  for (ColumnInfo l : labels) {
139  jcbLabel.addItem(l.labelName);
140  }
141  jcbLabel.addActionListener(this);
142  addPair(optPanel, "Label", jcbLabel, 0, 0);
143  jchCase = new JCheckBox();
144  addPair(optPanel, "Case sensitive", jchCase, 0, 1);
145  ButtonGroup btnGroup = new ButtonGroup();
146  jrbForward = new JRadioButton("Forward");
147  jrbForward.setSelected(true);
148  btnGroup.add(jrbForward);
149  JRadioButton jrb = new JRadioButton("Backward");
150  btnGroup.add(jrb);
151  addPair(optPanel, "Direction", jrbForward, 0, 2);
152  addPair(optPanel, "", jrb, 0, 3);
153 
154  // Add buttons
155  JPanel btnPanel = new JPanel(new GridBagLayout());
156 
157  btnFind = XmippWindowUtil.getTextButton("Find", this);
158  btnReplace = XmippWindowUtil.getTextButton("Replace", this);
159  btnReplaceFind = XmippWindowUtil.getTextButton("Replace/Find", this);
160  btnReplaceAll = XmippWindowUtil.getTextButton("Replace All", this);
161 
162  btnPanel.add(btnFind, XmippWindowUtil.getConstraints(gbc, 0, 0, 2));
163  btnPanel.add(btnReplaceFind,
164  XmippWindowUtil.getConstraints(gbc, 2, 0, 2));
165  btnPanel.add(btnReplace, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
166  btnPanel.add(btnReplaceAll,
167  XmippWindowUtil.getConstraints(gbc, 2, 1, 2));
168  gbc.anchor = GridBagConstraints.EAST;
169  mainPanel.add(btnPanel,
170  XmippWindowUtil.getConstraints(gbc, 0, row++, 2));
171 
172  panel.add(mainPanel);
173  enableActions();
174  }// function initComponents
175 
176 
177  protected void enableActions()
178  {
179  boolean isenabled = !data.isScipionInstance();
180  jtReplace.setEnabled(isenabled);
181  btnReplace.setEnabled(isenabled);
182  btnReplaceFind.setEnabled(isenabled);
183  btnReplaceAll.setEnabled(isenabled);
184  }
185 
186  @Override
187  public void handleActionPerformed(ActionEvent evt) {
188  Object o = evt.getSource();
189  if (o == jtFind || o == btnFind)
190  find();
191  else if (o == jcbLabel)
192  {
193  column = jcbLabel.getSelectedIndex();
194  label = labels.get(column);
195  }
196  else if (o == btnReplace)
197  replace(selected_index);
198  else if (o == btnReplaceFind) {
199  replace(selected_index);
200  find();
201  } else if (o == btnReplaceAll)
202  replaceAll();
203 
204  }// function actionPerformed
205 
206  private int nextIndex(int index, int direction) {
207  int next = 0;
208  if (index >= 0) {
209  next = (index + direction);
210  if (next < 0)
211  next = ids.length - 1;
212  else if (next >= ids.length)
213  next = 0;
214  }
215  return next;
216  }
217 
218  private void find() {
219  try {
220  int direction = jrbForward.isSelected() ? 1 : -1;
221  String findStr = jtFind.getText();
222  if (findStr.length() == 0)
223  return;
224 
225  int index = nextIndex(selected_index, direction);
226  selected_index = -1;
227 
228  for (int i = 0; i < ids.length && selected_index < 0; ++i) {
229  if (match(findStr, index))
230  selected_index = index;
231  else
232  index = nextIndex(index, direction);
233  }
234  if (selected_index > -1)
235  parent.selectItem(selected_index, column);
236  } catch (Exception e) {
237  showException(e);
238  }
239  }
240 
241  private boolean match(String findStr, int index) {
242  boolean caseSensitive = jchCase.isSelected();
243  String value = data.getValueString(label.label, ids[index]).trim();
244  String str = findStr.trim();
245  if (!caseSensitive) {
246  value = value.toLowerCase();
247  str = findStr.toLowerCase();
248  }
249  return (value.indexOf(str) >= 0);
250  }
251 
252  private void replace(int index) {
253  String replaceStr = jtReplace.getText().trim();
254  if (index > -1 && replaceStr.length() > 0) {
255  String value = data.getValueString(label.label, ids[index]);
256  String newValue = value.replace(jtFind.getText().trim(), replaceStr);
257  // table.setValueAt(newValue, index, jcbLabel.getSelectedIndex());
258  data.setValueString(label.label, newValue, ids[index]);
259  ((MetadataTableModel) table.getModel()).fireTableRowsUpdated(index,
260  index);
261  }
262  }
263 
264  private void replaceAll() {
265  String findStr = jtFind.getText().trim();
266  for (int i = 0; i < ids.length; ++i)
267  if (match(findStr, i))
268  replace(i);
269  }
270 
271 }// class AddFillLabelsJDialog
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boolean showException(Exception e)
Definition: XmippDialog.java:217
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xmipp.viewer.windows.MDSearchJDialog.MDSearchJDialog
MDSearchJDialog(JFrame parent, JTable table, GalleryData data)
Definition: MDSearchJDialog.java:86
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xmipp.viewer.models.GalleryData.setValueString
boolean setValueString(int label, String newValue, long l)
Definition: GalleryData.java:1431
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static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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String getValueString(int label, long id)
Definition: GalleryData.java:1427
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List< ColumnInfo > getColumns()
Definition: GalleryData.java:293
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void addPair(JPanel panel, String text, Component c, int col, int row)
Definition: MDSearchJDialog.java:104
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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void handleActionPerformed(ActionEvent evt)
Definition: MDSearchJDialog.java:187
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 import ij.ImagePlus;
4 import ij.gui.Roi;
5 import ij.process.ImageProcessor;
6 import java.awt.Rectangle;
7 import java.util.logging.Level;
8 import java.util.logging.Logger;
9 import javax.swing.ImageIcon;
10 import xmipp.ij.commons.XmippImageConverter;
11 import xmipp.jni.ImageGeneric;
12 import xmipp.utils.XmippMessage;
13 import xmipp.viewer.particlepicker.Micrograph;
14 import xmipp.viewer.particlepicker.ParticlePicker;
15 import xmipp.viewer.particlepicker.PickerParticle;
16 
17 public class ManualParticle extends PickerParticle{
18 
19  protected ParticlePicker picker;
20  protected ImageGeneric ig;
21 
22  protected double[] lastalign;
23 
24  public double[] getLastalign()
25  {
26  return lastalign;
27  }
28 
29  public void setLastalign(double[] lastalign)
30  {
31  this.lastalign = lastalign;
32  }
33 
34  public ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph)
35  {
36  this(x, y, picker, micrograph, 2);
37  }
38 
39  public ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)
40  {
41  super(x, y, micrograph, cost);
42  this.picker = picker;
43  }
44 
45 
46  public ParticlePicker getParticlePicker()
47  {
48  return picker;
49  }
50 
51 
52  public int getX0()
53  {
54  return getX() - picker.getRadius();
55  }
56 
57  public int getY0()
58  {
59  return getY() - picker.getRadius();
60  }
61 
62 
63 
64  public boolean contains(int x2, int y2 )
65  {
66  return super.contains(x2, y2, picker.getSize());
67  }
68 
69 
70  protected void loadImagePlus()
71  {
72  if(ig == null)
73  {
74  try {
75  int size = picker.getSize();
76  ImagePlus mimage = micrograph.getImagePlus();
77  int radius = size/2;
78  Rectangle r = new Rectangle(x - radius , y - radius, size, size);
79  Roi roi = mimage.getRoi();
80  mimage.setRoi(r);
81  ImageProcessor processor = mimage.getProcessor().crop();
82  ImagePlus img = new ImagePlus("", processor);
83  mimage.setRoi(roi);
84  ig = XmippImageConverter.convertToImageGeneric(img);
85  } catch (Exception ex) {
86  Logger.getLogger(ManualParticle.class.getName()).log(Level.SEVERE, null, ex);
87  throw new IllegalArgumentException(ex.getMessage());
88  }
89  }
90  }
91 
92  @Override
93  public void setPosition(int x, int y)
94  {
95  int radius = picker.getSize()/2;
96  if(!getMicrograph().fits(x, y, picker.getSize()))
97  throw new IllegalArgumentException(XmippMessage.getOutOfBoundsMsg(String.format("Particle centered at %s, %s with size %s", x, y, picker.getSize())));
98  super.setPosition(x, y);
99  ig = null;
100  }
101 
102 
103 
104  public void resetImage()
105  {
106 // if(ig != null)
107 // ig.destroy();
108  lastalign = null;
109  ig = null;
110  }
111 
112 
113  public ImageGeneric getImageGeneric() {
114  loadImagePlus();//to ensure there is an image generic setted
115  return ig;
116  }
117 
118  public double getTemplateRotation()
119  {
120  if(lastalign == null)
121  return -1;
122  return lastalign[1];
123  }
124 
125  public double getTemplateTilt()
126  {
127  if(lastalign == null)
128  return -1;
129  return lastalign[2];
130  }
131 
132 
133 
134  public double getTemplatePsi()
135  {
136  if(lastalign == null)
137  return -1;
138  return lastalign[3];
139  }
140 
141  public int getTemplateIndex()
142  {
143  if(lastalign == null)
144  return -1;
145  return (int)lastalign[0];
146  }
147 
148  public int getSize()
149  {
150  return picker.getSize();
151  }
152 
153 
154 
155 }
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Definition: XmippImageConverter.java:297
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ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph)
Definition: ManualParticle.java:34
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Definition: XmippMessage.java:56
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ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)
Definition: ManualParticle.java:39
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1 package xmipp.ij.plugins.maskstoolbar;
2 
3 import ij.IJ;
4 import ij.ImagePlus;
5 import ij.gui.Roi;
6 import ij.gui.Toolbar;
7 import ij.plugin.PlugIn;
8 import ij.plugin.frame.PlugInFrame;
9 import ij.process.ByteProcessor;
10 import java.awt.Color;
11 import java.awt.GridLayout;
12 import java.awt.event.ActionEvent;
13 import java.awt.event.ActionListener;
14 import java.awt.event.WindowEvent;
15 import java.lang.reflect.Method;
16 import javax.swing.Box;
17 import javax.swing.JButton;
18 import javax.swing.JToggleButton;
19 import xmipp.ij.plugins.maskstoolbar.ICONS;
20 import xmipp.ij.plugins.maskstoolbar.LABELS;
21 
22 /*
23  * To change this template, choose Tools | Templates
24  * and open the template in the editor.
25  */
30 public class MasksToolBarPlugin implements PlugIn {
31 
32  @Override
33  public void run(String args) {
34  MasksToolBar.getInstance().setVisible(true);
35  }
36 }
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.ij.plugins.maskstoolbar;
6 
7 import ij.IJ;
8 import ij.ImagePlus;
9 import ij.gui.Roi;
10 import ij.gui.Toolbar;
11 import ij.plugin.frame.PlugInFrame;
12 import ij.process.ByteProcessor;
13 import java.awt.Color;
14 import java.awt.GridLayout;
15 import java.awt.event.ActionEvent;
16 import java.awt.event.ActionListener;
17 import java.awt.event.WindowEvent;
18 import java.lang.reflect.Method;
19 import javax.swing.Box;
20 import javax.swing.JButton;
21 import javax.swing.JToggleButton;
22 import xmipp.ij.plugins.maskstoolbar.ICONS;
23 import xmipp.ij.plugins.maskstoolbar.LABELS;
24 
29 public class MasksToolBar extends PlugInFrame implements ActionListener {
30 
31  private static MasksToolBar instance = null; // To have an unique bar.
32  private ImagePlus mask = null;
33  private JButton jbSetBrushSize = new JButton();
34  private JButton jbCreateMask = new JButton();
35  private JButton jbCreateSelection = new JButton();
36  private JButton jbInvertMask = new JButton();
37  private JButton jbInvertSelection = new JButton();
38  private JButton jbSpecifySelection = new JButton();
39  private JToggleButton jtbBrush = new JToggleButton();
40  private JToggleButton jtbEllipse = new JToggleButton();
41  private JToggleButton jtbFreehand = new JToggleButton();
42  private JToggleButton jtbLockMask = new JToggleButton();
43  private JToggleButton jtbOval = new JToggleButton();
44  private JToggleButton jtbPolygon = new JToggleButton();
45  private JToggleButton jtbRectangle = new JToggleButton();
46  private JToggleButton jtbRoundRectangle = new JToggleButton();
47  private JToggleButton toolsButtons[] = new JToggleButton[]{
48  jtbRectangle,
49  jtbRoundRectangle,
50  jtbEllipse,
51  jtbOval,
52  jtbPolygon,
53  jtbFreehand,
54  jtbBrush};
55 
56  @SuppressWarnings("LeakingThisInConstructor")
57  public MasksToolBar() {
58  super(LABELS.TITLE);
59 
60  setLayout(new GridLayout(2, 8));
61 
62  jtbRectangle.setIcon(ICONS.TOOL_RECTANGLE);
63  jtbRoundRectangle.setIcon(ICONS.TOOL_ROUNDRECTANGLE);
64  jtbEllipse.setIcon(ICONS.TOOL_ELLIPSE);
65  jtbOval.setIcon(ICONS.TOOL_OVAL);
66  jtbPolygon.setIcon(ICONS.TOOL_POLYGON);
67  jtbFreehand.setIcon(ICONS.TOOL_FREEHAND);
68  jtbBrush.setIcon(ICONS.TOOL_BRUSH);
69  jbSetBrushSize.setIcon(ICONS.ACTION_BRUSHSIZE);
70  jtbLockMask.setIcon(ICONS.MASK_UNLOCKED);
71  jbCreateMask.setIcon(ICONS.ACTION_CREATEMASK);
72  jbCreateSelection.setIcon(ICONS.ACTION_CREATESELECTION);
73  jbInvertSelection.setIcon(ICONS.ACTION_INVERTSELECTION);
74  jbInvertMask.setIcon(ICONS.ACTION_INVERTMASK);
75  jbSpecifySelection.setIcon(ICONS.ACTION_SPECIFYSELECTION);
76 
77  jtbRectangle.setToolTipText(LABELS.TOOLTIP_RECTANGLE);
78  jtbRoundRectangle.setToolTipText(LABELS.TOOLTIP_ROUNDRECTANGLE);
79  jtbEllipse.setToolTipText(LABELS.TOOLTIP_ELLIPSE);
80  jtbOval.setToolTipText(LABELS.TOOLTIP_OVAL);
81  jtbPolygon.setToolTipText(LABELS.TOOLTIP_POLYGON);
82  jtbFreehand.setToolTipText(LABELS.TOOLTIP_FREEHAND);
83  jtbBrush.setToolTipText(LABELS.TOOLTIP_BRUSH);
84  jbSetBrushSize.setToolTipText(LABELS.TOOLTIP_SETBRUSHSIZE);
85  jtbLockMask.setToolTipText(LABELS.TOOLTIP_MASK_UNLOCKED);
86  jbCreateMask.setToolTipText(LABELS.TOOLTIP_CREATEMASK);
87  jbCreateSelection.setToolTipText(LABELS.TOOLTIP_CREATESELECTION);
88  jbInvertSelection.setToolTipText(LABELS.TOOLTIP_INVERTSELECTION);
89  jbInvertMask.setToolTipText(LABELS.TOOLTIP_INVERTMASK);
90  jbSpecifySelection.setToolTipText(LABELS.TOOLTIP_SPECIFYSELECTION);
91 
92  add(jtbRectangle);
93  add(jtbRoundRectangle);
94  add(jtbEllipse);
95  add(jtbOval);
96  add(jtbPolygon);
97  add(jtbFreehand);
98  add(jtbBrush);
99  add(jbSetBrushSize);
100  add(jtbLockMask);
101  add(jbCreateMask);
102  add(jbCreateSelection);
103  add(jbInvertSelection);
104  add(jbInvertMask);
105  add(jbSpecifySelection);
106  add(Box.createVerticalGlue());
107 
108  jtbRectangle.addActionListener(this);
109  jtbRoundRectangle.addActionListener(this);
110  jtbEllipse.addActionListener(this);
111  jtbOval.addActionListener(this);
112  jtbPolygon.addActionListener(this);
113  jtbFreehand.addActionListener(this);
114  jtbBrush.addActionListener(this);
115  jbSetBrushSize.addActionListener(this);
116  jtbLockMask.addActionListener(this);
117  jbCreateMask.addActionListener(this);
118  jbCreateSelection.addActionListener(this);
119  jbInvertSelection.addActionListener(this);
120  jbInvertMask.addActionListener(this);
121  jbSpecifySelection.addActionListener(this);
122  jtbRectangle.setSelected(true);
123 
124  pack();
125  setResizable(false);
126  }
127 
128  static void setTool(String tool) {
129  IJ.setTool(tool);
130  }
131 
132  private void uselectOthers(JToggleButton source) {
133  for (int i = 0; i < toolsButtons.length; i++) {
134  if (toolsButtons[i] != source) {
135  toolsButtons[i].setSelected(false);
136  }
137  }
138  }
139 
140  /*
141  * ij.gui.ToolBar.showBrushDialog() is protected.
142  * Using java reflection it becomes accessible.
143  */
144  void showBrushDialog() {
145  try {
146  Toolbar toolbar = Toolbar.getInstance();
147 
148  Class[] classes = {};
149  Method m = toolbar.getClass().getDeclaredMethod("showBrushDialog", classes);
150  m.setAccessible(true);
151 
152  Object[] arguments = {};
153  m.invoke(toolbar, arguments);
154  } catch (Exception e) {
155  IJ.error(e.getMessage());
156  }
157  }
158 
159  private void createMask() {
160  ImagePlus ip = IJ.getImage();
161 
162  if (ip != null) {
163  Roi roi = ip.getRoi();
164 
165  if (roi != null) {
166  if (mask == null || !mask.isVisible() || !jtbLockMask.isSelected()) {
167  ByteProcessor processor = new ByteProcessor(ip.getWidth(), ip.getHeight());
168  mask = new ImagePlus("Mask", processor);
169  }
170 
171  mask.getProcessor().setColor(Color.WHITE);
172  mask.getProcessor().fill(roi);
173  mask.updateAndDraw();
174  mask.show();
175  } else {
176  IJ.error("Area selection required.");
177  }
178  } else {
179  IJ.error("There are no images open.");
180  }
181  }
182 
183  void createSelection() {
184  ImagePlus ip = IJ.getImage();
185 
186  if (ip != null) {
187  if (ip.getType() == ImagePlus.GRAY8) {
188  IJ.run("Create Selection");
189  } else {
190  IJ.error("Image type is not valid: 8bit gray scale required.");
191  }
192  } else {
193  IJ.error("There are no images open.");
194  }
195  }
196 
197  void invertSelection() {
198  ImagePlus ip = IJ.getImage();
199 
200  if (ip != null) {
201  Roi roi = ip.getRoi();
202 
203  if (roi != null) {
204  IJ.run("Make Inverse");
205  } else {
206  IJ.error("Area selection required.");
207  }
208  } else {
209  IJ.error("There are no images open.");
210  }
211  }
212 
213  private void invertMask() {
214  if (mask != null) {
215  Roi roi = mask.getRoi(); // Stores current roi and...
216  mask.setRoi((Roi) null); // ...clears selection...
217  mask.getProcessor().invert();
218  mask.setRoi(roi); // ...to restore it later.
219  mask.updateAndDraw();
220  } else {
221  IJ.error("Mask has not been defined.");
222  }
223  }
224 
225  private void specifySelection() {
226  ImagePlus ip = IJ.getImage();
227 
228  if (ip != null) {
229  Roi roi = ip.getRoi();
230 
231  if (roi != null) {
232  IJ.run("Specify...");
233  } else {
234  IJ.error("Area selection required.");
235  }
236  } else {
237  IJ.error("There are no images open.");
238  }
239  }
240 
241  public void actionPerformed(ActionEvent ae) {
242  if (ae.getSource() == jtbRectangle) {
243  setTool("rectangle");
244  uselectOthers(jtbRectangle);
245  } else if (ae.getSource() == jtbRoundRectangle) {
246  setTool("roundrect");
247  uselectOthers(jtbRoundRectangle);
248  } else if (ae.getSource() == jtbEllipse) {
249  setTool("ellipse");
250  uselectOthers(jtbEllipse);
251  } else if (ae.getSource() == jtbOval) {
252  setTool("oval");
253  uselectOthers(jtbOval);
254  } else if (ae.getSource() == jtbPolygon) {
255  setTool("polygon");
256  uselectOthers(jtbPolygon);
257  } else if (ae.getSource() == jtbFreehand) {
258  setTool("freeroi");
259  uselectOthers(jtbFreehand);
260  } else if (ae.getSource() == jtbBrush) {
261  setTool("brush");
262  uselectOthers(jtbBrush);
263  } else if (ae.getSource() == jbSetBrushSize) {
264  showBrushDialog();
265  } else if (ae.getSource() == jtbLockMask) {
266  jtbLockMask.setIcon(jtbLockMask.isSelected() ? ICONS.MASK_LOCKED : ICONS.MASK_UNLOCKED);
267  jtbLockMask.setToolTipText(jtbLockMask.isSelected() ? LABELS.TOOLTIP_MASK_LOCKED : LABELS.TOOLTIP_MASK_UNLOCKED);
268  } else if (ae.getSource() == jbCreateMask) {
269  createMask();
270  } else if (ae.getSource() == jbCreateSelection) {
271  createSelection();
272  } else if (ae.getSource() == jbInvertSelection) {
273  invertSelection();
274  } else if (ae.getSource() == jbInvertMask) {
275  invertMask();
276  } else if (ae.getSource() == jbSpecifySelection) {
277  specifySelection();
278  }
279  }
280 
281  @Override
282  public void windowClosed(WindowEvent e) {
283  instance = null;
284  }
285 
286  public static MasksToolBar getInstance() {
287  if (instance == null) {
288  createInstance();
289  }
290 
291  return instance;
292  }
293 
294  private static void createInstance() {
295  instance = new MasksToolBar();
296  }
297 }
xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_ROUNDRECTANGLE
static final String TOOLTIP_ROUNDRECTANGLE
Definition: LABELS.java:15
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_RECTANGLE
static ImageIcon TOOL_RECTANGLE
Definition: ICONS.java:34
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_CREATEMASK
static final String TOOLTIP_CREATEMASK
Definition: LABELS.java:22
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_INVERTSELECTION
static final String TOOLTIP_INVERTSELECTION
Definition: LABELS.java:24
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_ELLIPSE
static ImageIcon TOOL_ELLIPSE
Definition: ICONS.java:36
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_MASK_UNLOCKED
static final String TOOLTIP_MASK_UNLOCKED
Definition: LABELS.java:28
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_POLYGON
static final String TOOLTIP_POLYGON
Definition: LABELS.java:18
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_INVERTSELECTION
static ImageIcon ACTION_INVERTSELECTION
Definition: ICONS.java:43
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_OVAL
static final String TOOLTIP_OVAL
Definition: LABELS.java:17
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_CREATESELECTION
static final String TOOLTIP_CREATESELECTION
Definition: LABELS.java:23
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_RECTANGLE
static final String TOOLTIP_RECTANGLE
Definition: LABELS.java:14
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xmipp.ij.plugins.maskstoolbar.ICONS.MASK_UNLOCKED
static ImageIcon MASK_UNLOCKED
Definition: ICONS.java:48
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_BRUSH
static final String TOOLTIP_BRUSH
Definition: LABELS.java:20
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_ELLIPSE
static final String TOOLTIP_ELLIPSE
Definition: LABELS.java:16
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_FREEHAND
static ImageIcon TOOL_FREEHAND
Definition: ICONS.java:39
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_CREATESELECTION
static ImageIcon ACTION_CREATESELECTION
Definition: ICONS.java:42
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_MASK_LOCKED
static final String TOOLTIP_MASK_LOCKED
Definition: LABELS.java:27
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_FREEHAND
static final String TOOLTIP_FREEHAND
Definition: LABELS.java:19
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_CREATEMASK
static ImageIcon ACTION_CREATEMASK
Definition: ICONS.java:41
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_INVERTMASK
static final String TOOLTIP_INVERTMASK
Definition: LABELS.java:25
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_SPECIFYSELECTION
static final String TOOLTIP_SPECIFYSELECTION
Definition: LABELS.java:26
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xmipp.ij.plugins.maskstoolbar.ICONS.MASK_LOCKED
static ImageIcon MASK_LOCKED
Definition: ICONS.java:47
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_INVERTMASK
static ImageIcon ACTION_INVERTMASK
Definition: ICONS.java:44
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xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_SETBRUSHSIZE
static final String TOOLTIP_SETBRUSHSIZE
Definition: LABELS.java:21
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_SPECIFYSELECTION
static ImageIcon ACTION_SPECIFYSELECTION
Definition: ICONS.java:45
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_POLYGON
static ImageIcon TOOL_POLYGON
Definition: ICONS.java:38
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_ROUNDRECTANGLE
static ImageIcon TOOL_ROUNDRECTANGLE
Definition: ICONS.java:35
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_BRUSHSIZE
static ImageIcon ACTION_BRUSHSIZE
Definition: ICONS.java:46
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Matrix.java File Reference
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class  xmipp.tomography.alignment.Matrix
 
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package  xmipp.tomography.alignment
 
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Xmipp -  v20.07 -
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Matrix.java
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1 package xmipp.tomography.alignment;
2 
3 
4 
5 public class Matrix {
6  private final int M; // number of rows
7  private final int N; // number of columns
8  private final double[][] data; // M-by-N array
9 
10  // create M-by-N matrix of 0's
11  public Matrix(int M, int N) {
12  this.M = M;
13  this.N = N;
14  data = new double[M][N];
15  }
16 
17  // create matrix based on 2d array
18  public Matrix(double[][] data) {
19  M = data.length;
20  N = data[0].length;
21  this.data = new double[M][N];
22  for (int i = 0; i < M; i++)
23  for (int j = 0; j < N; j++)
24  this.data[i][j] = data[i][j];
25  }
26 
27  // copy constructor
28  private Matrix(Matrix A) { this(A.data); }
29 
30  // create and return a random M-by-N matrix with values between 0 and 1
31  public static Matrix random(int M, int N) {
32  Matrix A = new Matrix(M, N);
33  for (int i = 0; i < M; i++)
34  for (int j = 0; j < N; j++)
35  A.data[i][j] = Math.random();
36  return A;
37  }
38 
39  // create and return the N-by-N identity matrix
40  public static Matrix identity(int N) {
41  Matrix I = new Matrix(N, N);
42  for (int i = 0; i < N; i++)
43  I.data[i][i] = 1;
44  return I;
45  }
46 
47  // swap rows i and j
48  private void swap(int i, int j) {
49  double[] temp = data[i];
50  data[i] = data[j];
51  data[j] = temp;
52  }
53 
54  // create and return the transpose of the invoking matrix
55  public Matrix transpose() {
56  Matrix A = new Matrix(N, M);
57  for (int i = 0; i < M; i++)
58  for (int j = 0; j < N; j++)
59  A.data[j][i] = this.data[i][j];
60  return A;
61  }
62 
63  // return C = A + B
64  public Matrix plus(Matrix B) {
65  Matrix A = this;
66  if (B.M != A.M || B.N != A.N) throw new RuntimeException("Illegal matrix dimensions.");
67  Matrix C = new Matrix(M, N);
68  for (int i = 0; i < M; i++)
69  for (int j = 0; j < N; j++)
70  C.data[i][j] = A.data[i][j] + B.data[i][j];
71  return C;
72  }
73 
74 
75  // return C = A - B
76  public Matrix minus(Matrix B) {
77  Matrix A = this;
78  if (B.M != A.M || B.N != A.N) throw new RuntimeException("Illegal matrix dimensions.");
79  Matrix C = new Matrix(M, N);
80  for (int i = 0; i < M; i++)
81  for (int j = 0; j < N; j++)
82  C.data[i][j] = A.data[i][j] - B.data[i][j];
83  return C;
84  }
85 
86  // does A = B exactly?
87  public boolean eq(Matrix B) {
88  Matrix A = this;
89  if (B.M != A.M || B.N != A.N) throw new RuntimeException("Illegal matrix dimensions.");
90  for (int i = 0; i < M; i++)
91  for (int j = 0; j < N; j++)
92  if (A.data[i][j] != B.data[i][j]) return false;
93  return true;
94  }
95 
96  // return C = A * B
97  public Matrix times(Matrix B) {
98  Matrix A = this;
99  if (A.N != B.M) throw new RuntimeException("Illegal matrix dimensions.");
100  Matrix C = new Matrix(A.M, B.N);
101  for (int i = 0; i < C.M; i++)
102  for (int j = 0; j < C.N; j++)
103  for (int k = 0; k < A.N; k++)
104  C.data[i][j] += (A.data[i][k] * B.data[k][j]);
105  return C;
106  }
107 
108 
109  // return x = A^-1 b, assuming A is square and has full rank
110  public Matrix solve(Matrix rhs) {
111  if (M != N || rhs.M != N || rhs.N != 1)
112  throw new RuntimeException("Illegal matrix dimensions.");
113 
114  // create copies of the data
115  Matrix A = new Matrix(this);
116  Matrix b = new Matrix(rhs);
117 
118  // Gaussian elimination with partial pivoting
119  for (int i = 0; i < N; i++) {
120 
121  // find pivot row and swap
122  int max = i;
123  for (int j = i + 1; j < N; j++)
124  if (Math.abs(A.data[j][i]) > Math.abs(A.data[max][i]))
125  max = j;
126  A.swap(i, max);
127  b.swap(i, max);
128 
129  // singular
130  if (A.data[i][i] == 0.0) throw new RuntimeException("Matrix is singular.");
131 
132  // pivot within b
133  for (int j = i + 1; j < N; j++)
134  b.data[j][0] -= b.data[i][0] * A.data[j][i] / A.data[i][i];
135 
136  // pivot within A
137  for (int j = i + 1; j < N; j++) {
138  double m = A.data[j][i] / A.data[i][i];
139  for (int k = i+1; k < N; k++) {
140  A.data[j][k] -= A.data[i][k] * m;
141  }
142  A.data[j][i] = 0.0;
143  }
144  }
145 
146  // back substitution
147  Matrix x = new Matrix(N, 1);
148  for (int j = N - 1; j >= 0; j--) {
149  double t = 0.0;
150  for (int k = j + 1; k < N; k++)
151  t += A.data[j][k] * x.data[k][0];
152  x.data[j][0] = (b.data[j][0] - t) / A.data[j][j];
153  }
154  return x;
155 
156  }
157 
158  // print matrix to standard output
159  public void show() {
160  for (int i = 0; i < M; i++) {
161  for (int j = 0; j < N; j++)
162  System.out.printf("%9.4f ", data[i][j]);
163  System.out.println();
164  }
165  }
166 
167 
168 
169  // test client
170  public static void main(String[] args) {
171  double[][] d = { { 1, 2, 3 }, { 4, 5, 6 }, { 9, 1, 3} };
172  Matrix D = new Matrix(d);
173  D.show();
174  System.out.println();
175 
176  Matrix A = Matrix.random(5, 5);
177  A.show();
178  System.out.println();
179 
180  A.swap(1, 2);
181  A.show();
182  System.out.println();
183 
184  Matrix B = A.transpose();
185  B.show();
186  System.out.println();
187 
188  Matrix C = Matrix.identity(5);
189  C.show();
190  System.out.println();
191 
192  A.plus(B).show();
193  System.out.println();
194 
195  B.times(A).show();
196  System.out.println();
197 
198  // shouldn't be equal since AB != BA in general
199  System.out.println(A.times(B).eq(B.times(A)));
200  System.out.println();
201 
202  Matrix b = Matrix.random(5, 1);
203  b.show();
204  System.out.println();
205 
206  Matrix x = A.solve(b);
207  x.show();
208  System.out.println();
209 
210  A.times(x).show();
211 
212  }
213 }
214 
215 
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xmipp.tomography.alignment.Matrix.main
static void main(String[] args)
Definition: Matrix.java:170
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xmipp.tomography.alignment.Matrix.solve
Matrix solve(Matrix rhs)
Definition: Matrix.java:110
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xmipp.tomography.alignment.Matrix.identity
static Matrix identity(int N)
Definition: Matrix.java:40
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xmipp.tomography.alignment.Matrix.random
static Matrix random(int M, int N)
Definition: Matrix.java:31
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.jni;
27 
28 import ij.IJ;
29 
30 import java.io.*;
31 import java.util.Arrays;
32 import java.util.HashMap;
33 import java.util.IllegalFormatCodePointException;
34 import java.util.logging.Level;
35 import java.util.logging.Logger;
36 
37 
41 public class MetaData {
42 
44  public static final int LABEL_NOTYPE = -1;
45  public static final int LABEL_INT = 0;
46  public static final int LABEL_BOOL = 1;
47  public static final int LABEL_DOUBLE = 2;
48  public static final int LABEL_STRING = 3;
49  public static final int LABEL_VECTOR_DOUBLE = 4;
50  public static final int LABEL_SIZET = 5;
51  public static final int LABEL_VECTOR_SIZET = 6;
52 
53  public static final String FILL_CONSTANT = "constant";
54  public static final String FILL_LINEAR = "linear";
55  public static final String FILL_RAND_UNIFORM = "random uniform";
56  public static final String FILL_RAND_GAUSSIAN = "random gaussian";
57 
58 
59 
60  //
61  // // Fields whose content is a path. They will be "fixed" conveniently.
62  // private final static int PATHS_FIELDS[] = {
63  // MDLabel.MDL_IMAGE1,
64  // MDLabel.MDL_IMAGE2,
65  // MDLabel.MDL_IMAGE3,
66  // MDLabel.MDL_IMAGE,
67  // MDLabel.MDL_PSD,
68  // MDLabel.MDL_CTF_MODEL
69  // };
70  //
71  // static {
72  // // Sorts it to use binary search later.
73  // // (It's executed just for the first time)
74  // Arrays.sort(PATHS_FIELDS);
75  // }
76 
77  public final static int GEOMETRY_LABELS[] = { MDLabel.MDL_FLIP,
78  MDLabel.MDL_ANGLE_PSI, MDLabel.MDL_SHIFT_X, MDLabel.MDL_SHIFT_Y};
79 
80  public final static int GEOMETRY_RELION_LABELS[] = { MDLabel.RLN_ORIENT_ORIGIN_X, MDLabel.RLN_ORIENT_ORIGIN_Y, MDLabel.RLN_ORIENT_PSI, MDLabel.RLN_ORIENT_FLIP};
81 
82  public final static int MICROGRAPH_BASIC_LABELS[] = {
83  MDLabel.MDL_MICROGRAPH, MDLabel.MDL_PSD, MDLabel.MDL_CTF_MODEL };
84 
85  public static final int MD_OVERWRITE = 0;
86  public static final int MD_APPEND = 1;
87  protected String filename;
88  // hold pointer to Image class in C++ space
89  private long peer;
90 
91  // keep labels for avoid read all the time
92  int[] activeLabels;
93 
94  protected HashMap<Long, EllipseCTF> ctfs = new HashMap<Long, EllipseCTF>();
95 
96 
97  static {
98  System.loadLibrary("XmippJNI");
99  // storeIds();
100  }
101 
103  public MetaData() {
104  //System.out.format("Java: Creating metadata\n");
105  //Exception ex = new Exception();
106  //ex.printStackTrace();
107  create();
108  }
109 
110 
111  // caching some ids
112  // private static native void storeIds();
113  // functions to create images
114  private native void create();
115 
116  // destructor
117  public synchronized native void destroy();
118 
119  // clear metadata
120  public native void clear();
121 
122  // reading
123  public native void read_(String filename);
124 
125  public final void read(String filename) {
126  this.filename = filename;
127  read_(filename);
128  activeLabels = getActiveLabels();
129  }
130 
131  public native int size();
132 
133  public native void setColumnFormat(boolean format);
134 
135  public native void write(String filename);
136 
137  public native void writeBlock(String filename);
138 
139  public native void print();
140 
141  public native boolean isColumnFormat();
142 
143  public native boolean containsLabel(int label);
144 
145  public native boolean removeLabel(int label);
146 
147  public boolean containsGeometryInfo(String type) {
148 
149 
150  if (type.equals("2D")) {
151  return containsGeometryInfo2D();
152 
153  } else {
154 
155  return containsGeometryInfo3D();
156  }
157 
158  }
159 
160 
161  private boolean containsGeometryInfo2D(){
162 
163  try {
164  boolean contains = containsLabel(GEOMETRY_LABELS) && !containsLabel(MDLabel.MDL_ANGLE_ROT);
165  if(!contains)
166  contains = containsLabel(GEOMETRY_RELION_LABELS) &&
167  ((!containsLabel(MDLabel.RLN_ORIENT_ROT)) || ( getColumnMax(MDLabel.RLN_ORIENT_ROT) == 0 )) ;
168  return contains;
169  } catch (Exception e) {
170  e.printStackTrace();
171  }
172  return false;
173 
174  }
175 
176  private boolean containsGeometryInfo3D(){
177 
178  try {
179  boolean contains = containsLabel(GEOMETRY_LABELS) && containsLabel(MDLabel.MDL_ANGLE_ROT);
180  if(!contains)
181  contains = containsLabel(GEOMETRY_RELION_LABELS) &&
182  ((containsLabel(MDLabel.RLN_ORIENT_ROT)) && ( getColumnMax(MDLabel.RLN_ORIENT_ROT) != 0 )) ;
183  return contains;
184  } catch (Exception e) {
185  e.printStackTrace();
186  }
187  return false;
188 
189  }
190 
191 
192 
193  public boolean containsLabel(int[] labels) {
194  try {
195  for (int i = 0; i < labels.length; i++)
196  if (containsLabel(labels[i]))
197  return true;
198 
199  } catch (Exception e) {
200  e.printStackTrace();
201  }
202  return false;
203  }
204 
205 
206  public boolean containsMicrographParticles() {
207  try {
208  int[] labels = new int[]{MDLabel.MDL_MICROGRAPH, MDLabel.MDL_XCOOR, MDLabel.MDL_YCOOR, MDLabel.MDL_ENABLED};
209  for (int i = 0; i < labels.length; i++)
210  if (!containsLabel(labels[i]))
211  return false;
212  } catch (Exception e) {
213  e.printStackTrace();
214  }
215  return true;
216  }
217 
218  public boolean containsMicrographsInfo() {
219  try {
220  // Should contain some micrographs labels
221  for (int i = 0; i < MICROGRAPH_BASIC_LABELS.length; i++)
222  if (!containsLabel(MICROGRAPH_BASIC_LABELS[i]))
223  return false;
224  } catch (Exception e) {
225  e.printStackTrace();
226  }
227  return true;
228  }
229 
230  public static boolean containsBlock(String file, String block)
231  {
232  try
233  {
234  return Arrays.asList(MetaData.getBlocksInMetaDataFile(file)).contains(block);
235  }
236  catch (Exception e)
237  {
238  throw new IllegalArgumentException(e);
239  }
240  }// function containsBlock
241 
242  public static native String label2Str(int label);
243 
244  public static native int str2Label(String labelName);
245 
247  public static String getLabelName(int label) {
248  try {
249  return label2Str(label);
250  } catch (Exception e) {
251  return null;
252  }
253  }
254 
255  public static native String[] getBlocksInMetaDataFile(String filename);
256 
257  public native int[] getActiveLabels();
258 
259  public static native int getLabelType(int label);
260 
261  public static Class getClassForType(int type) {
262  switch (type) {
263  case LABEL_INT:
264  return Integer.class;
265  case LABEL_BOOL:
266  return Boolean.class;
267  case LABEL_DOUBLE:
268  return Double.class;
269  case LABEL_SIZET:
270  return Long.class;
271  case LABEL_STRING:
272  case LABEL_VECTOR_DOUBLE:
273  case LABEL_VECTOR_SIZET:
274  return String.class;
275 
276  }
277  return null;
278  }
279 
280  public static Class getLabelClass(int label) {
281  int type = getLabelType(label);
282  return getClassForType(type);
283  }
284 
286  public static String getLabelTypeString(int labelType) {
287  switch (labelType) {
288  case LABEL_STRING:
289  return "STRING";
290  case LABEL_DOUBLE:
291  return "DOUBLE";
292  case LABEL_INT:
293  return "INT";
294  case LABEL_BOOL:
295  return "BOOL";
296  case LABEL_VECTOR_DOUBLE:
297  return "VECTOR(DOUBLE)";
298  case LABEL_SIZET:
299  return "SIZE_T";
300  case LABEL_VECTOR_SIZET:
301  return "VECTOR(SIZE_T)";
302  }
303  return "UNKNOWN";
304  }// function getLabelTypeString
305 
306  public static native String getLabelComment(int label);
307 
308  public static native boolean isTextFile(int label);
309 
310  public static native boolean isMetadata(int label);
311 
312  public static native boolean isCtfParam(int label);
313 
314  public static native boolean isImage(int label);
315 
316  public static native boolean isStack(int label);
317 
318  public static native boolean isMicrograph(int label);
319 
320  public static native boolean isPSD(int label);
321 
322  public native boolean isMetadataFile();
323 
324  public native void makeAbsPath(int label);
325 
326  // get values from metadata
327  public native int getValueInt(int label, long objId);
328 
329  public native long getValueLong(int label, long objId);
330 
331  public native double getValueDouble(int label, long objId);
332 
334  public native String getValueString(int label, long objId);
335 
336  public String getValueString(int label, long objId, boolean fixPaths) {
337  String value = getValueString(label, objId);
338 
339 // if(value == null)
340 // DEBUG.printFormat("label: %d, id: %d", label, objId);
341  // Try to fix paths.
342  if (fixPaths && filename != null && isPathField(label)) {
343  value = fixPath(value);
344  }
345 
346  return value;
347  }
348 
354  public String[] getRowValues(long objId) {
355  String[] values = new String[activeLabels.length];
356  for (int i = 0; i < activeLabels.length; ++i)
357  values[i] = getValueString(activeLabels[i], objId);
358  return values;
359  }
360 
361 // /** Return a new metadata containing the values of one row */
362 // public void getRow(long objId, MetaData mdRow){
363 // mdRow.importObjects(this, new long[]{objId});
364 // }
365 //
366 // public void setRow(MetaData mdRow, long objId){
367 // int[] labels = mdRow.getActiveLabels();
368 // String value;
369 // long rowId = mdRow.firstObject();
370 // for (int l : labels){
371 // value = mdRow.getValueString(l, rowId);
372 // setValueString(l, value, objId);
373 // }
374 // }
375 
376  public native void getRow(MDRow mdRow, long objId);
377 
378  public native void setRow(MDRow mdRow, long objId);
379 
384  public MetaData getMetaDataRow() {
385  MetaData md = null;
386  try {
387  md = new MetaData();
388  md.setColumnFormat(false);
389  int[] labels = getActiveLabels();
390  for (int l : labels)
391  md.addLabel(l);
392  md.addObject();
393  } catch (Exception e) {
394  e.printStackTrace();
395  }
396  return md;
397  }
398 
399  public static boolean isPathField(int label) {
400  return isTextFile(label) || isMetadata(label) || isCtfParam(label)
401  || isImage(label) || isStack(label) || isMicrograph(label)
402  || isPSD(label);
403  }
404 
405  // public static boolean isPathField(int label) {
406  // return Arrays.binarySearch(PATHS_FIELDS, label) >= 0;
407  // }
408  public String fixPath(String value) {
409  return Filename.findImagePath(value, getBaseDir(), true);
410  }
411 
412  public String fixPath(String value, String baseDir) {
413  return Filename.findImagePath(value, baseDir, false);
414  }
415 
416  public native boolean getValueBoolean(int label, long objId);
417 
418  public String getFilename() {
419  return filename != null ? Filename.getFilename(filename) : "";
420  }
421 
422  public String getBlock() {
423  return Filename.getPrefix(filename);
424  }
425 
426  public String getPath() {
427  return filename;
428  }
429 
430  public String getBaseDir() {
431  File f = new File(getFilename());
432  f = new File(f.toURI().normalize().getPath());
433 
434  return f.getParent();
435  }
436 
437  public native double[] getStatistics(boolean applyGeo, int label);
438 
439  public native double[] getColumnValues(int label);
440 
441  // set functions connection with MetaData class in C++
442  public boolean setEnabled(boolean value, long objId) {
443 
444  return setValueInt(MDLabel.MDL_ENABLED, value ? 1 : -1, objId);
445 
446  }
447 
448  public boolean getEnabled(long objId) {
449  if(!containsLabel(MDLabel.MDL_ENABLED))
450  return true;
451  return getValueInt(MDLabel.MDL_ENABLED, objId) > -1;
452  }
453 
454  public native boolean setValueInt(int label, int value, long objId);
455 
456  public native boolean setValueLong(int label, long value, long objId);
457 
458  public native boolean setValueDouble(int label, double value, long objId);
459 
460  //NOTE: if value contains spaces it should be quoted, otherwise string will be cut!!!
461  public native boolean setValueString(int label, String value, long objId);
462 
463  public native boolean setValueBoolean(int label, boolean value, long objId);
464 
466  public native long[] findObjects();
467 
471  public native void sort(int sortLabel, boolean ascending);
472 
474  public native void importObjects(MetaData from, long ids[]);
475 
477  public native long firstObject();
478 
480  public native long addObject();
481 
483  public native boolean removeObject(long objId);
484 
486  public native void removeDisabled();
487 
489  public native void addLabel(int label);
490 
492  public native void renameColumn(int oldLabel, int newLabel);
493 
495  public native void getStatsImages(ImageGeneric imageAvg,
496  ImageGeneric imageStd, boolean applyGeo, boolean wrap, int label);
497 
498  public native void writeMdToStack(String filename, boolean applyGeo, boolean wrap, int label);
499 
500 
501  public native void getPCAbasis(ImageGeneric basis, int label);
502 
503  public native void computeFourierStatistics(MetaData mdIn, int label);
504 
509  public native void unionAll(MetaData mdIn);
510 
517  public native void fillConstant(int label, String value);
518 
519 
520 
533  public native void fillRandom(int label, String mode, double op1, double op2);
534 
536  public native void fillLinear(int label, double start, double step);
537 
539  public native void enableDebug();
540 
541  /*********** Non-native functions ********************/
542 
544  public MetaData(String filename) {
545  //DEBUG.printFormat("Java: Creating metadata from filename: %s\n", filename);
546  //DEBUG.printStackTrace();
547 
548  create();
549  read(filename);
550  }
551 
556  @Override
557  protected void finalize() throws Throwable {
558  super.finalize();
559  destroy();
560  }
561 
568  public native void readPlain(String file, String columns);
569 
570 
571 
572 
573 
578  public native void operate(String operateStr);
579 
583  public native double getColumnMin(int column);
584 
585  public native double getColumnMax(int column);
586 
587 
588 
589 
590 
591  public boolean isCTFMd() {
592  try {
593  return containsLabel(MDLabel.MDL_PSD_ENHANCED) && containsLabel(MDLabel.MDL_PSD) && containsLabel(MDLabel.MDL_CTF_MODEL);
594  } catch (Exception e) {
595  e.printStackTrace();
596  }
597  return false;
598  }
599 
600  public String getCTFFile(long id)
601  {
602  return getValueString(MDLabel.MDL_CTF_MODEL, id);
603  }
604 
605  public EllipseCTF getEllipseCTF(long id) {
606  return getEllipseCTF(id, -1);
607  }
608 
609  public EllipseCTF getEllipseCTF(long id, int D) {
610  MetaData md = new MetaData(getCTFFile(id));
611  try {
612  double Q0, Cs, Ts, kV, downsampleFactor, defU, defV, defAngle;
613 
614  Q0 = md.getValueDouble(MDLabel.MDL_CTF_Q0, id);
615  Cs = md.getValueDouble(MDLabel.MDL_CTF_CS, id);
616  downsampleFactor = md.getValueDouble(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED, id);
617  Ts = md.getValueDouble(MDLabel.MDL_CTF_SAMPLING_RATE, id) * downsampleFactor;
618  kV = md.getValueDouble(MDLabel.MDL_CTF_VOLTAGE, id);
619 
620  defU = md.getValueDouble(MDLabel.MDL_CTF_DEFOCUSU, id);
621  defV = md.getValueDouble(MDLabel.MDL_CTF_DEFOCUSV, id);
622  defAngle = md.getValueDouble(MDLabel.MDL_CTF_DEFOCUS_ANGLE, id);
623 
624  return new EllipseCTF(id, Q0, Cs, downsampleFactor, Ts, kV, defU, defV, defAngle, D);
625  } catch (Exception ex) {
626  IJ.error(ex.getMessage());
627  throw new IllegalArgumentException(ex);
628  }
629 
630  }
631 
632 
633  public String getPSDFile(long id) {
634  return getValueString(MDLabel.MDL_PSD, id);
635  }
636 
637  public String getPSDEnhanced(long id) {
638  return getValueString(MDLabel.MDL_PSD_ENHANCED, id);
639  }
640 
641  public CTFDescription getCTFDescription(long id)
642  {
643  try {
644  return new CTFDescription(getCTFFile(id));
645  } catch (Exception ex) {
646  Logger.getLogger(MetaData.class.getName()).log(Level.SEVERE, null, ex);
647  throw new IllegalArgumentException(ex);
648  }
649  }
650 
651 
652 
653  public static boolean isPlainPos(String file)
654  {
655  try
656  {
657  InputStream in = new FileInputStream(file);
658  Reader reader = new InputStreamReader(in);
659  // buffer for efficiency
660  BufferedReader buffer = new BufferedReader(reader);
661  String line = buffer.readLine();//dismiss first line
662  if(line == null)
663  return true;//Empty file
664  int count = 0;//small statistics to detect if pos file
665  while ((line = buffer.readLine()) != null) {
666  for(char c: line.toCharArray())
667  if(!(Character.isDigit(c) || Character.isSpaceChar(c)))
668  return false;
669 
670 
671  if(count == 100)
672  break;
673  count ++;
674  }
675  } catch (IOException ex) {
676  return false;
677  }
678  return true;
679  }
680 
681 
682  public boolean hasRecalculateCTF() {
683  return !ctfs.isEmpty();
684  }
685 
686  public void removeCTF(long id) {
687  ctfs.remove(id);
688  }
689 
690  public boolean containsCTF(long id) {
691  return ctfs.containsKey(id);
692  }
693 
694  public void putCTF(long id, EllipseCTF ellipseCTF) {
695  ctfs.put(id, ellipseCTF);
696  }
697 
698  private long getFileTimeStamp(String filename){
699  File file = new File(filename);
700  return getFileTimeStamp(file);
701  }
702  private long getFileTimeStamp(File file){
703  return file.lastModified();
704  }
705 
706  public void writeWithException(String xmippFilename) throws IOException{
707 
708  String OSFilename = Filename.getFilename(xmippFilename);
709 
710  File fileObj = new File(OSFilename);
711 
712  boolean exist = fileObj.exists();
713  long fileTs = 0;
714  if (exist) {
715 
716  fileTs = getFileTimeStamp(fileObj);
717 
718  if (!fileObj.canWrite()){
719  throw new IOException("Can't write on " + OSFilename + ". Please check you have permissions to write.");
720  }
721  }
722 
723  this.write(xmippFilename);
724 
725  if (!exist && !fileObj.exists()) {
726 
727  throw new IOException("File: " + OSFilename + " couldn't be created. Check you have permission on the folder.");
728 
729  } else if (fileTs == getFileTimeStamp(fileObj)){
730 
731  throw new IOException("File: " + OSFilename + " couldn't be written. Something went wrong.");
732  }
733 
734 
735  }
736 
737 
738 
739 
740 }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
-
xmipp.jni.MetaData.getValueLong
native long getValueLong(int label, long objId)
-
xmipp.jni.MetaData.LABEL_VECTOR_DOUBLE
static final int LABEL_VECTOR_DOUBLE
Definition: MetaData.java:49
-
xmipp.jni.MetaData.MetaData
MetaData(String filename)
Definition: MetaData.java:544
-
xmipp.jni.MDLabel.MDL_ANGLE_PSI
static final int MDL_ANGLE_PSI
Special label to be used when gathering MDs in MpiMetadataPrograms.
Definition: MDLabel.java:8
-
xmipp.jni.MetaData.isMicrograph
static native boolean isMicrograph(int label)
-
xmipp.jni.MetaData.enableDebug
native void enableDebug()
-
xmipp.jni.MetaData.addObject
native long addObject()
-
xmipp.jni.MetaData.MICROGRAPH_BASIC_LABELS
static final int MICROGRAPH_BASIC_LABELS[]
Definition: MetaData.java:82
-
xmipp.jni.MetaData.setValueString
native boolean setValueString(int label, String value, long objId)
-
xmipp.jni.MetaData.LABEL_DOUBLE
static final int LABEL_DOUBLE
Definition: MetaData.java:47
-
xmipp.jni.MetaData.isCtfParam
static native boolean isCtfParam(int label)
-
xmipp.jni.MetaData.getPCAbasis
native void getPCAbasis(ImageGeneric basis, int label)
-
xmipp.jni.MetaData.LABEL_STRING
static final int LABEL_STRING
Definition: MetaData.java:48
-
xmipp.jni.MetaData.containsMicrographsInfo
boolean containsMicrographsInfo()
Definition: MetaData.java:218
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xmipp.jni.MetaData.isMetadataFile
native boolean isMetadataFile()
-
xmipp.jni.MetaData.LABEL_BOOL
static final int LABEL_BOOL
Definition: MetaData.java:46
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xmipp.jni.MetaData.write
native void write(String filename)
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xmipp.jni.MetaData.fillConstant
native void fillConstant(int label, String value)
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xmipp.jni.MetaData.getEllipseCTF
EllipseCTF getEllipseCTF(long id)
Definition: MetaData.java:605
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xmipp.jni.MetaData.clear
native void clear()
-
xmipp.jni.MetaData.LABEL_SIZET
static final int LABEL_SIZET
Definition: MetaData.java:50
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xmipp.jni.MetaData.getPSDFile
String getPSDFile(long id)
Definition: MetaData.java:633
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUSU
static final int MDL_CTF_DEFOCUSU
< average defocus (Angtroms)
Definition: MDLabel.java:86
-
xmipp.jni.MetaData.MD_OVERWRITE
static final int MD_OVERWRITE
Definition: MetaData.java:85
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xmipp.jni.MetaData.MD_APPEND
static final int MD_APPEND
Definition: MetaData.java:86
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xmipp.jni.MetaData.makeAbsPath
native void makeAbsPath(int label)
- -
xmipp.jni.MetaData.getColumnValues
native double [] getColumnValues(int label)
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xmipp.jni.MetaData.setColumnFormat
native void setColumnFormat(boolean format)
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xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MDLabel.MDL_SHIFT_Y
static final int MDL_SHIFT_Y
< difference in Shift along X axis (double)
Definition: MDLabel.java:367
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xmipp.jni.MetaData.writeBlock
native void writeBlock(String filename)
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xmipp.jni.MetaData.read
final void read(String filename)
Definition: MetaData.java:125
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xmipp.jni.MDLabel.RLN_ORIENT_ROT
static final int RLN_ORIENT_ROT
Definition: MDLabel.java:668
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xmipp.jni.MetaData.getBlocksInMetaDataFile
static native String [] getBlocksInMetaDataFile(String filename)
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xmipp.jni.MetaData.getLabelName
static String getLabelName(int label)
Definition: MetaData.java:247
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xmipp.jni.MDLabel.MDL_ANGLE_ROT
static final int MDL_ANGLE_ROT
< difference between psi angles (double,degrees)
Definition: MDLabel.java:12
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xmipp.jni.MetaData.LABEL_VECTOR_SIZET
static final int LABEL_VECTOR_SIZET
Definition: MetaData.java:51
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xmipp.jni.MetaData.getRow
native void getRow(MDRow mdRow, long objId)
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xmipp.jni.MetaData.print
native void print()
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xmipp.jni.MetaData.sort
native void sort(int sortLabel, boolean ascending)
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xmipp.jni.MetaData.removeDisabled
native void removeDisabled()
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xmipp.jni.MetaData.setValueBoolean
native boolean setValueBoolean(int label, boolean value, long objId)
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xmipp.jni.MDLabel.MDL_CTF_MODEL
static final int MDL_CTF_MODEL
< Parameters file for the CTF Model (std::string)
Definition: MDLabel.java:80
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xmipp.jni.MetaData.isMetadata
static native boolean isMetadata(int label)
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xmipp.jni.MetaData.isCTFMd
boolean isCTFMd()
Definition: MetaData.java:591
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xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_X
static final int RLN_ORIENT_ORIGIN_X
Definition: MDLabel.java:662
- - -
xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Y
static final int RLN_ORIENT_ORIGIN_Y
Definition: MDLabel.java:664
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xmipp.jni.MetaData.GEOMETRY_RELION_LABELS
static final int GEOMETRY_RELION_LABELS[]
Definition: MetaData.java:80
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MetaData.containsBlock
static boolean containsBlock(String file, String block)
Definition: MetaData.java:230
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xmipp.jni.MetaData.unionAll
native void unionAll(MetaData mdIn)
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xmipp.jni.MetaData.getColumnMin
native double getColumnMin(int column)
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xmipp.jni.MetaData.str2Label
static native int str2Label(String labelName)
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.jni.MetaData.size
native int size()
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xmipp.jni.MetaData.addLabel
native void addLabel(int label)
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xmipp.jni.MetaData.getLabelClass
static Class getLabelClass(int label)
Definition: MetaData.java:280
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xmipp.jni.MetaData.fillLinear
native void fillLinear(int label, double start, double step)
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xmipp.jni.MDLabel.MDL_PSD_ENHANCED
static final int MDL_PSD_ENHANCED
< A Power Spectrum Density file name (std::string)
Definition: MDLabel.java:309
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xmipp.jni.MetaData.getActiveLabels
native int [] getActiveLabels()
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xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
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xmipp.jni.MetaData.getClassForType
static Class getClassForType(int type)
Definition: MetaData.java:261
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xmipp.jni.MDLabel.MDL_CTF_DEFOCUSV
static final int MDL_CTF_DEFOCUSV
< Defocus U (Angstroms)
Definition: MDLabel.java:87
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xmipp.jni.Filename.findImagePath
static String findImagePath(String filename, String mdFilename, boolean shouldExist)
Definition: Filename.java:225
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xmipp.jni.MetaData.removeLabel
native boolean removeLabel(int label)
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.jni.MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED
static final int MDL_CTF_DOWNSAMPLE_PERFORMED
< Iceness of the micrograph
Definition: MDLabel.java:155
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xmipp.jni.MetaData.LABEL_INT
static final int LABEL_INT
Definition: MetaData.java:45
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xmipp.jni.MetaData.getRowValues
String [] getRowValues(long objId)
Definition: MetaData.java:354
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.jni.MetaData.readPlain
native void readPlain(String file, String columns)
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xmipp.jni.MetaData.containsLabel
boolean containsLabel(int[] labels)
Definition: MetaData.java:193
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xmipp.jni.MetaData.label2Str
static native String label2Str(int label)
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xmipp.jni.MetaData.writeWithException
void writeWithException(String xmippFilename)
Definition: MetaData.java:706
-
xmipp.jni.MDLabel.MDL_CTF_VOLTAGE
static final int MDL_CTF_VOLTAGE
< Sampling rate in Z direction
Definition: MDLabel.java:84
-
xmipp.jni.MetaData.writeMdToStack
native void writeMdToStack(String filename, boolean applyGeo, boolean wrap, int label)
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xmipp.jni.MetaData.FILL_LINEAR
static final String FILL_LINEAR
Definition: MetaData.java:54
-
xmipp.jni.MetaData.getPSDEnhanced
String getPSDEnhanced(long id)
Definition: MetaData.java:637
-
xmipp.jni.MetaData.GEOMETRY_LABELS
static final int GEOMETRY_LABELS[]
Definition: MetaData.java:77
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xmipp.jni.MetaData.setValueDouble
native boolean setValueDouble(int label, double value, long objId)
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xmipp.jni.MetaData.isPlainPos
static boolean isPlainPos(String file)
Definition: MetaData.java:653
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.jni.MetaData.firstObject
native long firstObject()
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xmipp.jni.MetaData.ctfs
HashMap< Long, EllipseCTF > ctfs
Definition: MetaData.java:94
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xmipp.jni.MetaData.setRow
native void setRow(MDRow mdRow, long objId)
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xmipp.jni.MDLabel.MDL_SHIFT_X
static final int MDL_SHIFT_X
< A collection of micrographs, e.g. a tilt serie (std::string)
Definition: MDLabel.java:363
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xmipp.jni.MetaData.getStatsImages
native void getStatsImages(ImageGeneric imageAvg, ImageGeneric imageStd, boolean applyGeo, boolean wrap, int label)
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xmipp.jni.MDLabel.MDL_PSD
static final int MDL_PSD
Definition: MDLabel.java:308
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xmipp.jni.MetaData.putCTF
void putCTF(long id, EllipseCTF ellipseCTF)
Definition: MetaData.java:694
-
xmipp.jni.MetaData.fixPath
String fixPath(String value)
Definition: MetaData.java:408
-
xmipp.jni.MetaData.getCTFFile
String getCTFFile(long id)
Definition: MetaData.java:600
-
xmipp.jni.MetaData.getFilename
String getFilename()
Definition: MetaData.java:418
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xmipp.jni.MetaData.setEnabled
boolean setEnabled(boolean value, long objId)
Definition: MetaData.java:442
-
xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_ANGLE
static final int MDL_CTF_DEFOCUS_ANGLE
< Defocus = A*x+B*y+C
Definition: MDLabel.java:102
-
xmipp.jni.MetaData.getEnabled
boolean getEnabled(long objId)
Definition: MetaData.java:448
-
xmipp.jni.MDLabel.MDL_CTF_CS
static final int MDL_CTF_CS
< Defocus angle (degrees)
Definition: MDLabel.java:103
-
xmipp.jni.MetaData.getLabelComment
static native String getLabelComment(int label)
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xmipp.jni.MetaData.hasRecalculateCTF
boolean hasRecalculateCTF()
Definition: MetaData.java:682
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xmipp.jni.MetaData.removeObject
native boolean removeObject(long objId)
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xmipp.jni.MetaData.getEllipseCTF
EllipseCTF getEllipseCTF(long id, int D)
Definition: MetaData.java:609
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xmipp.jni.MetaData.read_
native void read_(String filename)
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xmipp.jni.MetaData.isPSD
static native boolean isPSD(int label)
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xmipp.jni.MetaData.FILL_RAND_GAUSSIAN
static final String FILL_RAND_GAUSSIAN
Definition: MetaData.java:56
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xmipp.jni.Filename.getFilename
static String getFilename(String filename)
Definition: Filename.java:302
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xmipp.jni.MetaData.getColumnMax
native double getColumnMax(int column)
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xmipp.jni.MDLabel.MDL_FLIP
static final int MDL_FLIP
Definition: MDLabel.java:180
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xmipp.jni.MetaData.operate
native void operate(String operateStr)
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xmipp.jni.MetaData.setValueLong
native boolean setValueLong(int label, long value, long objId)
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xmipp.jni.MDLabel.MDL_CTF_Q0
static final int MDL_CTF_Q0
< Transversal displacemente
Definition: MDLabel.java:113
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xmipp.jni.MetaData.isStack
static native boolean isStack(int label)
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xmipp.jni.MetaData.getLabelTypeString
static String getLabelTypeString(int labelType)
Definition: MetaData.java:286
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xmipp.jni.MDLabel.RLN_ORIENT_PSI
static final int RLN_ORIENT_PSI
Definition: MDLabel.java:672
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xmipp.jni.MetaData.isTextFile
static native boolean isTextFile(int label)
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xmipp.jni.MetaData.LABEL_NOTYPE
static final int LABEL_NOTYPE
Definition: MetaData.java:44
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xmipp.jni.MetaData.getStatistics
native double [] getStatistics(boolean applyGeo, int label)
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xmipp.jni.MetaData.isImage
static native boolean isImage(int label)
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xmipp.jni.MetaData.removeCTF
void removeCTF(long id)
Definition: MetaData.java:686
-
xmipp.jni.MetaData.containsCTF
boolean containsCTF(long id)
Definition: MetaData.java:690
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xmipp.jni.MetaData.importObjects
native void importObjects(MetaData from, long ids[])
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xmipp.jni.Filename.getPrefix
static String getPrefix(String filename)
Definition: Filename.java:339
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xmipp.jni.MetaData.fixPath
String fixPath(String value, String baseDir)
Definition: MetaData.java:412
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xmipp.jni.MetaData.getLabelType
static native int getLabelType(int label)
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xmipp.jni.MetaData.getValueString
String getValueString(int label, long objId, boolean fixPaths)
Definition: MetaData.java:336
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xmipp.jni.MetaData.computeFourierStatistics
native void computeFourierStatistics(MetaData mdIn, int label)
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xmipp.jni.MetaData.getBaseDir
String getBaseDir()
Definition: MetaData.java:430
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xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.jni.MetaData.isColumnFormat
native boolean isColumnFormat()
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xmipp.jni.MetaData.renameColumn
native void renameColumn(int oldLabel, int newLabel)
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xmipp.jni.MetaData.getValueBoolean
native boolean getValueBoolean(int label, long objId)
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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xmipp.jni.MetaData.FILL_CONSTANT
static final String FILL_CONSTANT
Definition: MetaData.java:53
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xmipp.jni.MetaData.getMetaDataRow
MetaData getMetaDataRow()
Definition: MetaData.java:384
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xmipp.jni.MDLabel.MDL_CTF_SAMPLING_RATE
static final int MDL_CTF_SAMPLING_RATE
< Name for another CTF model (std::string)
Definition: MDLabel.java:82
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xmipp.jni.MetaData.FILL_RAND_UNIFORM
static final String FILL_RAND_UNIFORM
Definition: MetaData.java:55
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xmipp.jni.MetaData.containsGeometryInfo
boolean containsGeometryInfo(String type)
Definition: MetaData.java:147
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xmipp.jni.MDLabel.RLN_ORIENT_FLIP
static final int RLN_ORIENT_FLIP
Definition: MDLabel.java:660
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xmipp.jni.MetaData.containsMicrographParticles
boolean containsMicrographParticles()
Definition: MetaData.java:206
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xmipp.jni.MetaData.getCTFDescription
CTFDescription getCTFDescription(long id)
Definition: MetaData.java:641
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xmipp.jni.MetaData.isPathField
static boolean isPathField(int label)
Definition: MetaData.java:399
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xmipp.jni.MetaData.fillRandom
native void fillRandom(int label, String mode, double op1, double op2)
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MetadataGalleryTableModel.java File Reference
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package  xmipp.viewer.models
 
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MetadataGalleryTableModel.java
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.models;
27 
28 import ij.ImagePlus;
29 
30 import java.util.ArrayList;
31 import java.util.List;
32 
33 import xmipp.ij.commons.ImagePlusLoader;
34 import xmipp.ij.commons.XmippImageConverter;
35 import xmipp.jni.Filename;
36 import xmipp.jni.ImageGeneric;
37 import xmipp.utils.DEBUG;
38 import xmipp.utils.XmippMessage;
39 import xmipp.utils.XmippPopupMenuCreator;
40 import xmipp.viewer.ImageDimension;
41 import xmipp.viewer.windows.ImagesWindowFactory;
42 
43 //Gallery mode!!!!!!!!!!
44 public class MetadataGalleryTableModel extends ImageGalleryTableModel
45 {
46 
47  private static final long serialVersionUID = 1L;
48  // Label to be rendered
49  protected ColumnInfo renderLabel;
50  // Also store the visible ones to fast access
51  public ArrayList<ColumnInfo> visibleLabels;
52 
53  public MetadataGalleryTableModel(GalleryData data, boolean[] selection) throws Exception
54  {
55  super(data, selection);
56  data.normalize = false;
57  }
58 
60  public void updateColumnInfo(List<ColumnInfo> newInfo)
61  {
62  int n = newInfo.size();
63  boolean changed = false;
64  data.renderImages = false;
65  data.ciFirstRender = null;
66 
67  for (int i = 0; i < n; ++i)
68  for (int j = 0; j < n; ++j)
69  {
70  ColumnInfo ci1 = data.labels.get(i);
71  ColumnInfo ci2 = newInfo.get(j);
72  if (ci1.label == ci2.label)
73  {
74  if (ci1.updateInfo(ci2))
75  changed = true;
76 
77  if (ci1.visible)
78  {
79  visibleLabels.add(ci1);
80  if (data.ciFirstRender == null && ci1.allowRender)
81  data.ciFirstRender = ci1;
82  }
83  if (ci1.render)
84  data.renderImages = true;
85  if (i != j)
86  changed = true;
87  }
88  }
89 
90  if (changed)
91  {
92  data.labels = newInfo;
93  visibleLabels.clear();
94  for (ColumnInfo ci : data.labels)
95  if (ci.visible)
96  visibleLabels.add(ci);
97  calculateCellSize();
98  cols = visibleLabels.size();
99  // fireTableDataChanged();
100  fireTableStructureChanged();
101  }
102  }
103 
104  public ImagePlus getImage(long id, String imagepath, ColumnInfo renderLabel)
105  {
106  ImagePlus imp = null;
107  if (imagepath != null && Filename.exists(imagepath))
108  {
109  try
110  {
111  ImagePlusLoader loader;
112  if(Filename.isStackOrVolume(imagepath))
113  loader = new ImagePlusLoader(imagepath, null, null, data.useGeo, data.wrap, data.inverty, ImageGeneric.MID_SLICE);
114  else
115  loader = new ImagePlusLoader(imagepath, data.useGeo, data.wrap, data.inverty);
116  loader.setGeometry(data.getGeometry(id, renderLabel));
117  loader.setInvertY(data.inverty);
118  loader.setDimension(thumb_width, thumb_height);
119  return loader.getImagePlus();
120  }
121  catch (Exception ex)
122  {
123  imp = null;
124  }
125  }
126  return imp;
127  }
128 
129 
130  protected void openXmippImageWindow(int index, ColumnInfo ci)
131  {
132  String file = getImageFilename(index, ci.label);
133  if(file == null)
134  throw new IllegalArgumentException(XmippMessage.getPathNotExistsMsg(data.getValueFromLabel(index, ci.label)));
135  ImagePlusLoader loader = new ImagePlusLoader(file, data.useGeo, data.wrap, data.inverty);
136  if(data.containsGeometryInfo())
137  loader.setGeometry(data.getGeometry(data.ids[index], ci));
138  if (data.getNormalized())
139  loader.setNormalize(normalize_min, normalize_max);
140  ImagesWindowFactory.openXmippImageWindow(loader, data.parameters);
141  }
142 
143 
144  // Load initial dimensions
145  @Override
146  protected ImageDimension loadDimension() throws Exception
147  {
148  // Set information about columns
149  visibleLabels = new ArrayList<ColumnInfo>();
150  // data.globalRender = false;
151 
152  for (ColumnInfo ci : data.labels)
153  {
154  if (ci.visible)
155  visibleLabels.add(ci);
156  // if (ci.render)
157  // data.globalRender = true;
158  }
159  ImageDimension dim = null;
160  int width = 50, height = 50;
161  if (data.hasRenderLabel() && data.renderImages)
162  {
163  renderLabel = data.ciFirstRender;
164  // if (renderLabels) {
165  String imageFn = data.getSampleImage(renderLabel);
166  if(imageFn != null)
167  {
168  ImagePlusLoader loader;
169  if(Filename.isStackOrVolume(imageFn))
170  loader = new ImagePlusLoader(imageFn, null, null, false, false, false, ImageGeneric.MID_SLICE);
171  else
172  loader = new ImagePlusLoader(imageFn);
173  ImagePlus image = loader.getImagePlus();
174  if(image != null && image.getWidth() > 0)
175  {
176  width = image.getWidth();
177  height = image.getHeight();
178  dim = new ImageDimension(width, height);
179  }
180  }
181 
182  }
183 
184  if (dim == null)
185  dim = new ImageDimension(width);
186  // Zdim will always be used as number of elements to display
187  dim.setZDim(data.ids.length);
188  n = dim.getZDim();
189  image_width = dim.getXDim();
190  image_height = dim.getYDim();
191  return dim;
192  }
193 
194  @Override
195  protected ImageItem createItem(int index, String key, ColumnInfo ci) throws Exception
196  {
197  return createImageItem(index, ci);
198  }
199 
200 
201 
202  public String getLabel(int row, int col)
203  {
204  try
205  {
206  int index = getIndex(row, col);
207  long objId = data.ids[index];
208  return data.getDisplayLabel(objId);
209 
210  }
211  catch (Exception e)
212  {
213  e.printStackTrace();
214  }
215  return null;
216  }
217 
221  protected ImageItem createImageItem(int index, ColumnInfo renderLabel) throws Exception
222  {
223  String imageFn = getImageFilename(index, renderLabel.label);
224  long objId = data.ids[index];
225  ImagePlus imp = getImage(objId, imageFn, renderLabel);
226  ImageItem item = new ImageItem(index, imp);
227  return item;
228  }
229 
230  @Override
231  public String getItemKey(int index) throws Exception
232  {
233  return getItemKey(index, renderLabel.label);
234 
235  }
236 
237  @Override
238  public String getTitle()
239  {
240  String title = "Metadata: " + (data.getFileName() != null ? Filename.getBaseName(data.getFileName()) : "");
241  if (n > 1)
242  title += String.format(" %d items", n);
243  if (data.hasRenderLabel())
244  title += String.format(" (%d x %d)", image_width, image_height);
245 
246  return title;
247  }// function getTitle
248 
249  public String getImageFilename(int index, int label)
250  {
251  try
252  {
253  String file = data.getValueFromLabel(index, label);
254  String mddir = data.md.getBaseDir();
255  file = Filename.findImagePath(file, mddir, true);
256  return file;
257  }
258  catch (Exception e)
259  {
260  e.printStackTrace();
261  }
262  return null;
263  }// function getImageFilename
264 
265  // @Override
266  // public String getImageFilenameAt(int row, int col) {
267  // return data.isImageFile(renderLabel) ? data.getValueFromCol(row,
268  // renderLabel) : null;
269  // }
270 
271  @Override
272  public boolean handleDoubleClick(int row, int col)
273  {
274  try
275  {
276  if (data.isImageFile(renderLabel))
277  {
278  int index = getIndex(row, col);
279  openXmippImageWindow(index, getColumn(row, col));
280  return true;
281  }
282  }
283  catch (Exception e)
284  {
285  e.printStackTrace();
286  }
287  return false;
288  }// function handleDoubleClick
289 
290 
291  @Override
292  protected double[] getMinAndMax()
293  {
294  try
295  {
296  return data.md.getStatistics(false, data.ciFirstRender.label);
297  }
298  catch (Exception ex)
299  {
300  DEBUG.printException(ex);
301  }
302  return null;
303  }// function getMinAndMax
304 
306  public void setUseGeometry(boolean geo, boolean wrap)
307  {
308  if (!geo)
309  wrap = false;
310  boolean changed = data.useGeo != geo || data.wrap != wrap;
311  data.useGeo = geo;
312  data.wrap = wrap;
313  if (changed)
314  fireTableDataChanged();
315  }// function setUseGeometry
316 
317  @Override
318  public ImagePlusLoader getImageLoader()
319  {
320  try
321  {
322  ImagePlus imp = XmippImageConverter.readMetadataToImagePlus(renderLabel.label, data.md, data.useGeo, data.wrap, data.inverty);
323  return new ImagePlusLoader(imp, data.inverty);
324  }
325  catch (Exception e)
326  {
327  e.printStackTrace();
328  }
329  return null;
330  }// function getImageLoader
331 
332  @Override
333  public boolean handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)
334  {
335  return true;
336  }// function handleRightClick
337 
338  // Extension of the ImagePlusLoader, read an image from a Metadata row
339 
340  @Override
341  public boolean showLabels() {
342  return true;
343  }
344 
345 
346 
347 
348 
349 }
xmipp.viewer.models.MetadataGalleryTableModel.MetadataGalleryTableModel
MetadataGalleryTableModel(GalleryData data, boolean[] selection)
Definition: MetadataGalleryTableModel.java:53
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xmipp.viewer.models.GalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: GalleryData.java:1779
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xmipp.ij.commons.XmippImageConverter.readMetadataToImagePlus
static ImagePlus readMetadataToImagePlus(int label, MetaData md, boolean useGeo, boolean wrap, boolean inverty)
Definition: XmippImageConverter.java:226
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xmipp.jni.Filename.getBaseName
static String getBaseName(String path)
Definition: Filename.java:458
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xmipp.ij.commons.ImagePlusLoader.setNormalize
void setNormalize(double normalize_min, double normalize_max)
Definition: ImagePlusLoader.java:97
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xmipp.viewer.models.GalleryData.getValueFromLabel
String getValueFromLabel(int index, int label)
Definition: GalleryData.java:1190
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String getSampleImage(ColumnInfo ci)
Definition: GalleryData.java:580
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xmipp.jni.Filename.isStackOrVolume
static boolean isStackOrVolume(String filename)
Definition: Filename.java:130
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xmipp.viewer.models.MetadataGalleryTableModel.getImage
ImagePlus getImage(long id, String imagepath, ColumnInfo renderLabel)
Definition: MetadataGalleryTableModel.java:104
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xmipp.viewer.models.MetadataGalleryTableModel.createImageItem
ImageItem createImageItem(int index, ColumnInfo renderLabel)
Definition: MetadataGalleryTableModel.java:221
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xmipp.jni.Filename.findImagePath
static String findImagePath(String filename, String mdFilename, boolean shouldExist)
Definition: Filename.java:225
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xmipp.viewer.models.ColumnInfo.updateInfo
boolean updateInfo(ColumnInfo ci)
Definition: ColumnInfo.java:78
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xmipp.jni.Filename.exists
static boolean exists(String path)
Definition: Filename.java:266
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xmipp.viewer.models.MetadataGalleryTableModel.handleRightClick
boolean handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)
Definition: MetadataGalleryTableModel.java:333
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xmipp.utils.DEBUG.printException
static void printException(Exception ex)
Definition: DEBUG.java:30
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xmipp.ij.commons.ImagePlusLoader.setDimension
void setDimension(int width, int height)
Definition: ImagePlusLoader.java:183
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xmipp.utils.XmippMessage.getPathNotExistsMsg
static String getPathNotExistsMsg(String path)
Definition: XmippMessage.java:71
- -
xmipp.viewer.windows.ImagesWindowFactory.openXmippImageWindow
static XmippIJWindow openXmippImageWindow(ImagePlus imp, Params params)
Definition: ImagesWindowFactory.java:134
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xmipp.jni.ImageGeneric.MID_SLICE
static final int MID_SLICE
Definition: ImageGeneric.java:12
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xmipp.jni.MetaData.getStatistics
native double [] getStatistics(boolean applyGeo, int label)
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xmipp.viewer.models.MetadataGalleryTableModel.createItem
ImageItem createItem(int index, String key, ColumnInfo ci)
Definition: MetadataGalleryTableModel.java:195
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xmipp.jni.MetaData.getBaseDir
String getBaseDir()
Definition: MetaData.java:430
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xmipp.ij.commons.ImagePlusLoader.setGeometry
void setGeometry(Geometry geometry)
Definition: ImagePlusLoader.java:172
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class  xmipp.viewer.models.MetadataRowTableModel
 
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package  xmipp.viewer.models
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.models;
27 
28 
29 import javax.swing.JTable;
30 
31 import xmipp.jni.MetaData;
32 import xmipp.utils.Params;
33 import xmipp.utils.XmippPopupMenuCreator;
34 import xmipp.viewer.windows.GalleryJFrame;
35 
37 @SuppressWarnings("serial")
38 public class MetadataRowTableModel extends MetadataTableModel {
39  protected long id;
40 
42  public MetadataRowTableModel(GalleryJFrame window, MetaData md) throws Exception {
43  this(new GalleryData(window, new Params(), md));
44  }
45 
46  public MetadataRowTableModel(GalleryData data) throws Exception {
47  super(data, null);
48  cols = 1;
49  rows = visibleLabels.size();
50  id = data.md.firstObject();
51  // TODO Auto-generated constructor stub
52  selection = new boolean[rows];
53  }
54 
55  @Override
56  public String getColumnName(int column) {
57  return "Value";
58  }
59 
60  @Override
61  public Class getColumnClass(int column) {
62  return String.class;
63  }
64 
65  @Override
66  public Object getValueAt(int row, int column){
67  return super.getValueAt(0, row);
68  }
69 
70  @Override
71  public void setValueAt(Object value, int row, int column) {
72  data.setValueToCol(0, data.getColumnInfo(row), value.toString());
73  }// function setValueAt
74 
75  @Override
77  public GalleryColumnModel createColumnModel() {
78  return new GalleryColumnModel(cellDim.width);
79  }//function createColumnModel
80 
81  @Override
82  public void setupTable(JTable table) {
83  super.setupTable(table);
84  table.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
85  }
86 
87  @Override
88  public boolean handleRightClick(int row, int col, XmippPopupMenuCreator xpopup) {
89  boolean result = super.handleRightClick(0, row, xpopup);
90  xpopup.setItemVisible(XmippPopupMenuCreator.SELECT, false);
91  xpopup.setItemVisible(XmippPopupMenuCreator.ENABLED, false);
92  xpopup.setItemVisible(XmippPopupMenuCreator.DISABLED, false);
93  return result;
94  }
95 
96  @Override
97  public int getIndex(int row, int col) {
98 
99  return 0;
100 
101  }
102 
103  public ColumnInfo getColumn(int row, int col)
104  {
105  return visibleLabels.get(row);
106  }
107 
109  @Override
110  public void touchItem(int row, int col) {
111  setSelected(row, !isSelected(row));
112  adjustWidth = false;
113  //fireTableCellUpdated(row, col);//item was clicked
114  }
115 
116  public boolean isSelected(int row, int col) {
117 
118  return isSelected(row);
119  }
120 
121  public void setSelected(int row, int col, boolean b) {
122  setSelected(row, b);
123  }
124 
125  //** Select a range of elements given the coordinates */
126  @Override
127  public void selectRange(int first_row, int first_col, int last_row, int last_col) {
128  int min = Math.min(first_row, last_row);
129  int max = Math.max(first_row, last_row);
130  for (int i = min; i <= max; i++)
131  if(!isSelected(i))
132  {
133  setSelected(i, true);
134  fireTableCellUpdated(i, 0);
135  }
136  }
137 
138  @Override
139  public boolean showLabels() {
140  return false;
141  }
142 }//class MetadataRow
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xmipp.viewer.models.MetadataRowTableModel.setValueAt
void setValueAt(Object value, int row, int column)
Definition: MetadataRowTableModel.java:71
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xmipp.viewer.models.MetadataRowTableModel.MetadataRowTableModel
MetadataRowTableModel(GalleryJFrame window, MetaData md)
Definition: MetadataRowTableModel.java:42
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xmipp.viewer.models.MetadataRowTableModel.handleRightClick
boolean handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)
Definition: MetadataRowTableModel.java:88
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xmipp.viewer.models.MetadataRowTableModel.setSelected
void setSelected(int row, int col, boolean b)
Definition: MetadataRowTableModel.java:121
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xmipp.utils.XmippMenuCreator.setItemVisible
void setItemVisible(String key, boolean value)
Definition: XmippMenuCreator.java:160
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xmipp.viewer.models.MetadataRowTableModel.selectRange
void selectRange(int first_row, int first_col, int last_row, int last_col)
Definition: MetadataRowTableModel.java:127
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class  xmipp.viewer.models.MetadataTableModel
 
class  xmipp.viewer.models.MetadataTableModel.MetadataColumnModel
 
class  xmipp.viewer.models.MetadataTableModel.MetadataTableHeader
 
class  xmipp.viewer.models.MetadataTableModel.MetadataColumnListener
 
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package  xmipp.viewer.models
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.models;
27 
28 import java.awt.Component;
29 import java.awt.Point;
30 import java.awt.event.MouseAdapter;
31 import java.awt.event.MouseEvent;
32 
33 import javax.swing.*;
34 import javax.swing.table.JTableHeader;
35 import javax.swing.table.TableCellRenderer;
36 import javax.swing.table.TableColumn;
37 import javax.swing.table.TableColumnModel;
38 
39 import xmipp.ij.commons.XmippApplication;
40 import xmipp.ij.commons.XmippUtil;
41 import xmipp.jni.Filename;
42 import xmipp.jni.MetaData;
43 import xmipp.utils.Params;
44 import xmipp.utils.ScipionParams;
45 import xmipp.utils.XmippDialog;
46 import xmipp.utils.XmippMessage;
47 import xmipp.utils.XmippPopupMenuCreator;
48 import xmipp.utils.XmippWindowUtil;
49 import xmipp.viewer.FloatRenderer;
50 import xmipp.viewer.windows.ImagesWindowFactory;
51 
52 public class MetadataTableModel extends MetadataGalleryTableModel {
53  private static final long serialVersionUID = 1L;
54  final static int NO_COLUMN_INDEX = -1;
55  int sortColumnIndex = NO_COLUMN_INDEX;
56  boolean ascending = true;
57 
58 
59  public MetadataTableModel(GalleryData data, boolean[] selection) throws Exception {
60  super(data, selection);
61  cols = visibleLabels.size();
62  rows = n;
63  renderer.hackBorders = false;
64 
65  }
66 
67  @Override
68  public String getColumnName(int column) {
69  return visibleLabels.get(column).labelName;
70  }
71 
72  @Override
73  public Class getColumnClass(int column) {
74  ColumnInfo ci = visibleLabels.get(column);
75  Class c = null;
76  try {
77  if (ci.render)
78  c = ImageItem.class;
79  else if (ci.isEnable())
80  c = Boolean.class;//This way a JCheckBox is rendered
81  else
82  c = MetaData.getClassForType(ci.type);
83 
84  } catch (Exception e) {
85  e.printStackTrace();
86  }
87  return c;
88  }
89 
90 
94  @Override
95  public Object getValueAt(int row, int column) {
96  // DEBUG.printMessage(String.format("MetadataTable.getValueAt(%d, %d)",
97  // row, column));
98  try {
99 
100  ColumnInfo ci = visibleLabels.get(column);
101  if (ci.render) {
102 
103  String key = getItemKey(row, ci.label);
104  ImageItem item;
105  // If the element is on cache, just return it
106  if (cache.containsKey(key))
107  item = cache.get(key);
108  else {
109  // If not, create the item and store it for future
110  item = createImageItem(row, ci);
111  cache.put(key, item);
112  }
113  setupItem(item);
114  return item;
115  }
116  int label = ci.label;
117  long id = data.ids[row];
118 
119  int type = ci.type;
120  MetaData md = data.md;
121  switch (type) {
122  case MetaData.LABEL_INT:
123 
124  int value = md.getValueInt(label, id);
125  // treat special case of MDL_ENABLED
126  if (ci.isEnable())
127  return (value > 0);
128  return value;
129  case MetaData.LABEL_BOOL:
130  return md.getValueBoolean(label, id);
131  case MetaData.LABEL_DOUBLE:
132  return md.getValueDouble(label, id);
133  case MetaData.LABEL_SIZET:
134  return md.getValueLong(label, id);
135  case MetaData.LABEL_STRING:
136  String str = md.getValueString(label, data.ids[row]);
137  if (ci.labelName.contains("_transform._matrix"))
138  return String.format("<html>%s</html>", XmippUtil.formatNumbers(str).replace("],", "]<br>"));
139 
140  return str;
141  case MetaData.LABEL_VECTOR_DOUBLE:
142  case MetaData.LABEL_VECTOR_SIZET:
143  return md.getValueString(label, data.ids[row]);
144 
145  }
146  return null;
147 
148  } catch (Exception e) {
149  e.printStackTrace();
150 
151  }
152  return null;
153  }// function getValueAt
154 
155 
156 
157  @Override
158  public void setValueAt(Object value, int row, int column) {
159 
160  ColumnInfo ci = visibleLabels.get(column);
161  if (value == null || value.equals("")) {
162  XmippDialog.showError(null,
163  XmippMessage.getEmptyFieldMsg(ci.labelName));
164  return;// empty values are not allowed
165  }
166  try {
167  long id = data.ids[row];
168  setMdValueAt(value, row, column, ci, id);
169  data.setMdChanges(true);
170  } catch (Exception e) {
171  e.printStackTrace();
172  }
173 
174  }// function setValueAt
175 
181  protected void setMdValueAt(Object value, int row, int column,
182  ColumnInfo ci, long id) throws Exception {
183  if (!ci.render) {
184  int label = ci.label;
185  int type = ci.type;
186  MetaData md = data.md;
187  switch (type) {
188  case MetaData.LABEL_BOOL:
189  md.setValueBoolean(label, (Boolean) value, id);
190  break;
191  case MetaData.LABEL_INT:
192  if (ci.isEnable()) {
193  md.setEnabled((Boolean) value, id);
194  } else
195  md.setValueInt(label, ((Integer) value).intValue(), id);
196  break;
197  case MetaData.LABEL_DOUBLE:
198  md.setValueDouble(label, ((Double) value).doubleValue(), id);
199  break;
200  case MetaData.LABEL_SIZET:
201  md.setValueLong(label, ((Long) value).longValue(), id);
202  break;
203  case MetaData.LABEL_STRING:
204  case MetaData.LABEL_VECTOR_DOUBLE:
205  case MetaData.LABEL_VECTOR_SIZET:
206  // TODO: Implement a better editor for vectors
207  md.setValueString(label, value.toString(), id);
208  break;
209  }
210  adjustWidth = false;
211  fireTableRowsUpdated(row, row);
212  }
213  }
214 
215  @Override
216  public boolean isCellEditable(int row, int column) {
217  ColumnInfo ci = visibleLabels.get(column);
218  if(ci.isEnable())
219  return ci.allowEdit;//maybe on metadatas sometimes is disabled
220  if(data.isScipionInstance() || data.isChimeraClient())
221  return false;
222 
223  return ci.allowEdit && !ci.render;
224  }
225 
226  // @Override
227  // public String getImageFilenameAt(int row, int col){
228  // ColumnInfo ci = visibleLabels.get(col);
229  // return (ci.render && data.isImageFile(ci))
230  // ? data.getValueFromCol(row, ci) : null;
231  // }
232  @Override
233  public boolean handleDoubleClick(int row, int col) {
234  try {
235 
236  ColumnInfo ci = visibleLabels.get(col);
237  if (ci.allowRender && data.isImageFile(ci)) {
238  int index = getIndex(row, col);
239  String file = getImageFilename(index, ci.label);
240  if(Filename.isVolume(file))
241  {
242  Params params = XmippApplication.isScipion()? ((ScipionParams)data.parameters).getScipionParams(): new Params();
243  ImagesWindowFactory.openMetadata(file, params, Params.OPENING_MODE_GALLERY);
244  }
245  else
246  openXmippImageWindow(index, ci);
247  return true;
248  }
249  if(data.isChimeraClient())//
250  {
251  String cmd = data.getChimeraProjectionCmd(row);
252  XmippWindowUtil.runCommand(cmd, data.parameters.getChimeraPort());
253  }
254  } catch (Exception e) {
255  if(e.getMessage() == null)
256  e.printStackTrace();
257  else
258  XmippDialog.showError(null, e.getMessage());
259 
260  }
261  return false;
262  }// function handleDoubleClick
263 
264  @Override
265  public void setColumns(int cols) {
266 
267  }
268 
269  @Override
270  public boolean adjustColumn(int width) {
271  return false;
272  }
273 
275  public void setRenderImages(boolean value) {
276  boolean changed = false;
277  for (ColumnInfo ci : data.labels)
278  if (ci.allowRender && ci.render != value) {
279  ci.render = value;
280  changed = true;
281  if(data.ciFirstRender == null && value)
282  data.ciFirstRender = ci;
283  }
284  try
285  {
286  if (changed) {
287  data.renderImages = value;
288  loadDimension();
289  calculateCellSize();
290  fireTableDataChanged();
291  }
292 
293  }
294  catch (Exception e)
295  {
296  // TODO Auto-generated catch block
297  e.printStackTrace();
298  }
299  }
300 
301  @Override
302  public boolean showLabels() {
303  return data.renderImages;
304  }
305 
306  @Override
307  protected void calculateCellSize() {
308  //System.out.println(String.format("MetadataTable:calculateSize renderLabel %s hasRenderLabel %s", data.renderImages, data.hasRenderLabel()));
309  if (data.renderImages && data.hasRenderLabel()) {
310  super.calculateCellSize();
311  //System.out.println(String.format("MetadataTable:calculateSize w:%d, h:%d", cellDim.width, cellDim.height));
312 
313  } else {
314  int font_height;
315  font_height = renderer.getFontMetrics(renderer.getFont())
316  .getHeight();
317  font_height += renderer.getIconTextGap(); // Adds the extra gap.
318  cellDim.setSize(200, font_height + 5);
319  }
320  }
321 
322  @Override
323  public void setupTable(JTable table) {
324  table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
325  table.setDefaultRenderer(ImageItem.class, renderer);
326  table.setDefaultRenderer(Double.class, new FloatRenderer());
327  // MetadataTableHeader header = new MetadataTableHeader(columnModel);
328  // JTableHeader header = new JTableHeader(table.getColumnModel());
329  // table.setTableHeader(header);
330  JTableHeader header = table.getTableHeader();
331  header.setUpdateTableInRealTime(true);
332  header.addMouseListener(new MetadataColumnListener(table));
333  // header.setReorderingAllowed(true);
334  updateTableSelection(table);
335  }
336 
337  @Override
338  public JTableHeader getTableHeaderModel() {
339  return new MetadataTableHeader(columnModel);
340  }
341 
343  @Override
344  public void updateTableSelection(JTable table) {
345  table.clearSelection();
346  for (int i = 0; i < selection.length; ++i)
347  if (selection[i]) {
348  table.addRowSelectionInterval(i, i);
349  }
350  }
351 
352  @Override
353  public boolean handleRightClick(int row, int col,
354  XmippPopupMenuCreator xpopup) {
355  if (isBusy(row, col))
356  return false;
357  xpopup.initItems();
358 
359  if (data.isFile(visibleLabels.get(col))) {
360 
361  xpopup.setItemVisible(XmippPopupMenuCreator.OPEN, true);
362  if (!data.isImageFile(visibleLabels.get(col)))
363  xpopup.setItemVisible(XmippPopupMenuCreator.OPEN_ASTEXT, true);
364  }
365 
366  return true;
367  }
368 
369  @Override
371  public GalleryColumnModel createColumnModel() {
372  return new MetadataColumnModel();
373  }
374 
375  public class MetadataColumnModel extends GalleryColumnModel {
376  public MetadataColumnModel() {
377  super(0);
378  }
379 
380  @Override
381  public void adjustColumnsWidth(JTable table) {
382  try {
383  if (visibleLabels.size() != getColumnCount())
384  return;
385 
386  //DEBUG.printStackTrace();
387 
388  calculateCellSize();
389  // String[] row = md.getRowValues(data.ids[0]);
390  // table.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
391  int width = 0;
392  TableCellRenderer rend;
393  Component comp;
394  boolean non_empty = data.md.size() > 0;
395  TableColumn tc;
396  ColumnInfo col;
397  for (int i = 0; i < visibleLabels.size(); i++) {
398  col = visibleLabels.get(i);
399  tc = getColumn(i);
400  width = 0;
401  // Calculate width of the cell
402  if (col.render) {
403  width = cellDim.width;
404  } else if (non_empty) {
405  // else {
406 
407  rend = table.getCellRenderer(0, i);
408  if(rend != null)
409  {
410  Object value = table.getValueAt(0, i);
411  //If columns are reordered Renderer may be related to column according to visual order but value is related to real order
412  comp = rend.getTableCellRendererComponent(table, value, false, false, 0, i);
413  width = comp.getPreferredSize().width + 10;
414  }
415  }
416  // Calculate width of the header
417  rend = tc.getHeaderRenderer();
418  if (rend == null)
419  rend = table.getTableHeader().getDefaultRenderer();
420  Object value = tc.getHeaderValue();
421  comp = rend.getTableCellRendererComponent(table, value,
422  false, false, 0, i);
423  // Take max width
424  width = Math.max(width, comp.getPreferredSize().width);
425  getColumn(i).setPreferredWidth(width + 10);
426  // DEBUG.printMessage(String.format("col: %d, width: %d", i,
427  // width));
428  }
429  } catch (Exception e) {
430  // TODO Auto-generated catch block
431  e.printStackTrace();
432  }
433  }// function adjustColumnsWidth
434 
435  }// class MetadataColumnModel
436 
437  public class MetadataTableHeader extends JTableHeader {
438  public MetadataTableHeader(TableColumnModel columnModel) {
439  super(columnModel);
440  }
441 
443  public String getToolTipText(MouseEvent e) {
444  java.awt.Point p = e.getPoint();
445  int index = columnModel.getColumnIndexAtX(p.x);
446  if (index > -1){
447  int col = table.convertColumnIndexToModel(index);
448  return visibleLabels.get(col).comment;
449  }
450 
451  return null;
452  }
453  }
454 
455  public class MetadataColumnListener extends MouseAdapter {
456  public static final String ASCENDING_PREFIX = "\u25B2 ";
457  public static final String DESCENDING_PREFIX = "\u25BC ";
458  protected JTable table;
459 
460  public MetadataColumnListener(JTable t) {
461  table = t;
462  }
463 
464  public void mouseClicked(MouseEvent e) {
465 
466  TableColumnModel colModel = table.getColumnModel();
467  // Get the clicked column index
468  int columnModelIndex = colModel.getColumnIndexAtX(e.getX());
469 
470  // Get the column
471  final TableColumn column = colModel.getColumn(columnModelIndex);
472 
473  // Take into account a possible reordering of columns
474  int modelIndex = column.getModelIndex();
475 
476  // Take into account possible invisible columns indexing
477  modelIndex = data.getVisibleColumnIndex(modelIndex);
478  if (modelIndex < 0)
479  return;
480  if (sortColumnIndex == modelIndex)
481  ascending = !ascending;
482  else
483 
484  // Remove previous sorting icon
485  removePreviousSortingIcon();
486  sortColumnIndex = modelIndex;
487 
488 
489  final String columnName = data.labels.get(sortColumnIndex).labelName;
490 
491  column.setHeaderValue( "\u231B " + columnName);
492  Runnable sort = new Runnable() {
493  @Override
494  public void run() {
495 
496  data.sortMd(data.labels.get(sortColumnIndex), ascending);
497  column.setHeaderValue((ascending? ASCENDING_PREFIX : DESCENDING_PREFIX)+columnName);
498  table.getTableHeader().repaint();
499  clearSelection();
500  updateTableSelection(table);
501  cache.clear();
502  table.repaint();
503 
504  }
505  };
506 
507  SwingUtilities.invokeLater(sort);
508 
509  }
510 
511  protected void removePreviousSortingIcon() {
512 
513  // If there is a previous column sorted
514  if (sortColumnIndex != NO_COLUMN_INDEX){
515  // Get the column model
516  TableColumnModel colModel = table.getColumnModel();
517 
518  // For each column
519  for (int i=0; i<colModel.getColumnCount();i++){
520  TableColumn col = colModel.getColumn(i);
521  String header = col.getHeaderValue().toString();
522 
523  // If it has the ascending prefix
524  if (header.startsWith(ASCENDING_PREFIX) ){
525  // remove it
526  col.setHeaderValue(header.replaceFirst(ASCENDING_PREFIX, ""));
527  return;
528  } else if (header.startsWith(DESCENDING_PREFIX)) {
529  // remove it
530  col.setHeaderValue(header.replaceFirst(DESCENDING_PREFIX, ""));
531  return;
532  }
533  }
534  }
535  }
536  }
537 
538  @Override
539  public int getIndex(int row, int col) {
540  return row;
541  }
542 
543  public ColumnInfo getColumn(int row, int col)
544  {
545  return visibleLabels.get(col);
546  }
547 
548  @Override
549  public Point getCoords(int index) {
550 
551  Point p = new Point();
552  p.x = 0;
553  p.y = index;
554  return p;
555  }
556 
557 
558 
559 
560 }// class MetadataTable
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static final int LABEL_VECTOR_DOUBLE
Definition: MetaData.java:49
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native boolean setValueString(int label, String value, long objId)
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boolean isCellEditable(int row, int column)
Definition: MetadataTableModel.java:216
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xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
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xmipp.jni.MetaData.LABEL_DOUBLE
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Definition: MetaData.java:47
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xmipp.ij.commons.XmippUtil.formatNumbers
static String formatNumbers(String str)
Definition: XmippUtil.java:131
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xmipp.jni.MetaData.LABEL_STRING
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Definition: MetaData.java:48
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Definition: MetaData.java:46
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Definition: MetaData.java:50
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xmipp.viewer.models.GalleryData.sortMd
void sortMd(ColumnInfo sortci, boolean asc)
Definition: GalleryData.java:624
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xmipp.viewer.models.MetadataTableModel.setValueAt
void setValueAt(Object value, int row, int column)
Definition: MetadataTableModel.java:158
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xmipp.jni.MetaData.LABEL_VECTOR_SIZET
static final int LABEL_VECTOR_SIZET
Definition: MetaData.java:51
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xmipp.jni.MetaData.setValueBoolean
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xmipp.jni.Filename.isVolume
static boolean isVolume(String filename)
Definition: Filename.java:134
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MetadataTableModel(GalleryData data, boolean[] selection)
Definition: MetadataTableModel.java:59
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xmipp.jni.MetaData.size
native int size()
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xmipp.jni.MetaData.getClassForType
static Class getClassForType(int type)
Definition: MetaData.java:261
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ImageItem createImageItem(int index, ColumnInfo renderLabel)
Definition: MetadataGalleryTableModel.java:221
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xmipp.jni.MetaData.LABEL_INT
static final int LABEL_INT
Definition: MetaData.java:45
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Definition: MetadataTableModel.java:543
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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static GalleryJFrame openMetadata(String filename, MetaData md, Params parameters, String mode)
Definition: ImagesWindowFactory.java:180
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Integer getChimeraPort()
Definition: Params.java:339
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native String getValueString(int label, long objId)
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String getChimeraProjectionCmd(int row)
Definition: GalleryData.java:202
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boolean isFile(ColumnInfo ci)
Definition: GalleryData.java:827
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xmipp.jni.MetaData.setEnabled
boolean setEnabled(boolean value, long objId)
Definition: MetaData.java:442
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xmipp.utils.Params.OPENING_MODE_GALLERY
static final String OPENING_MODE_GALLERY
Definition: Params.java:29
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static void runCommand(String command, Integer port)
Definition: XmippWindowUtil.java:342
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Object getValueAt(int row, int column)
Definition: MetadataTableModel.java:95
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boolean showError(String message)
Definition: XmippDialog.java:211
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void setItemVisible(String key, boolean value)
Definition: XmippMenuCreator.java:160
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void setMdValueAt(Object value, int row, int column, ColumnInfo ci, long id)
Definition: MetadataTableModel.java:181
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xmipp.utils.XmippMessage.getEmptyFieldMsg
static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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boolean handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)
Definition: MetadataTableModel.java:353
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  * Roberto Marabini (roberto@cnb.csic.es)
4  *
5  *
6  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
7  *
8  * This program is free software; you can redistribute it and/or modify
9  * it under the terms of the GNU General Public License as published by
10  * the Free Software Foundation; either version 2 of the License, or
11  * (at your option) any later version.
12  *
13  * This program is distributed in the hope that it will be useful,
14  * but WITHOUT ANY WARRANTY; without even the implied warranty of
15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  * GNU General Public License for more details.
17  *
18  * You should have received a copy of the GNU General Public License
19  * along with this program; if not, write to the Free Software
20  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
21  * 02111-1307 USA
22  *
23  * All comments concerning this program package may be sent to the
24  * e-mail address 'xmipp@cnb.csic.es'
25  ***************************************************************************/
26 package xmipp.test;
27 
28 import java.io.File;
29 
30 import org.junit.After;
31 import org.junit.AfterClass;
32 import org.junit.Before;
33 import org.junit.BeforeClass;
34 import org.junit.Test;
35 
36 import xmipp.jni.Filename;
37 import xmipp.jni.ImageGeneric;
38 import xmipp.jni.MDLabel;
39 import xmipp.jni.MDRow;
40 import xmipp.jni.MetaData;
41 import xmipp.utils.DEBUG;
42 import xmipp.utils.XmippWindowUtil;
43 import xmipp.viewer.windows.GalleryJFrame;
44 import static org.junit.Assert.*;
45 
57 public class MetadataTest
58 {
59  static String mdFn = XmippTest.getTestFilename("tux.xmd");
60  // Values expected from the metadata
61  String[] imageValues = { "000001@tux.stk", "000002@tux.stk", "000003@tux.stk", "000004@tux.stk" };
62 
63  double[] shiftXValues = { 0.000000, 1.404060, 1.715445, 1.266333 };
64  double[] shiftXSorted = { 0.000000, 1.266333, 1.404060, 1.715445 };
65  int[] refValues = { 3, 4, 1, 2 };
66  int[] refSorted = { 4, 3, 2, 1 };
67 
68  @BeforeClass
69  public static void setUpClass() throws Exception
70  {
71  }
72 
73  @AfterClass
74  public static void tearDownClass() throws Exception
75  {
76  }
77 
78  @Before
79  public void setUp()
80  {
81  }
82 
83  @After
84  public void tearDown()
85  {
86  }
87 
88  @Test
89  public void testRead() throws Exception
90  {
91  MetaData md = new MetaData(mdFn);
92  MDRow row = new MDRow();
93 
94  long[] ids = md.findObjects();
95  long id;
96  for (int i = 0; i < ids.length; ++i)
97  {
98  id = ids[i];
99  assertEquals(imageValues[i], md.getValueString(MDLabel.MDL_IMAGE, id));
100  assertEquals(shiftXValues[i], md.getValueDouble(MDLabel.MDL_SHIFT_X, id), XmippTest.EQUAL_ACCURACY);
101  assertEquals(refValues[i], md.getValueInt(MDLabel.MDL_REF, id));
102 
103  //Test MDRow
104  md.getRow(row, id);
105  assertEquals(imageValues[i], row.getValueString(MDLabel.MDL_IMAGE));
106  assertEquals(shiftXValues[i], row.getValueDouble(MDLabel.MDL_SHIFT_X), XmippTest.EQUAL_ACCURACY);
107  assertEquals(refValues[i], row.getValueInt(MDLabel.MDL_REF));
108  }
109  md.destroy();
110  }// function testRead
111 
112  @Test
113  public void testLabelType() throws Exception
114  {
115  int type = MetaData.getLabelType(MDLabel.MDL_IMAGE);
116  assertEquals(MetaData.LABEL_STRING, type);
117  }// function testLabelType
118 
119  @Test
120  public void testSort() throws Exception
121  {
122  MetaData md = new MetaData(mdFn);
123  // Sort by MDL_SHIFT_X ascending
124  md.sort(MDLabel.MDL_SHIFT_X, true);
125  long[] ids = md.findObjects();
126  for (int i = 0; i < ids.length; ++i)
127  assertEquals(shiftXSorted[i], md.getValueDouble(MDLabel.MDL_SHIFT_X, ids[i]), XmippTest.EQUAL_ACCURACY);
128  // Sort by MDL_REF descending
129  md.sort(MDLabel.MDL_REF, false);
130  ids = md.findObjects();
131  for (int i = 0; i < ids.length; ++i)
132  assertEquals(refSorted[i], md.getValueInt(MDLabel.MDL_REF, ids[i]));
133  md.destroy();
134  }// function testSort
135 
136  @Test
137  public void testMakeAbsPath() throws Exception
138  {
139  MetaData md = new MetaData(mdFn), md2 = new MetaData(mdFn);
140  md2.makeAbsPath(MDLabel.MDL_IMAGE);
141  long[] ids = md.findObjects();
142  long[] ids2 = md2.findObjects();
143 
144  for (int i = 0; i < ids.length; ++i)
145  {
146  String path = md.getValueString(MDLabel.MDL_IMAGE, ids[i]);
147  File f = new File(Filename.getFilename(path));
148  path = md2.getValueString(MDLabel.MDL_IMAGE, ids2[i]);
149  assertEquals(Filename.getFilename(path), f.getAbsolutePath());
150  }
151  //md.print();
152  //md2.print();
153 
154  md.destroy();
155  md2.destroy();
156 
157  }// function testSort
158 
159  @Test
160  public void testFill() throws Exception
161  {
162  // Test fillConstant
163  String imagePath = "resources/test/singleImage.img";
164  MetaData md = new MetaData(mdFn);
165  md.fillConstant(MDLabel.MDL_IMAGE1, imagePath);
166  long[] ids = md.findObjects();
167  for (int i = 0; i < ids.length; ++i)
168  assertEquals(imagePath, md.getValueString(MDLabel.MDL_IMAGE1, ids[i]));
169 
170  // Test fillLinear
171  md.fillLinear(MDLabel.MDL_SHIFT_Y, 0.0, 0.5);
172  double value = 0.0;
173  for (int i = 0; i < ids.length; ++i)
174  {
175  assertEquals(value, md.getValueDouble(MDLabel.MDL_SHIFT_Y, ids[i]), XmippTest.EQUAL_ACCURACY);
176  value += 0.5;
177  }
178  // md.print();
179 
180  // Test fillRandom
181  // md.fillRandom(MDLabel.MDL_SHIFT_Y, "uniform", 2.0, 3.0);
182  // md.print();
183  md.destroy();
184  }// function testFill
185 
186  @Test
187  public void testRemoveObject() throws Exception
188  {
189  double[] localShiftXValues = { shiftXValues[1], shiftXValues[3] };
190  MetaData md = new MetaData(mdFn);
191  long[] ids = md.findObjects();
192  md.removeObject(ids[0]);
193  md.removeObject(ids[2]);
194  assertEquals(2, md.size());
195  ids = md.findObjects();
196  for (int i = 0; i < ids.length; ++i)
197  assertEquals(localShiftXValues[i], md.getValueDouble(MDLabel.MDL_SHIFT_X, ids[i]), XmippTest.EQUAL_ACCURACY);
198  // md.print();
199  md.destroy();
200  }
201 
202  @Test
203  public void testReadQuotedString() throws Exception
204  {
205  // MetaData md = new MetaData("kk.xmd");
206  // long[] ids = md.findObjects();
207  // md.print();
208  // System.out.println("------------------------------------");
209  // for (int i=0; i < ids.length; ++i){
210  // System.out.println(md.getValueString(MDLabel.MDL_IMAGE, ids[i]));
211  // System.out.println(md.getValueString(MDLabel.MDL_ANGLE_DIFF,
212  // ids[i]));
213  // }
214  // md.print();
215  }
216 
217  // @Test
218  // public void createBigMetadata() throws Exception {
219  // MetaData md = new MetaData();
220  // int n = 1000000;
221  // long id;
222  //
223  // DEBUG.tic();
224  // System.out.println("Creating big md....");
225  // for (int i = 0; i < n; ++i){
226  // id = md.addObject();
227  // md.setValueString(MDLabel.MDL_IMAGE, String.format("image%06d.xmp", i),
228  // id);
229  // }
230  // DEBUG.toc();
231  // DEBUG.tic();
232  // System.out.println("Filling big md....");
233  // md.fillLinear(MDLabel.MDL_ANGLE_PSI, 0.0, 0.5);
234  // md.fillRandom(MDLabel.MDL_SHIFT_X, "gaussian", 0., 3.);
235  // md.fillRandom(MDLabel.MDL_SHIFT_Y, "gaussian", 0., 3.);
236  // DEBUG.toc();
237  // md.write("big_md.xmd");
238  // }
239 
240  // public void createBigMetadata(MetaData md, int n) {
241  // System.out.println("Creating big md....");
242  // long id;
243  // double v = 0.;
244  //
245  // for (int i = 0; i < n; ++i) {
246  // id = md.addObject();
247  // md.setValueString(MDLabel.MDL_IMAGE,
248  // String.format("image%06d.xmp", i), id);
249  // md.setValueDouble(MDLabel.MDL_ANGLE_PSI, v, id);
250  // md.setValueDouble(MDLabel.MDL_SHIFT_X, 100.0, id);
251  // md.setValueDouble(MDLabel.MDL_SHIFT_Y, 100.0, id);
252  // v+=0.5;
253  // }
254  // }
255 
256 // @Test
257 // public void readBigMetadata() throws Exception
258 // {
259 // try
260 // {
261 //
262 // DEBUG.tic();
263 // System.out.println("Creating big md....");
264 // MetaData md = new MetaData("javaMdTest/big_md.xmd");
265 // // MetaData md = new MetaData();
266 // // createBigMetadata(md, 1000000);
267 // DEBUG.toc();
268 // System.out.println("Finding objects big md....");
269 // long[] ids = md.findObjects();
270 // DEBUG.toc();
271 // long counter = 0, total = ids.length;
272 // String image;
273 // double angle = 0, x = 0, y = 0;
274 //
275 // System.out.println("Looping objects big md....");
276 // for (long id : ids)
277 // {
278 // image = md.getValueString(MDLabel.MDL_IMAGE, id);
279 // angle += md.getValueDouble(MDLabel.MDL_ANGLE_PSI, id);
280 // x += md.getValueDouble(MDLabel.MDL_SHIFT_X, id);
281 // y += md.getValueDouble(MDLabel.MDL_SHIFT_Y, id);
282 // if (++counter % 10000 == 0)
283 // System.out.format("%d of %d\n", counter, total);
284 // }
285 // System.out.format("sums angle: %f x: %f y: %f %n", angle, x, y);
286 // md.destroy();
287 // }
288 // catch (Exception ex)
289 // {
290 // ex.printStackTrace();
291 // }
292 // }
293 
294  public class Worker implements Runnable
295  {
296  MetaData imagesmd;
297  MetaData md;
298 
299  public Worker(MetaData md,MetaData imagesmd)
300  {
301  this.imagesmd = imagesmd;
302  this.md = md;
303  }
304 
305  public void run()
306  {
307  String imagepath;
308  int idlabel = MDLabel.MDL_IMAGE;
309 
310  long id2;
311  for (long id : md.findObjects())
312  {
313  imagepath = md.getValueString(idlabel, id, true);
314  if (imagepath != null && ImageGeneric.exists(imagepath))
315  {
316  id2 = imagesmd.addObject();
317  imagesmd.setValueString(idlabel, imagepath, id2);
318  }
319  }
320 
321  for (long id : imagesmd.findObjects())
322  {
323  imagepath = imagesmd.getValueString(idlabel, id, true);
324  System.out.printf("%d %s\n", id, imagepath);
325  }
326 
327  imagesmd.destroy();
328  }
329  }
330  @Test
331  public void readRuntimeMd() throws Exception
332  {
333  try
334  {
335  System.out.println("read runtime md...");
336 
337  MetaData md = new MetaData(XmippTest.getTestFilename("images.stk"));
338  MetaData imagesmd = new MetaData();
339  String imagepath;
340  int idlabel = MDLabel.MDL_IMAGE;
341 
342 
343 
344  Worker w = new Worker(md, imagesmd);
345  //w.run();
346 
347  Thread th = new Thread(w);
348  th.start();
349 
350  md.destroy();
351 
352  System.out.println("read runtime md ended...");
353  }
354  catch (Exception ex)
355  {
356  ex.printStackTrace();
357  }
358  }
359 
360  @Test
361  public void updateMetaDataRowWithRow() throws Exception
362  {
363  try
364  {
365  System.out.println("updateMetaDataRowWithRow");
366 
367  MetaData md = new MetaData(XmippTest.getTestFilename("images.stk"));
368  MetaData imagesmd = new MetaData();
369  String imagepath;
370  int idlabel = MDLabel.MDL_IMAGE;
371  MDRow mdRow = new MDRow();
372  long[] ids = md.findObjects();
373 
374  long id2;
375  for (long id: ids)
376  {
377  imagepath = md.getValueString(idlabel, id, true);
378  if (imagepath != null && ImageGeneric.exists(imagepath))
379  {
380  id2 = imagesmd.addObject();
381  md.getRow(mdRow, id);
382  mdRow.setValueString(idlabel, imagepath);
383  imagesmd.setRow(mdRow, id2);
384  }
385  }
386 
387  long[] ids2 = imagesmd.findObjects();
388  for (int i=0; i < ids.length; i++)
389  {
390  assertEquals(md.getValueString(idlabel, ids[i]),
391  imagesmd.getValueString(idlabel, ids2[i]));
392  }
393 
394  //imagesmd.print();
395 
396  imagesmd.destroy();
397  md.destroy();
398  mdRow.destroy();
399 
400  System.out.println("updateMetaDataRowWithRow ended...");
401  }
402  catch (Exception ex)
403  {
404  ex.printStackTrace();
405  }
406  }
407 
408 // @Test
409 // public void readTinyMetadatas() throws Exception
410 // {
411 // try
412 // {
413 // MetaData md = new MetaData("javaMdTest/all_tiny.xmd");
414 // MetaData md2 = new MetaData();
415 //
416 // long[] ids = md.findObjects();
417 // long[] ids2;
418 // String tinyFn;
419 // double angle, x, y;
420 //
421 // for (long id : ids)
422 // {
423 // tinyFn = md.getValueString(MDLabel.MDL_IMAGE, id);
424 // md2.read(tinyFn);
425 // System.out.println("Tiny md: " + tinyFn);
426 // ids2 = md2.findObjects();
427 // for (long id2 : ids2)
428 // {
429 // angle = md2.getValueDouble(MDLabel.MDL_ANGLE_PSI, id2);
430 // x = md2.getValueDouble(MDLabel.MDL_SHIFT_X, id2);
431 // y = md2.getValueDouble(MDLabel.MDL_SHIFT_Y, id2);
432 // // System.out.format(" image: %s, angle: %f x: %f y: %f %n",
433 // // tinyFn, angle, x, y);
434 // }
435 // }
436 // md.destroy();
437 // md2.destroy();
438 // }
439 // catch (Exception ex)
440 // {
441 // ex.printStackTrace();
442 // }
443 // }
444 
445  @Test
446  public void testOperate() throws Exception
447  {
448  MetaData md = new MetaData(mdFn);
449  md.operate("shiftX=2*shiftX, ref=ref+10");
450  long[] ids = md.findObjects();
451  long id;
452  for (int i = 0; i < ids.length; ++i)
453  {
454  id = ids[i];
455  assertEquals(shiftXValues[i] * 2, md.getValueDouble(MDLabel.MDL_SHIFT_X, id), XmippTest.EQUAL_ACCURACY);
456  assertEquals(refValues[i] + 10, md.getValueInt(MDLabel.MDL_REF, id));
457  }
458  }// function testRead
459 
460 }// class MetadataTest
xmipp.test.MetadataTest.tearDownClass
static void tearDownClass()
Definition: MetadataTest.java:74
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xmipp.jni.MDRow.setValueString
native boolean setValueString(int label, String value)
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xmipp.jni.MetaData.addObject
native long addObject()
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native double getValueDouble(int label)
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xmipp.jni.MetaData.LABEL_STRING
static final int LABEL_STRING
Definition: MetaData.java:48
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xmipp.jni.MetaData.fillConstant
native void fillConstant(int label, String value)
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xmipp.jni.ImageGeneric.exists
static boolean exists(String imagepath)
Definition: ImageGeneric.java:291
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xmipp.jni.MDLabel.MDL_SHIFT_Y
static final int MDL_SHIFT_Y
< difference in Shift along X axis (double)
Definition: MDLabel.java:367
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xmipp.test.XmippTest.getTestFilename
static String getTestFilename(String file)
Definition: XmippTest.java:40
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xmipp.jni.MetaData.getRow
native void getRow(MDRow mdRow, long objId)
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native void sort(int sortLabel, boolean ascending)
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synchronized native void destroy()
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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synchronized native void destroy()
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native int size()
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native void fillLinear(int label, double start, double step)
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native int getValueInt(int label, long objId)
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xmipp.jni.MDRow.getValueInt
native int getValueInt(int label)
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xmipp.test.MetadataTest.setUpClass
static void setUpClass()
Definition: MetadataTest.java:69
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.jni.MDLabel.MDL_SHIFT_X
static final int MDL_SHIFT_X
< A collection of micrographs, e.g. a tilt serie (std::string)
Definition: MDLabel.java:363
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xmipp.test.MetadataTest.Worker.Worker
Worker(MetaData md, MetaData imagesmd)
Definition: MetadataTest.java:299
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xmipp.jni.MDLabel.MDL_IMAGE1
static final int MDL_IMAGE1
< Name of Metadata file for all images (string)
Definition: MDLabel.java:199
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xmipp.jni.MDLabel.MDL_IMAGE
static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
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xmipp.jni.MetaData.removeObject
native boolean removeObject(long objId)
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xmipp.jni.Filename.getFilename
static String getFilename(String filename)
Definition: Filename.java:302
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xmipp.jni.MetaData.operate
native void operate(String operateStr)
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xmipp.jni.MDLabel.MDL_REF
static final int MDL_REF
< 3D Class to which the image belongs (int)
Definition: MDLabel.java:312
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xmipp.jni.MetaData.getLabelType
static native int getLabelType(int label)
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xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.jni.MDRow.getValueString
native String getValueString(int label)
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1 package xmipp.viewer.particlepicker.extract;
2 
3 import ij.gui.ImageWindow;
4 
5 import java.awt.Color;
6 import java.awt.Dimension;
7 import java.awt.Graphics;
8 import java.awt.Graphics2D;
9 import java.awt.Image;
10 import java.util.List;
11 import xmipp.ij.commons.XmippImageCanvas;
12 import xmipp.jni.Particle;
13 import xmipp.viewer.particlepicker.Shape;
14 
15 public class MicrographCanvas extends XmippImageCanvas
16 {
17 
18 
19  private List<Particle> particles;
20  private int size;
21  private MicrographData micdata;
22 
23  public MicrographCanvas(MicrographData loader, int size)
24  {
25  super(loader.getMicrograph().getImagePlus());
26  this.micdata = loader;
27  this.particles = loader.getParticles();
28  this.size = size;
29  }
30 
31  protected ImageWindow iw;
32 
33  public void display()
34  {
35  if (iw != null && iw.isVisible())
36  {
37  iw.setImage(getImage());
38  iw.updateImage(getImage());
39  }
40  else
41  this.iw = new ImageWindow(getImage(), this);// if you don't provide
42  // iw, I init mine
43  // iw.maximize();
44  iw.pack();
45  }
46 
47  public void paint(Graphics g)
48  {
49  Graphics offgc;//Off screen graphic
50  Image offscreen = null;//Off screen image
51  Dimension d = getSize();
52  // create the offscreen buffer and associated Graphics
53  offscreen = createImage(d.width, d.height);
54  offgc = offscreen.getGraphics();
55  super.paint(offgc);//super paint in off screen
56  //my paint in offscreen
57  Graphics2D g2 = (Graphics2D) offgc;
58  doCustomPaint(g2);
59  //drawing offscreen image
60  g.drawImage(offscreen, 0, 0, this);
61  }
62 
63  protected void drawShape(Graphics2D g2, Shape shape, int x, int y, int radius)
64  {
65  int size = 2 * radius;
66  if (shape == Shape.Rectangle)
67  g2.drawRect(x - radius, y - radius, size, size);
68  else if (shape == Shape.Circle)
69  g2.drawOval(x - radius, y - radius, size, size);
70  else if (shape == Shape.Center)
71  {
72  int distance = (int) (radius / 5. * magnification);
73  g2.drawLine(x, y - distance, x, y + distance);
74  g2.drawLine(x + distance, y, x - distance, y);
75  }
76 
77  }
78 
79  protected void doCustomPaint(Graphics2D g2)
80  {
81  g2.setColor(Color.GREEN);
82  for (Particle p : particles)
83  {
84  drawShape(g2, Shape.Rectangle, getXOnImage(p.getX()), getYOnImage(p.getY()), size);
85  drawShape(g2, Shape.Center, getXOnImage(p.getX()), getYOnImage(p.getY()), size);
86  }
87  }
88 
89 }
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xmipp.viewer.particlepicker.extract.MicrographCanvas.drawShape
void drawShape(Graphics2D g2, Shape shape, int x, int y, int radius)
Definition: MicrographCanvas.java:63
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1 package xmipp.viewer.particlepicker.extract;
2 
3 import java.util.ArrayList;
4 import java.util.List;
5 
6 import xmipp.jni.MDLabel;
7 import xmipp.jni.MetaData;
8 import xmipp.jni.Particle;
9 import xmipp.viewer.particlepicker.Micrograph;
10 
11 public class MicrographData
12 {
13  private String mdfile;
14  private List<Particle> particles;
15  private Micrograph micrograph;
16  private String micfile;
17 
18  public MicrographData(String mdfile, String micfile)
19  {
20  this.mdfile = mdfile;
21  this.particles = new ArrayList<Particle>();
22  this.micfile = micfile;
23  this.micrograph = new Micrograph(micfile)
24  {
25 
26 
27 
28  @Override
29  public boolean hasData()
30  {
31  return !particles.isEmpty();
32  }
33  };
34  loadData();
35  }
36 
37  public Micrograph getMicrograph()
38  {
39  return micrograph;
40  }
41 
42  public static void openMicrographs(String mdfile)
43  {
44 
45 
46  List<MicrographData> micdatas = MicrographData.getMicrographData(mdfile);
47  MicrographCanvas mc;
48  for(MicrographData pl: micdatas)
49  {
50  mc = new MicrographCanvas(pl, 30);
51  mc.display();
52  }
53  }
54 
55 
56 
57  private void loadData()
58  {
59  particles.clear();
60  MetaData md = new MetaData(mdfile);
61  Particle p;
62  int x, y;
63  String file;
64  for (long id : md.findObjects())
65  {
66  file = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
67  if (this.micfile.equals(file))
68  {
69  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
70  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
71  p = new Particle(x, y);
72  particles.add(p);
73  }
74  }
75  md.destroy();
76  }
77 
78  public List<Particle> getParticles()
79  {
80  return particles;
81  }
82 
83  public String getMicrographFile()
84  {
85  return micfile;
86  }
87 
88  public static List<MicrographData> getMicrographData(String file)
89  {
90  List<MicrographData> loaders = new ArrayList<MicrographData>();
91  MetaData md = new MetaData(file);
92  Particle p;
93  int x, y;
94  String micfileiter;
95  boolean exists;
96  MicrographData data = null;
97  for (long id : md.findObjects())
98  {
99  exists = false;
100  micfileiter = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
101  for (MicrographData dataiter : loaders)
102  if (dataiter.getMicrographFile().equals(micfileiter))
103  {
104  exists = true;
105  data = dataiter;
106  break;
107  }
108  if (!exists)
109  {
110  data = new MicrographData(file, micfileiter);
111  loaders.add(data);
112  }
113  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
114  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
115  p = new Particle(x, y);
116  data.addParticle(p);
117  }
118  md.destroy();
119  return loaders;
120  }
121 
122  private void addParticle(Particle p)
123  {
124  particles.add(p);
125  }
126 
127 }
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xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.viewer.particlepicker.extract.MicrographData.getMicrographData
static List< MicrographData > getMicrographData(String file)
Definition: MicrographData.java:88
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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- - diff --git a/html/MicrographPairsTableModel_8java.html b/html/MicrographPairsTableModel_8java.html deleted file mode 100644 index 81c7ec4a..00000000 --- a/html/MicrographPairsTableModel_8java.html +++ /dev/null @@ -1,95 +0,0 @@ - - - - - - - -Xmipp: xmippViz/java/src/xmipp/viewer/particlepicker/tiltpair/gui/MicrographPairsTableModel.java File Reference - - - - - - - - - -
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1 package xmipp.viewer.particlepicker.tiltpair.gui;
2 
3 import java.util.List;
4 
5 import javax.swing.table.AbstractTableModel;
6 
7 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph;
8 
9 
10 public class MicrographPairsTableModel extends AbstractTableModel {
11 
12 
13 
14  private List<UntiltedMicrograph> micrographs;
15  private String[] columns = new String[]{"", "Name", "Pair Name", "Particles", "Tilt Angle"};
16 
17  public MicrographPairsTableModel(TiltPairPickerJFrame frame)
18  {
19  this.micrographs = frame.getParticlePicker().getMicrographs();
20  }
21 
22  @Override
23  public int getColumnCount() {
24  return columns.length;
25  }
26  @Override
27  public String getColumnName(int c)
28  {
29  return columns[c];
30  }
31 
32  @Override
33  public int getRowCount() {
34  return micrographs.size();
35  }
36 
37  @Override
38  public Object getValueAt(int rowIndex, int columnIndex) {
39  UntiltedMicrograph m = micrographs.get(rowIndex);
40  if(columnIndex == 0)
41  return rowIndex + 1;
42  if(columnIndex == 1)
43  return m.getName();
44  if(columnIndex == 2)
45  return m.getTiltedMicrograph().getName();
46  if(columnIndex == 3)
47  return m.getParticles().size();
48  if(columnIndex == 4)
49  return String.format("%.2f", m.getTiltAngle());
50  return null;
51  }
52 
53  public int getParticlesPosition()
54  {
55  return 2;
56  }
57 
58 }
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xmipp.viewer.particlepicker.Micrograph.getName
static String getName(String file, int level)
Definition: Micrograph.java:140
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enum  xmipp.viewer.particlepicker.training.model.MicrographState
 
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 public enum MicrographState {
4  Manual, Supervised, Corrected, Available, Auto, Review, Automatic
5 }
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package  xmipp.viewer.particlepicker
 
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1 package xmipp.viewer.particlepicker;
2 
3 import ij.IJ;
4 import ij.ImagePlus;
5 
6 import java.awt.Image;
7 import java.io.File;
8 import java.util.List;
9 import java.util.logging.Level;
10 import java.util.logging.Logger;
11 
12 import javax.swing.Icon;
13 import javax.swing.ImageIcon;
14 
15 import xmipp.ij.commons.IJCommand;
16 import xmipp.ij.commons.XmippImageConverter;
17 import xmipp.ij.commons.XmippUtil;
18 import xmipp.jni.Filename;
19 import xmipp.jni.ImageGeneric;
20 import xmipp.jni.Particle;
21 import xmipp.utils.XmippMessage;
22 
23 public abstract class Micrograph {
24 
25  private static Icon noimageicon;
26  private String file;
27  private String name;
28  private ImagePlus imp;
29  private String pos24file;
30  public static final String ext = ".pos";
31  private int width, height;
32  private String posfile;
33  private CtfInfo ctfInfo;
34  private Icon ctficon;
35 
36  public void setPosFileFromXmipp24(String posfile) {
37  this.pos24file = posfile;
38  }
39 
40  public String getPosFileFromXmipp24() {
41  return pos24file;
42  }
43 
44  public Micrograph(String file) {
45  this(file, getName(file, 1), null);
46  }
47 
48  public Micrograph(String file, String name) {
49  this(file, name, null);
50  }
51 
52  public Micrograph(String file, CtfInfo ctfInfo) {
53  this(file, getName(file, 1), ctfInfo);
54  }
55 
56  public Micrograph(String file, String name, CtfInfo ctfInfo) {
57  this.file = file;
58  this.ctfInfo = ctfInfo;
59  String path = file;
60  if(Filename.hasPrefix(file))
61  path = Filename.removePrefix(file);
62  if (!new File(path).exists())
63  {
64  System.out.printf("path %s selfile %s\n", path, ParticlePicker.getPicker().selfile);
65  file = Filename.findImagePath(path, ParticlePicker.getPicker().selfile, true);
66  if(file == null)
67  throw new IllegalArgumentException(XmippMessage.getNoSuchFieldValueMsg("micrograph", path));
68  }
69 
70  this.name = name;
71  this.posfile = name + ext;
72  //loadDimensions(); // ensure width and height get updated
73 
74  }
75 
76  public String getPSD() {
77  return ctfInfo == null ? null : ctfInfo.psd;
78  }
79 
80  public ImagePlus getPSDImage() {
81  String psd = getPSD();
82 
83  if (psd == null || !(new File(psd).exists()))
84  return null;
85  return XmippUtil.getImagePlus(psd);
86 
87  }
88 
89  public Icon getCTFIcon() {
90  String file;
91  if (ctficon == null) {
92  String psd = getPSD();
93  if (psd == null || !(new File(psd).exists()))
94  file = (Filename.getXmippPath("resources" + File.separator
95  + "no-image.jpg"));
96  else
97  file = psd;
98  ImagePlus imp = XmippUtil.getImagePlus(file);
99  Image image = imp.getImage().getScaledInstance(120, 110,
100  Image.SCALE_SMOOTH);
101  ctficon = new ImageIcon(image);
102 
103  }
104  return ctficon;
105  }
106 
107  public static Icon getNoImageIcon() {
108  String file;
109  if (noimageicon == null) {
110  file = (Filename.getXmippPath("resources" + File.separator
111  + "no-image.jpg"));
112  ImagePlus imp = XmippUtil.getImagePlus(file);
113  Image image = imp.getImage().getScaledInstance(120, 110,
114  Image.SCALE_SMOOTH);
115  noimageicon = new ImageIcon(image);
116 
117  }
118  return noimageicon;
119  }
120 
121  public String getCTF() {
122  return ctfInfo == null ? null : ctfInfo.ctf;
123  }
124 
125  public CtfInfo getCtfInfo() {
126  return ctfInfo;
127  }
128 
129  public boolean fits(int x, int y, int size) {
130  if (x < 0 || y < 0)
131  return false;
132 
133  int radius = size / 2;
134  if (x - radius < 0 || x + radius > getWidth() || y - radius < 0
135  || y + radius > getHeigth())
136  return false;
137  return true;
138  }
139 
140  public static String getName(String file, int level) {
141  if (file == null)
142  return null;
143  // level can start at 1 for file name, 2 is for parent directory name
144  String[] tokens = file.split(File.separator);
145  if (tokens.length < level)
146  throw new IllegalArgumentException(
147  String.format(
148  "Name for micrograph is taken from level %s, invalid path ",
149  level, file));
150  String name = tokens[tokens.length - level];
151  if (level == 1) {
152  int pos = name.lastIndexOf('.');
153  if (pos != -1)
154  name = name.substring(0, pos);
155 
156  pos = tokens[0].lastIndexOf('@');
157  if (pos != -1) {
158  name = tokens[0].substring(0, pos) + "_at_" + name;
159  }
160  }
161  return name;
162  }
163 
164  public String getPosFile() {
165  return posfile;
166  }
167 
168  /* Load width and height after loaded ImagePlus */
169  public void loadDimensions() {
170 
171  if (imp != null) {
172  width = imp.getWidth();
173  height = imp.getHeight();
174  } else {
175  try {
176  ImageGeneric img = new ImageGeneric(file); // this reads the header
177  width = img.getXDim();
178  height = img.getYDim();
179  img.destroy();
180  } catch (Exception e) {
181  e.printStackTrace();
182  }
183  }
184  }
185 
186 
187 
188  public ImagePlus getImagePlus() {
189  try {
190 
191  if (imp == null) {
192  imp = XmippImageConverter.loadImage(file);
193  if (imp == null)
194  imp = new ImagePlus(file);
195 
196  }
197  return imp;
198  } catch (Exception e) {
199  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
200  throw new IllegalArgumentException(e.getMessage());
201  }
202  }
203 
204  public ImagePlus getImagePlus(List<IJCommand> filters) {
205  try {
206  if (filters.isEmpty())
207  return getImagePlus();
208 
209  if (imp == null) {
210  ImageGeneric ig = new ImageGeneric(file);
211  ig.read(ImageGeneric.FIRST_IMAGE);
212 
213  // Smooth filter should be the first one
214  // because it is applied in Xmipp
215  for (IJCommand f : filters)
216  if (f.getCommand().equals(ParticlePicker.xmippsmoothfilter)) {
217  ig.convert2Datatype(ImageGeneric.UChar);
218  ImageGeneric igsmooth = new ImageGeneric(
219  ImageGeneric.UChar);
220  igsmooth.resize(ig.getXDim(), ig.getYDim());
221  ig.smooth(igsmooth);
222  break;
223  }
224  imp = XmippImageConverter.convertToImagePlus(ig);
225  ig.destroy();
226 
227  }
228  return imp;
229  } catch (Exception e) {
230  throw new IllegalArgumentException(e.getMessage());
231  }
232  }
233 
234  public void runImageJFilters(List<IJCommand> filters) {
235  for (IJCommand f : filters)
236  // this filter was applied
237  if (!f.getCommand().equals(ParticlePicker.xmippsmoothfilter))
238  {
239  IJ.run(imp, f.getCommand(), f.getOptions());
240  }
241  }
242 
243 
244 
245  public String getFile() {
246  return file;
247  }
248 
249  public String getName() {
250  return name;
251  }
252 
253  public String toString() {
254  return name;
255  }
256 
257  public abstract boolean hasData();
258 
259  public int getWidth()
260  {
261  if(width == 0)
262  loadDimensions();
263  return width;
264  }
265 
266  public int getHeigth()
267  {
268  if(height == 0)
269  loadDimensions();
270  return height;
271  }
272 
273  public void releaseImage()
274  {
275  imp = null;
276 
277  }
278 
279  public List<? extends PickerParticle> getParticleList(){
280  return null;
281  };
282 }
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xmipp.jni.ImageGeneric.smooth
native void smooth(ImageGeneric imgResult)
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xmipp.jni.ImageGeneric.destroy
synchronized native void destroy()
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xmipp.viewer.particlepicker.Micrograph.Micrograph
Micrograph(String file, String name, CtfInfo ctfInfo)
Definition: Micrograph.java:56
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xmipp.viewer.particlepicker.Micrograph.setPosFileFromXmipp24
void setPosFileFromXmipp24(String posfile)
Definition: Micrograph.java:36
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xmipp.viewer.particlepicker.Micrograph.getParticleList
List<? extends PickerParticle > getParticleList()
Definition: Micrograph.java:279
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xmipp.viewer.particlepicker.Micrograph.Micrograph
Micrograph(String file, CtfInfo ctfInfo)
Definition: Micrograph.java:52
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xmipp.jni.Filename.hasPrefix
static boolean hasPrefix(String filename)
Definition: Filename.java:331
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xmipp.jni.ImageGeneric.convert2Datatype
final native void convert2Datatype(int dataType)
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xmipp.ij.commons.XmippUtil.getImagePlus
static ImagePlus getImagePlus(String file)
Definition: XmippUtil.java:55
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xmipp.viewer.particlepicker.Micrograph.getName
static String getName(String file, int level)
Definition: Micrograph.java:140
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xmipp.ij.commons.XmippImageConverter.loadImage
static ImagePlus loadImage(String filename)
Definition: XmippImageConverter.java:49
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xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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xmipp.jni.Filename.getXmippPath
static native String getXmippPath()
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xmipp.jni.Filename.removePrefix
static String removePrefix(String filename)
Definition: Filename.java:373
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xmipp.jni.ImageGeneric.getYDim
native int getYDim()
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xmipp.jni.ImageGeneric.getXDim
native int getXDim()
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static String findImagePath(String filename, String mdFilename, boolean shouldExist)
Definition: Filename.java:225
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static final int UChar
Definition: ImageGeneric.java:16
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void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.viewer.particlepicker.Micrograph.runImageJFilters
void runImageJFilters(List< IJCommand > filters)
Definition: Micrograph.java:234
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void resize(int w, int h)
Definition: ImageGeneric.java:90
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xmipp.viewer.particlepicker.Micrograph.getImagePlus
ImagePlus getImagePlus(List< IJCommand > filters)
Definition: Micrograph.java:204
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Micrograph(String file, String name)
Definition: Micrograph.java:48
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static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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static String getNoSuchFieldValueMsg(String field, Object value)
Definition: XmippMessage.java:52
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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1 package xmipp.viewer.particlepicker.training.gui;
2 
3 import java.util.List;
4 
5 import javax.swing.table.AbstractTableModel;
6 
7 import xmipp.viewer.particlepicker.CtfInfo;
8 import xmipp.viewer.particlepicker.training.model.Mode;
9 import xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph;
10 
11 
12 public class MicrographsTableModel extends AbstractTableModel {
13 
14 
15 
16  private List<SupervisedPickerMicrograph> micrographs;
17  private String[] columns;
18  private SupervisedPickerJFrame frame;
19 
20  public MicrographsTableModel(SupervisedPickerJFrame frame)
21  {
22  this.micrographs = frame.getParticlePicker().getMicrographs();
23  CtfInfo ctfInfo = micrographs.get(0).getCtfInfo();
24  if (ctfInfo == null || ctfInfo.defocusU == null)
25  columns = new String[]{"", "Name", "Particles", "State"};
26  else
27  columns = new String[]{"", "Name", "Particles", "State", "DefocusU"};
28  this.frame = frame;
29  }
30 
31  @Override
32  public int getColumnCount() {
33  return columns.length;
34  }
35  @Override
36  public String getColumnName(int c)
37  {
38 
39  return columns[c];
40  }
41 
42  @Override
43  public int getRowCount() {
44  return micrographs.size();
45  }
46 
47  @Override
48  public Object getValueAt(int rowIndex, int columnIndex) {
49  SupervisedPickerMicrograph m = micrographs.get(rowIndex);
50  switch (columnIndex) {
51  case 0: return rowIndex + 1;
52  case 1: return m.getName();
53  case 2:
54  if(m.getStep() == Mode.Manual)
55  return Integer.toString(m.getManualParticles().size());
56  if(m.getStep() == Mode.Available)
57  return "0";
58  if(m.getStep() == Mode.Supervised)
59  return String.format("%s + %s", m.getManualParticles().size(),
60  m.getAutomaticParticlesNumber(m.getThreshold()));
61  case 3: return m.getState();
62  case 4:
63  CtfInfo ctfInfo = m.getCtfInfo();
64  return ctfInfo.defocusU.toString();
65  default:
66  return null;
67  }
68  }
69 
70 }
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 public enum Mode {
4  Manual, // Only user-selected particles
5  Supervised, // User trains the picker, some particles are manual and others automatic
6  Available, // Micrograph is available to autopick in Xmipp
7  Review, // User checks results from autopicking and can edit
8  ReadOnly, // User can only see the coordinates
9  Extract,
10  Automatic; // Used in GenericPicker, user can setup parameters, but not modify coordinates manually
11 
12 
13  public static Mode getMode(String s)
14  {
15  if(s.equalsIgnoreCase(Mode.Manual.toString()))
16  return Mode.Manual;
17  else if(s.equalsIgnoreCase(Mode.Supervised.toString()))
18  return Mode.Supervised;
19  else if(s.equalsIgnoreCase(Mode.Review.toString()))
20  return Mode.Review;
21  else if(s.equalsIgnoreCase(Mode.Available.toString()))
22  return Mode.Available;
23  else if(s.equalsIgnoreCase(Mode.ReadOnly.toString()))
24  return Mode.ReadOnly;
25  else if(s.equalsIgnoreCase(Mode.Extract.toString()))
26  return Mode.Extract;
27  else if (s.equalsIgnoreCase(Mode.Automatic.toString()))
28  return Mode.Automatic;
29 
30  return null;
31  }
32 
33 }
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1 package xmipp.utils;
2 
3 import javax.swing.*;
4 import javax.swing.table.*;
5 import javax.swing.border.*;
6 import java.awt.*;
7 
12 public class MultilineCellRenderer extends JTextArea implements TableCellRenderer {
13 
14  public MultilineCellRenderer() {
15  setLineWrap(true);
16  setWrapStyleWord(true);
17  setOpaque(true);
18  }
19 
20  public Component getTableCellRendererComponent(JTable table, Object value,
21  boolean isSelected, boolean hasFocus, int row, int column) {
22  if (isSelected) {
23  setForeground(table.getSelectionForeground());
24  setBackground(table.getSelectionBackground());
25  } else {
26  setForeground(table.getForeground());
27  setBackground(table.getBackground());
28  }
29  setFont(table.getFont());
30  if (hasFocus) {
31  setBorder( UIManager.getBorder("Table.focusCellHighlightBorder") );
32  if (table.isCellEditable(row, column)) {
33  setForeground( UIManager.getColor("Table.focusCellForeground") );
34  setBackground( UIManager.getColor("Table.focusCellBackground") );
35  }
36  } else {
37  setBorder(new EmptyBorder(1, 2, 1, 2));
38  }
39  setText((value == null) ? "" : value.toString());
40  return this;
41  }
42 }
xmipp.utils.MultilineCellRenderer.getTableCellRendererComponent
Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)
Definition: MultilineCellRenderer.java:20
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package  xmipp.ij.plugins.maskstoolbar
 
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.ij.plugins.maskstoolbar;
6 
7 import ij.ImagePlus;
8 
13 public class Operations {
14 
15  public static void binarize(ImagePlus ip) {
16  byte pixels[] = (byte[]) ip.getProcessor().getPixels();
17 
18  for (int i = 0; i < pixels.length; i++) {
19  if (pixels[i] > 0) {
20  pixels[i] = 1;
21  }
22  }
23 
24  ip.getProcessor().setPixels(pixels);
25  //ip.updateImage();
26  }
27 }
xmipp.ij.plugins.maskstoolbar.Operations.binarize
static void binarize(ImagePlus ip)
Definition: Operations.java:15
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Params.java
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1 package xmipp.utils;
2 
3 import org.apache.commons.cli.BasicParser;
4 import org.apache.commons.cli.CommandLine;
5 import org.apache.commons.cli.Option;
6 import org.apache.commons.cli.Options;
7 import xmipp.jni.ImageGeneric;
8 
9 
14 public class Params {
15 
16  //Some constants definitions
17  public final static String FILE = "i";
18  public final static String DIRECTORY = "dir";
19  public final static String INPUT_VECTORSFILE = "vectors";
20  public final static String INPUT_CLASSESFILE = "classes";
21  public final static String INPUT_DATAFILE = "data";
22  public final static String POLL = "poll";
23  public final static String TABLE_ROWS = "rows";
24  public final static String TABLE_COLUMNS = "columns";
25  public final static String ZOOM = "zoom";
26  public final static String OPENING_MODE = "mode";
27  public final static String OPENING_MODE_DEFAULT = "default";
28  public final static String OPENING_MODE_IMAGE = "image";
29  public final static String OPENING_MODE_GALLERY = "gallery";
30  public final static String OPENING_MODE_METADATA = "metadata";
31  public final static String RENDER_IMAGES = "render";
32  public final static String VISIBLE_LABELS = "visible";
33  public final static String ORDER_LABELS = "order";
34  public final static String SORTBY_LABEL = "sortby";
35  public final static String DISPLAY_LABELS = "labels";
36  public final static String FILTER = "filter";
37  public final static String FILTERS_SEPARATOR = ",";
38  public final static String PORT = "port";
39  public final static String DOWNSAMPLING = "downsampling";
40  public final static String BAD_PIXELS_FACTOR = "factor";
41  public final static String W1 = "w1";
42  public final static String W2 = "w2";
43  public final static String RAISED_W = "raised_w";
44  public final static String MASK = "mask";
45  public final static String DEBUG = "debug";
46  public final static String MASKTOOLBAR = "mask_toolbar";
47  public final static String VIEW = "view";
48  public final static String NO_GEO = "dont_apply_geo";
49  public final static String NO_WRAP = "dont_wrap";
50  public final static String OBJECT_CMDS = "object_commands";
51  public final static String SAMPLINGRATE = "sampling_rate";
52  public final static String CHIMERAPORT = "chimera_port";
53  public final static String INVERTY = "inverty";
54  private static final String NO_RECALCULATE_CTF = "dont_recalc_ctf";
55 
56 
57  public String directory;
58  public String files[];
59  public Integer port;
60  public boolean singleSelection;
61  public String mode = OPENING_MODE_DEFAULT;
62  public boolean poll;
63  public Integer zoom;
64  public String[] renderLabels = new String[]{"first"}; //Label to render, by default first
65  public String renderLabel;
66  public String[] displayLabels;
67  public boolean debug = false;
68  public boolean mask_toolbar = false;
69  public int rows = -1, columns = -1;
70  public double bad_pixels_factor;
71  public double w1;
72  public double w2;
73  public double raised_w;
74  public double downsampling;
75  public String maskFilename;
76  public String vectorsFilename;
77  public String classesFilename;
78  public String dataFilename;
79  public int resliceView = ImageGeneric.Z_NEG;
80  public boolean useGeo = true;
81  public boolean wrap = true;
82  protected Options options;
83  protected CommandLine cmdLine;
84  public String[] visibleLabels;
85  public String[] orderLabels;
86  public String[] sortby;
87  private String block;
88  public String[] objectCommands;
89  private Float samplingRate;
90  public Integer chimeraPort;
91  public boolean inverty;
92  public boolean renderImages = true;
93  public boolean recalculateCTF = true;
94 
95 
96  public Params() {
97  }
98 
99  public Params(String args[]) {
100  options = new Options();
101  defineArgs();
102  processArgs(args);
103  }
104 
105  public void defineArgs()
106  {
107  options.addOption(FILE, true, "");
108  // It should be able to handle multiple files.
109  options.getOption(FILE).setOptionalArg(true);
110  options.getOption(FILE).setArgs(Integer.MAX_VALUE);
111 
112  options.addOption(DIRECTORY, true, "");
113  options.addOption(PORT, true, "");
114 
115  options.addOption(OPENING_MODE, true, "");
116  options.addOption(POLL, false, "");
117  options.addOption(ZOOM, true, "");
118  Option opt = new Option(RENDER_IMAGES, true, "");
119  opt.setArgs(Integer.MAX_VALUE);
120  options.addOption(opt);
121  opt = new Option(VISIBLE_LABELS, "");
122  opt.setArgs(Integer.MAX_VALUE);
123  options.addOption(opt);
124  opt = new Option(ORDER_LABELS, "");
125  opt.setArgs(Integer.MAX_VALUE);
126  options.addOption(opt);
127 
128  opt = new Option(SORTBY_LABEL, "");
129  opt.setArgs(2);
130  options.addOption(opt);
131 
132  opt = new Option(DISPLAY_LABELS, "");
133  opt.setArgs(Integer.MAX_VALUE);
134  options.addOption(opt);
135  options.addOption(DEBUG, false, "");
136  options.addOption(MASKTOOLBAR, false, "");
137  options.addOption(TABLE_ROWS, true, "");
138  options.addOption(TABLE_COLUMNS, true, "");
139 
140  options.addOption(BAD_PIXELS_FACTOR, true, "");
141 
142  options.addOption(W1, true, "");
143  options.addOption(W2, true, "");
144  options.addOption(RAISED_W, true, "");
145 
146  options.addOption(DOWNSAMPLING, true, "");
147 
148  options.addOption(MASK, false, "");
149 
150  options.addOption(INPUT_VECTORSFILE, true, "");
151  options.addOption(INPUT_CLASSESFILE, true, "");
152  options.addOption(INPUT_DATAFILE, true, "");
153  options.addOption(VIEW, true, "z");
154  options.addOption(NO_GEO, false, "");
155  options.addOption(NO_WRAP, false, "");
156  opt = new Option(OBJECT_CMDS, "");
157  opt.setArgs(Integer.MAX_VALUE);
158  options.addOption(opt);
159  options.addOption(SAMPLINGRATE, true, "");
160  options.addOption(CHIMERAPORT, true, "");
161  options.addOption(INVERTY, false, "");
162  // Do not offer to recalculate CFT if true
163  options.addOption(NO_RECALCULATE_CTF, false, "");
164 
165 
166  }
167 
168 
169  public void processArgs(String args[]) {
170 
171 
172  try {
173  BasicParser parser = new BasicParser();
174  cmdLine = parser.parse(options, args);
175 
176  if (cmdLine.hasOption(FILE)) {
177  files = cmdLine.getOptionValues(FILE);
178  }
179 
180  if (cmdLine.hasOption(DIRECTORY)) {
181  directory = cmdLine.getOptionValue(DIRECTORY);
182  }
183 
184  if (cmdLine.hasOption(PORT)) {
185  port = Integer.parseInt(cmdLine.getOptionValue(PORT));
186  }
187 
188  if (cmdLine.hasOption(OPENING_MODE)) {
189  mode = cmdLine.getOptionValue(OPENING_MODE);
190  } else {
191  mode = OPENING_MODE_DEFAULT;
192  }
193 
194  poll = cmdLine.hasOption(POLL);
195 
196  if (cmdLine.hasOption(ZOOM)) {
197  zoom = Integer.parseInt(cmdLine.getOptionValue(ZOOM));
198  }
199 
200  if(cmdLine.hasOption(RENDER_IMAGES))
201  {
202  renderLabels = cmdLine.getOptionValues(RENDER_IMAGES);
203  renderImages = !(renderLabels.length == 1 && renderLabels[0].equalsIgnoreCase("no"));
204 
205  }
206  if(cmdLine.hasOption(VISIBLE_LABELS))
207  {
208  visibleLabels = cmdLine.getOptionValues(VISIBLE_LABELS);
209  }
210  if(cmdLine.hasOption(ORDER_LABELS))
211  {
212  orderLabels = cmdLine.getOptionValues(ORDER_LABELS);
213  }
214  if(cmdLine.hasOption(SORTBY_LABEL))
215  {
216 
217  sortby = cmdLine.getOptionValues(SORTBY_LABEL);
218 
219  }
220  if(cmdLine.hasOption(DISPLAY_LABELS))
221  displayLabels = cmdLine.getOptionValues(DISPLAY_LABELS);
222 
223  debug = cmdLine.hasOption(DEBUG);
224  mask_toolbar = cmdLine.hasOption(MASKTOOLBAR);
225 
226  if (cmdLine.hasOption(TABLE_ROWS)) {
227  rows = Integer.parseInt(cmdLine.getOptionValue(TABLE_ROWS));
228  }
229 
230  if (cmdLine.hasOption(TABLE_COLUMNS)) {
231  columns = Integer.parseInt(cmdLine.getOptionValue(TABLE_COLUMNS));
232  }
233 
234  if (cmdLine.hasOption(BAD_PIXELS_FACTOR)) {
235  bad_pixels_factor = Double.parseDouble(cmdLine.getOptionValue(BAD_PIXELS_FACTOR));
236  System.out.println("bad_pixels.-.. "+bad_pixels_factor);
237  }
238 
239  if (cmdLine.hasOption(W1)) {
240  w1 = Double.parseDouble(cmdLine.getOptionValue(W1));
241  }
242 
243  if (cmdLine.hasOption(W2)) {
244  w2 = Double.parseDouble(cmdLine.getOptionValue(W2));
245  }
246 
247  if (cmdLine.hasOption(RAISED_W)) {
248  raised_w = Double.parseDouble(cmdLine.getOptionValue(RAISED_W));
249  }
250 
251  if (cmdLine.hasOption(DOWNSAMPLING)) {
252  downsampling = Double.parseDouble(cmdLine.getOptionValue(DOWNSAMPLING));
253  }
254 
255 
256 
257  if (cmdLine.hasOption(INPUT_VECTORSFILE)) {
258  vectorsFilename = cmdLine.getOptionValue(INPUT_VECTORSFILE);
259  }
260 
261  if (cmdLine.hasOption(INPUT_CLASSESFILE)) {
262  classesFilename = cmdLine.getOptionValue(INPUT_CLASSESFILE);
263  }
264 
265  if (cmdLine.hasOption(INPUT_DATAFILE)) {
266  dataFilename = cmdLine.getOptionValue(INPUT_DATAFILE);
267  }
268 
269 
270  useGeo = !cmdLine.hasOption(NO_GEO);
271  wrap = !cmdLine.hasOption(NO_WRAP);
272  recalculateCTF = !cmdLine.hasOption(NO_RECALCULATE_CTF);
273 
274  if (cmdLine.hasOption(VIEW)){
275  String view = cmdLine.getOptionValue(VIEW);
276  if (view.equals("z"))
277  resliceView = ImageGeneric.Z_NEG;
278  else if (view.equals("y"))
279  resliceView = ImageGeneric.Y_NEG;
280  else if (view.equals("x"))
281  resliceView = ImageGeneric.X_NEG;
282  else if (view.equals("z_pos"))
283  resliceView = ImageGeneric.Z_POS;
284  else if (view.equals("y_pos"))
285  resliceView = ImageGeneric.Y_POS;
286  else if (view.equals("x_pos"))
287  resliceView = ImageGeneric.X_POS;
288  }
289 
290  if(cmdLine.hasOption(OBJECT_CMDS))
291  objectCommands = cmdLine.getOptionValues(OBJECT_CMDS);
292 
293  if (cmdLine.hasOption(SAMPLINGRATE)) {
294  samplingRate = Float.parseFloat(cmdLine.getOptionValue(SAMPLINGRATE));
295  }
296  if (cmdLine.hasOption(CHIMERAPORT)) {
297  chimeraPort = Integer.parseInt(cmdLine.getOptionValue(CHIMERAPORT));
298  }
299  inverty = cmdLine.hasOption(INVERTY);
300 
301 
302 
303  } catch (Exception ex) {
304  ex.printStackTrace();
305  }
306  }
307 
308  public String getRenderLabel()
309  {
310  return renderLabels[0];
311  }
312 
313  public String[] getDisplayLabels()
314  {
315  return displayLabels;
316  }
317 
318  public void setBlock(String block)
319  {
320  this.block = block;
321  }
322 
323  public String getBlock()
324  {
325  return block;
326  }
327 
328  public boolean isMask() {
329  if(cmdLine == null)
330  return false;
331  return cmdLine.hasOption("mask");
332  }
333 
334  public Float getSamplingRate()
335  {
336  return samplingRate;
337  }
338 
339  public Integer getChimeraPort()
340  {
341  return chimeraPort;
342  }
343 
344  public void setChimeraPort(int i) {
345  chimeraPort = i;
346  }
347 
348 }
xmipp.utils.Params.displayLabels
String [] displayLabels
Definition: Params.java:66
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xmipp.utils.Params.DIRECTORY
static final String DIRECTORY
Definition: Params.java:18
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Definition: Params.java:24
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boolean useGeo
Definition: Params.java:80
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Integer chimeraPort
Definition: Params.java:90
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Options options
Definition: Params.java:82
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String [] sortby
Definition: Params.java:86
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Definition: Params.java:83
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xmipp.utils.Params.W1
static final String W1
Definition: Params.java:41
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void processArgs(String args[])
Definition: Params.java:169
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xmipp.utils.Params.MASKTOOLBAR
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Definition: Params.java:46
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Definition: Params.java:17
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Definition: Params.java:75
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static final String PORT
Definition: Params.java:38
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static final String W2
Definition: Params.java:42
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Definition: Params.java:74
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Definition: Params.java:48
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xmipp.jni.ImageGeneric.Y_POS
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Definition: ImageGeneric.java:38
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Definition: Params.java:70
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xmipp.utils.Params.mask_toolbar
boolean mask_toolbar
Definition: Params.java:68
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static final String DISPLAY_LABELS
Definition: Params.java:35
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Definition: ImageGeneric.java:39
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xmipp.utils.Params.getDisplayLabels
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Definition: Params.java:313
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static final String ORDER_LABELS
Definition: Params.java:33
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xmipp.utils.Params.vectorsFilename
String vectorsFilename
Definition: Params.java:76
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xmipp.utils.Params.OPENING_MODE
static final String OPENING_MODE
Definition: Params.java:26
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static final String VIEW
Definition: Params.java:47
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xmipp.utils.Params.isMask
boolean isMask()
Definition: Params.java:328
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xmipp.utils.Params.getBlock
String getBlock()
Definition: Params.java:323
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xmipp.utils.Params.NO_WRAP
static final String NO_WRAP
Definition: Params.java:49
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xmipp.utils.Params.TABLE_ROWS
static final String TABLE_ROWS
Definition: Params.java:23
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String [] orderLabels
Definition: Params.java:85
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xmipp.utils.Params.renderImages
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Definition: Params.java:92
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Definition: Params.java:37
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Params(String args[])
Definition: Params.java:99
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Definition: Params.java:27
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Definition: Params.java:31
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xmipp.utils.Params.getChimeraPort
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Definition: Params.java:339
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Definition: Params.java:78
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Definition: Params.java:19
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xmipp.utils.Params.ZOOM
static final String ZOOM
Definition: Params.java:25
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xmipp.jni.ImageGeneric.Z_NEG
static final int Z_NEG
Definition: ImageGeneric.java:35
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xmipp.utils.Params.recalculateCTF
boolean recalculateCTF
Definition: Params.java:93
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xmipp.utils.Params.directory
String directory
Definition: Params.java:57
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xmipp.utils.Params.classesFilename
String classesFilename
Definition: Params.java:77
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xmipp.jni.ImageGeneric.Z_POS
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Definition: ImageGeneric.java:36
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xmipp.utils.Params.OPENING_MODE_GALLERY
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Definition: Params.java:29
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xmipp.utils.Params.objectCommands
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Definition: Params.java:88
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xmipp.utils.Params.FILTER
static final String FILTER
Definition: Params.java:36
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xmipp.utils.Params.OPENING_MODE_METADATA
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Definition: Params.java:30
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xmipp.utils.Params.OPENING_MODE_IMAGE
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Definition: Params.java:28
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Definition: Params.java:22
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Definition: Params.java:344
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Definition: Params.java:40
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xmipp.utils.Params.INPUT_CLASSESFILE
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Definition: Params.java:20
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Definition: Params.java:53
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Definition: Params.java:52
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Definition: Params.java:60
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xmipp.utils.Params.SAMPLINGRATE
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Definition: Params.java:51
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xmipp.utils.Params.INPUT_DATAFILE
static final String INPUT_DATAFILE
Definition: Params.java:21
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Definition: Params.java:43
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Definition: Params.java:50
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Definition: Params.java:65
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xmipp.jni.ImageGeneric.Y_NEG
static final int Y_NEG
Definition: ImageGeneric.java:37
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xmipp.utils.Params.MASK
static final String MASK
Definition: Params.java:44
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Definition: Params.java:334
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Definition: Params.java:34
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Definition: Params.java:318
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Definition: ImageGeneric.java:40
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Definition: Params.java:64
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Definition: Params.java:91
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Definition: Params.java:32
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package  xmipp.viewer.particlepicker
 
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1 package xmipp.viewer.particlepicker;
2 
3 import ij.gui.ImageCanvas;
4 
5 import java.awt.Color;
6 import java.awt.Graphics;
7 import java.awt.Rectangle;
8 import java.awt.event.*;
9 import javax.swing.SwingUtilities;
10 import xmipp.utils.XmippDialog;
11 import xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame;
12 import xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph;
13 import xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle;
14 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph;
15 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle;
16 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame;
17 import xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph;
18 
19 public class ParticleCanvas extends ImageCanvas implements MouseMotionListener, MouseListener
20 {
21 
22  private PickerParticle particle;
23  private int size;
24  private int lastx, lasty;
25  private boolean dragged;
26  private ParticlePickerJFrame frame;
27  private ParticlePickerCanvas canvas;
28  private int side;
29 
30 
31  public ParticleCanvas(PickerParticle pickerParticle, ParticlePickerJFrame frame)
32  {
33  super(pickerParticle.getMicrograph().getImagePlus());
34  this.particle = pickerParticle;
35  this.frame = frame;
36  this.canvas = (pickerParticle instanceof TiltedParticle) ? ((TiltPairPickerJFrame) frame).getTiltedCanvas() : frame.getCanvas();
37 
38  this.size = (int) (frame.getParticlePicker().getSize());
39  side = frame.getSide();
40  setMagnification((float) side / size);
41  setDrawingSize(side, side);
42  addMouseMotionListener(this);
43  addMouseListener(this);
44  }
45 
46  public void paint(Graphics g)
47  {
48  Rectangle source = new Rectangle(particle.getX0(size), particle.getY0(size), size, size);
49  setSourceRect(source);
50  super.paint(g);
51  g.setColor(Color.white);
52  g.drawRect(0, 0, side - 1, side - 1);
53 
54  if(particle instanceof UntiltedParticle){
55  String type = "U";
56  g.drawString(type, 5, side - 2);
57  } else if(particle instanceof TiltedParticle) {
58  String type = "T";
59  g.drawString(type, 5, side - 2);
60  }
61  }
62 
63  @Override
64  public void mouseDragged(MouseEvent e)
65  {
66  if (dragged)
67  {
68  int movex = lastx - e.getX();
69  int movey = lasty - e.getY();
70  int x = particle.getX() + movex;
71  int y = particle.getY() + movey;
72  try
73  {
74  particle.setPosition(x, y);
75  repaint();
76  canvas.repaint();
77  frame.setChanged(true);
78  }
79  catch (Exception ex)
80  {
81  canvas.repaint();
82  repaint();
83  XmippDialog.showInfo(frame, ex.getMessage());
84 
85  }
86  }
87  lastx = e.getX();
88  lasty = e.getY();
89  }
90 
91  @Override
92  public void mousePressed(MouseEvent e)
93  {
94  if (frame.isPickingAvailable(e))
95  {
96  dragged = true;
97  lastx = e.getX();
98  lasty = e.getY();
99 
100  if (SwingUtilities.isLeftMouseButton(e) && e.isShiftDown()) {
101  if (frame instanceof SupervisedPickerJFrame)
102  ((SupervisedPickerMicrograph) frame.getMicrograph()).removeParticle(particle, ((SupervisedPickerJFrame) frame).getParticlePicker());
103  else if (frame instanceof TiltPairPickerJFrame) {
104  if (frame.getMicrograph() instanceof UntiltedMicrograph)
105  ((UntiltedMicrograph) frame.getMicrograph()).removeParticle((UntiltedParticle) particle);
106  else if (frame.getMicrograph() instanceof TiltedMicrograph)
107  ((TiltedMicrograph) frame.getMicrograph()).removeParticle((TiltedParticle) particle);
108  }
109  canvas.repaint();
110  frame.updateMicrographsModel();
111  frame.loadParticles(false);
112  }else
113  {
114  canvas.moveTo(particle);
115  canvas.refreshActive(particle);
116  }
117  }
118 
119  }
120 
121  @Override
122  public void mouseReleased(MouseEvent e)
123  {
124  dragged = false;
125 
126  }
127 }
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xmipp.jni.Particle.setPosition
void setPosition(int x, int y)
Definition: Particle.java:65
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xmipp.viewer.particlepicker.ParticlePickerJFrame.setChanged
abstract void setChanged(boolean changed)
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
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xmipp.viewer.particlepicker.ParticleCanvas.ParticleCanvas
ParticleCanvas(PickerParticle pickerParticle, ParticlePickerJFrame frame)
Definition: ParticleCanvas.java:31
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xmipp.viewer.particlepicker.ParticlePickerCanvas.refreshActive
abstract void refreshActive(PickerParticle p)
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ParticlePickerCanvas.java
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1 package xmipp.viewer.particlepicker;
2 
3 import ij.gui.ImageWindow;
4 
5 import java.awt.BasicStroke;
6 import java.awt.Color;
7 import java.awt.Cursor;
8 import java.awt.Dimension;
9 import java.awt.Graphics;
10 import java.awt.Graphics2D;
11 import java.awt.Image;
12 import java.awt.Point;
13 import java.awt.Rectangle;
14 import java.awt.Stroke;
15 import java.awt.Toolkit;
16 import java.awt.event.KeyEvent;
17 import java.awt.event.MouseEvent;
18 import java.awt.event.MouseWheelEvent;
19 import java.util.ArrayList;
20 import java.util.List;
21 
22 import xmipp.ij.commons.XmippImageCanvas;
23 import xmipp.ij.commons.XmippImageWindow;
24 import xmipp.jni.Particle;
25 import xmipp.utils.XmippDialog;
26 import xmipp.utils.XmippResource;
27 import xmipp.viewer.particlepicker.training.model.ManualParticle;
28 
29 import javax.swing.*;
30 
31 public abstract class ParticlePickerCanvas<P extends PickerParticle> extends XmippImageCanvas
32 {
33  public final static BasicStroke dashedst = new BasicStroke(2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 10.0f, new float[] { 10.0f }, 0.0f);
34  public final static BasicStroke continuousst = new BasicStroke(2.0f);
35  public final static BasicStroke thinContinuousSt = new BasicStroke(1.5f);
36  public final static BasicStroke activest = new BasicStroke(1.5f);
37 
38  protected ParticlePickerJFrame frame;
39  protected Micrograph micrograph;
40  protected ParticlePicker picker;
41  protected XmippImageWindow iw;
42  protected Cursor eraserCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("eraserC.png").getImage(), new Point(3, 31), "Eraser");
43  protected Cursor linearCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("linearPickingC.png").getImage(), new Point(0, 0), "Linear");
44  private byte pickingCursorIndex = 1;
45  protected Cursor pickingCursor = getPickingCursor(pickingCursorIndex);
46  protected P active;
47 
48  Dimension size;
49  public void setMicrograph(Micrograph m)
50  {
51  micrograph = m;
52 
53  }
54 
55  protected boolean activemoved;
56 
57  private static boolean tongleSetSelected = false;
58 
59  public ParticlePickerCanvas(ParticlePickerJFrame frame)
60  {
61  this(frame, frame.getMicrograph());
62  }
63 
64  public ParticlePickerCanvas(ParticlePickerJFrame frame, Micrograph micrograph)
65  {
66  super(micrograph.getImagePlus(frame.getParticlePicker().getFilters()));
67  this.frame = frame;
68  this.picker = frame.getParticlePicker();
69  this.micrograph = micrograph;
70  micrograph.runImageJFilters(picker.getFilters());
71 
72  addKeyListener(this);
73  addMouseMotionListener(this);
74 
75  this.iw = new XmippImageWindow(getImage(), this, null);
76  getFrame().displayZoom(getMagnification());
77  iw.setTitle(getMicrograph().getName());
78 
79  }
80 
81  public void keyPressed(KeyEvent e)
82  {
83  super.keyPressed(e);
84 
85  P active = getActive();
86  int step = 1;
87  int code = e.getKeyCode();
88 // int x = screenX(imp.getWidth()/2);
89 // int y = screenY(imp.getHeight()/2);
90  if(active != null)
91  {
92  if (code == KeyEvent.VK_UP)
93  {
94  setActiveMoved(true);
95  manageActive(active.getX(), active.getY() - step);
96  }
97  else if (code == KeyEvent.VK_DOWN)
98  {
99  setActiveMoved(true);
100  manageActive(active.getX(), active.getY() + step);
101  }
102  else if (code == KeyEvent.VK_LEFT)
103  {
104  setActiveMoved(true);
105  manageActive(active.getX() - step, active.getY());
106  }
107  else if (code == KeyEvent.VK_RIGHT)
108  {
109  setActiveMoved(true);
110  manageActive(active.getX() + step, active.getY());
111  }
112  else if (code == ParticlePickerJFrame.ERASE_ACTIVE)
113  {
114  removeParticle((P) active);
115  this.active = getLastParticle();
116  refresh();
117  }
118  }
119  if (code == ParticlePickerJFrame.TOGGLE_MARKER_KEY)
120  {
121  getFrame().circlechb.setSelected(tongleSetSelected);
122  getFrame().rectanglechb.setSelected(tongleSetSelected);
123  tongleSetSelected = !tongleSetSelected;
124  }else if (code == ParticlePickerJFrame.TOGGLE_ERASE_MODE_KEY){
125  // Toggle erase mode.
126  getFrame().activateEraseMode();
127  } else if (code == ParticlePickerJFrame.NEXT_MICROGRAPH_KEY)
128  {
129  getFrame().moveToNextMicrograph();
130  } else if (code == ParticlePickerJFrame.PREVIOUS_MICROGRAPH_KEY)
131  {
132  getFrame().moveToPreviousMicrograph();
133  }else if (code == ParticlePickerJFrame.TOGGLE_LINEAR_MODE_KEY){
134  // Toggle linear mode
135  getFrame().activateLinearMode();
136  }else if (code == ParticlePickerJFrame.TOGGLE_NORMAL_MODE_KEY){
137  // Toggle linear mode
138  getFrame().activateNormalMode();
139 
140  }else if (code == KeyEvent.VK_PLUS){
141  changePickingCursor((byte) (pickingCursorIndex+1));
142 
143  }else if (code == KeyEvent.VK_MINUS){
144  changePickingCursor((byte) (pickingCursorIndex-1));
145 
146  }else
147  return;// do not repaint if not needed
148  repaint();
149  }
150 
151  private void changePickingCursor(byte index) {
152  Cursor newCursor = getPickingCursor(index);
153 
154  if (newCursor != null){
155  pickingCursorIndex = index;
156  pickingCursor = newCursor;
157  setCustomCursor();
158  }
159  }
160 
161  private Cursor getPickingCursor(int index) {
162 
163  String pickingCursorImageName = "pickingC" + index + ".png";
164 
165  ImageIcon icon = XmippResource.getIcon(pickingCursorImageName);
166 
167  if (icon.getIconHeight() == -1) {
168  // Fall back on crosshair cursor
169  return crosshairCursor;
170  } else {
171  return Toolkit.getDefaultToolkit().createCustomCursor(icon.getImage(), new Point(2, 0), "Picking");
172  }
173 
174  }
175 
176  protected void captureWindowSize(){
177  size = this.imp.getWindow().getSize();
178  this.imp.getWindow().setIgnoreRepaint(true);
179 
180  }
181  protected void restoreWindowSize(){
182  if (size != null) {
183  this.imp.getWindow().setSize(size);
184  this.imp.getWindow().setIgnoreRepaint(false);
185  }
186  }
187 
188  public void zoomIn(int sx, int sy)
189  {
190 
191  captureWindowSize();
192 
193  super.zoomIn(sx, sy);
194  getFrame().displayZoom(getMagnification());
195 
196  restoreWindowSize();
197  }
198 
199  public void zoomOut(int sx, int sy)
200  {
201  captureWindowSize();
202 
203  super.zoomOut(sx, sy);
204  getFrame().displayZoom(getMagnification());
205 
206  restoreWindowSize();
207  }
208 
209  protected abstract P getLastParticle();
210 
211  protected abstract void manageActive(int x, int y);
212 
213  public boolean hasActiveParticle()
214  {
215  return active != null;
216  }
217 
218  protected void setActiveMoved(boolean b)
219  {
220  activemoved = b;
221  }
222 
223  protected void refresh()
224  {
225  getFrame().updateMicrographsModel();
226  getFrame().setChanged(true);
227  repaint();
228  }
229 
230  public ImageWindow getIw()
231  {
232  return iw;
233  }
234 
235  public void moveTo(PickerParticle p)
236  {
237  int width = (int) getSrcRect().getWidth();
238  int height = (int) getSrcRect().getHeight();
239  int x0 = p.getX() - width / 2;
240  if (x0 < 0)
241  x0 = 0;
242  if (x0 + width > imp.getWidth())
243  x0 = imp.getWidth() - width;
244  int y0 = p.getY() - height / 2;
245  if (y0 < 0)
246  y0 = 0;
247  if (y0 + height > imp.getHeight())
248  y0 = imp.getHeight() - height;
249  Rectangle r = new Rectangle(x0, y0, width, height);
250  if (!getSrcRect().contains(r))
251  {
252  setSourceRect(r);
253  repaint();
254  }
255  }
256 
257  public void mouseEntered(MouseEvent e)
258  {
259  super.mouseEntered(e);
260  this.requestFocus();
261  setCustomCursor(e);
262  }
263 
264  public void mouseExited(MouseEvent e)
265  {
266  super.mouseExited(e);
267  setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
268 
269  }
270 
271  public void setCustomCursor(){
272  setCustomCursor(null);
273  }
274  protected void setCustomCursor(MouseEvent e)
275  {
276  boolean proceed = true;
277 
278  if (e != null) {
279  proceed = getFrame().isPickingAvailable(e);
280  }
281 
282  if (proceed) {
283  if (getFrame().isEraserMode(null))
284  setCursor(eraserCursor);
285 
286  else if (getFrame().isLinearMode())
287  setCursor(linearCursor);
288 
289  else
290  setCursor(pickingCursor);
291  }
292  }
293 
294  public abstract void refreshActive(PickerParticle p);
295 
296 
297  public abstract P getActive();
298 
299 
300  public abstract ParticlePickerJFrame getFrame();
301 
302 
303  protected void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
304  {
305  drawShape(g2, p.getX(), p.getY(), picker.getSize(), all, stroke);
306  }
307 
308  protected void drawShape(Graphics2D g2, ManualParticle p, boolean all)
309  {
310  drawShape(g2, p, all, continuousst);
311  }
312 
313  protected void drawShape(Graphics2D g2, int x, int y, int size, boolean all)
314  {
315  drawShape(g2, x, y, size, all, continuousst);
316 
317  }
318  protected void drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)
319  {
320  g2.setColor(color);
321  drawShape(g2, x, y, size, all, stroke);
322  }
323  protected void drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)
324  {
325 
326  g2.setStroke(stroke);
327  int length = (int) (size * magnification);
328  int radius = (int) (size / 2. * magnification);
329  x = getXOnImage(x);
330  y = getYOnImage(y);
331  int distance = Math.min(10, (int) (radius/4. * magnification));
332 
333  if (getFrame().isShapeSelected(Shape.Rectangle) || all)
334  g2.drawRect(x - radius, y - radius, length, length);
335  if (getFrame().isShapeSelected(Shape.Circle) || all)
336  g2.drawOval(x - radius, y - radius, length, length);
337  if (getFrame().isShapeSelected(Shape.Center) || all)
338  {
339  g2.setStroke(activest);
340  g2.drawLine(x, y - distance, x, y + distance);
341  g2.drawLine(x + distance, y, x - distance, y);
342  }
343  }
344 
345 
346  protected void drawLine(double alpha, Graphics2D g2)
347  {
348  int width = imp.getWidth();
349  int height = imp.getHeight();
350  double m;
351  double x1, y1, x2, y2;
352  if (alpha != Math.PI / 2)
353  {
354  m = Math.tan(alpha - Math.PI / 2);
355 
356  double y = height / 2.f;
357  double x = y / m;
358 
359  if (Math.abs(x) > width / 2.f)// cuts in image sides
360  {
361  x1 = width;// on image
362  y1 = getYCutOnImage(m, width / 2.f);
363  x2 = 0;
364  y2 = getYCutOnImage(m, -width / 2.f);
365  }
366  else
367  // cuts in image top and bottom
368  {
369  y1 = 0;
370  x1 = getXCutOnImage(m, height / 2.f);
371  y2 = height;
372  x2 = getXCutOnImage(m, -height / 2.f);
373  }
374  }
375  else
376  {
377  x1 = 0;
378  y1 = y2 = height / 2.f;
379  x2 = width;
380 
381  }
382  Color ccolor = g2.getColor();
383  g2.setColor(Color.yellow);
384  g2.drawLine((int) (x1 * magnification), (int) (y1 * magnification), (int) (x2 * magnification), (int) (y2 * magnification));
385  g2.setColor(ccolor);
386  }
387 
388 
389  public int getXOnImage(int x)
390  {
391  int x0 = (int) getSrcRect().getX();
392  return (int) ((x - x0) * magnification);
393  }
394 
395  public int getYOnImage(int y)
396  {
397  int y0 = (int) getSrcRect().getY();
398  return (int) ((y - y0) * magnification);
399  }
400 
401  private double getYCutOnImage(double m, double x)
402  {
403  int height = imp.getHeight();
404  return height / 2.f - m * x;
405  }
406 
407 
408  private double getXCutOnImage(double m, double y)
409  {
410  int width = imp.getWidth();
411  return y / m + width / 2.f;
412  }
413 
414  public void updateMicrograph()
415  {
416  Micrograph m = getFrame().getMicrograph();
417  updateMicrograph(m);
418  }
419 
420  public void updateMicrograph(Micrograph m)
421  {
422  getMicrograph().releaseImage();
423  setMicrograph(m);
424  imp = m.getImagePlus(picker.getFilters());
425  m.runImageJFilters(picker.getFilters());
426  refreshActive(null);
427  Rectangle previousRect = (Rectangle)srcRect.clone();
428  int previousDstWidth = dstWidth;
429  int previousDstHeight = dstHeight;
430  if(iw.isClosing())
431  iw = new XmippImageWindow(getImage(), this, null);
432  iw.setImage(imp);
433  double zoom = getParticlePicker().getZoom();
434  int imageWidth = imp.getWidth();
435  int imageHeight = imp.getHeight();
436  if(zoom != -1)
437  {
438 
439  setDrawingSize(previousDstWidth, previousDstHeight);
440  if (previousRect.width < imageWidth && previousRect.height < imageHeight)
441  setSourceRect(previousRect);
442  setMagnification(zoom);
443  iw.pack();
444  }
445  else
446  iw.maximize();
447  getFrame().displayZoom(getMagnification());
448  iw.setTitle(getMicrograph().getName());
449 
450  }
451 
452  protected void erase(MouseEvent e)
453  {
454  // Get the eraser size and coordinates and apply zoom
455  int size = getFrame().getEraserSize()/2;
456  double distance = (size);
457 
458  // Add the radio of the particles: we want to eras particle if eraser touches the circle of the particle
459  distance = distance + (getParticlePicker().getSize()/2);
460 
461 
462  int cursorX = offScreenX(e.getX());
463  int cursorY = offScreenY (e.getY());
464 
465  List<PickerParticle> particlesToDelete = new ArrayList<PickerParticle>();
466  // Go through the list of particles
467  for (PickerParticle particle : getMicrograph().getParticleList()) {
468 
469  // if particle is within the distance (inside eraser)
470  int length = length(particle.getX(),particle.getY(), cursorX, cursorY);
471 
472  if (length <= distance){
473  particlesToDelete.add(particle);
474  }
475  }
476 
477  // For each particle to delete
478  for (PickerParticle particle : particlesToDelete) {
479  removeParticle((P) particle);
480  }
481 
482  active = getLastParticle();
483  refresh();
484  paintEraser(e);
485  }
486 
487  private int length (int x, int y, int x1, int y1) {
488 
489  return (int) Math.ceil(Math.sqrt(Math.pow((x - x1), 2) + Math.pow((y - y1), 2)));
490 
491  }
492 
493  protected abstract void removeParticle(P particleToRemove);
494 
495  public abstract Micrograph getMicrograph();
496 
497  protected void moveActiveParticle(int x, int y)
498  {
499  if (active == null)
500  return;
501  try{
502  active.setPosition(x, y);
503 
504  }catch (Exception e){
505  XmippDialog.showError(getFrame(), e.getMessage());
506  }
507  if (getFrame().getParticlesJDialog() != null)
508  active.getParticleCanvas(getFrame()).repaint();
509  }
510 
511  public void paint(Graphics g) {
512  Graphics offgc;//Off screen graphic
513  Image offscreen = null;//Off screen image
514  Dimension d = getSize();
515 
516  // create the offscreen buffer and associated Graphics
517  offscreen = createImage(d.width, d.height);
518  offgc = offscreen.getGraphics();
519 
520  super.paint(offgc);//super paint in off screen
521  //my paint in offscreen
522  Graphics2D g2 = (Graphics2D) offgc;
523  doCustomPaint(g2);
524  //drawing offscreen image
525  g.drawImage(offscreen, 0, 0, this);
526  }
527 
528  public void mouseMoved(MouseEvent e) {
529  super.mouseMoved(e);
530 
531  if (getFrame().isEraserMode(e)){
532  paintEraser(e);
533  }
534  }
535 
536  protected abstract void doCustomPaint(Graphics2D g2);
537 
538  public abstract ParticlePicker getParticlePicker();
539 
540  protected void paintEraser(MouseEvent e){
541 
542  paintEraser(e.getX(),e.getY());
543 
544  }
545 
546  private void paintEraser(int x, int y){
547 
548  Graphics2D g = (Graphics2D) this.getGraphics();
549 
550  // Repaint
551  this.paint(g);
552  // Draw a circle from the center
553  g.setColor(Color.CYAN);
554  int r = getFrame().getEraserSize();
555 
556  // Apply magnification
557  r = (int) Math.round((getMagnification()*r));
558 
559  int ovalX = x-(r/2);
560  int ovalY = y-(r/2);
561 
562  g.setStroke(continuousst);//2 pixel width
563  g.drawOval(ovalX,ovalY,r,r);
564 
565  }
566 
567  @Override
568  public void mouseWheelMoved(MouseWheelEvent e) {
569  // Resize the eraser brush
570  if (!e.isShiftDown()){
571  // if erase mode
572  if (getFrame().isEraserMode(e)){
573  getFrame().setEraserSize(getFrame().getEraserSize()+(e.getWheelRotation()*50));
574  paintEraser(e);
575  } else {
576  getFrame().processSizeMouseWheelEvent(e);
577  }
578 
579  } else {
580  super.mouseWheelMoved(e);
581 
582  }
583  }
584 
585 }
xmipp.viewer.particlepicker.ParticlePickerCanvas.doCustomPaint
abstract void doCustomPaint(Graphics2D g2)
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)
Definition: ParticlePickerCanvas.java:318
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xmipp.viewer.particlepicker.Micrograph.getParticleList
List<? extends PickerParticle > getParticleList()
Definition: Micrograph.java:279
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:323
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all)
Definition: ParticlePickerCanvas.java:308
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xmipp.viewer.particlepicker.ParticlePickerJFrame.setChanged
abstract void setChanged(boolean changed)
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xmipp.viewer.particlepicker.Micrograph.runImageJFilters
void runImageJFilters(List< IJCommand > filters)
Definition: Micrograph.java:234
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xmipp.utils.XmippResource.getIcon
static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, int x, int y, int size, boolean all)
Definition: ParticlePickerCanvas.java:313
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xmipp.viewer.particlepicker.ParticlePickerCanvas.ParticlePickerCanvas
ParticlePickerCanvas(ParticlePickerJFrame frame, Micrograph micrograph)
Definition: ParticlePickerCanvas.java:64
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.viewer.particlepicker.ParticlePickerCanvas.removeParticle
abstract void removeParticle(P particleToRemove)
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xmipp.viewer.particlepicker.ParticlePickerCanvas.refreshActive
abstract void refreshActive(PickerParticle p)
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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ParticlePickerJFrame.java File Reference
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class  xmipp.viewer.particlepicker.ParticlePickerJFrame
 
class  xmipp.viewer.particlepicker.ParticlePickerJFrame.MicrographsSelectionListener
 
class  xmipp.viewer.particlepicker.ParticlePickerJFrame.ColorActionListener
 
class  xmipp.viewer.particlepicker.ParticlePickerJFrame.ShapeItemListener
 
class  xmipp.viewer.particlepicker.NoneSelectedButtonGroup
 
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package  xmipp.viewer.particlepicker
 
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ParticlePickerJFrame.java
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1 package xmipp.viewer.particlepicker;
2 
3 import ij.IJ;
4 import ij.ImageListener;
5 import ij.ImagePlus;
6 import ij.plugin.frame.Recorder;
7 
8 import java.awt.*;
9 import java.awt.event.*;
10 import java.io.File;
11 import java.net.URL;
12 import java.net.URLClassLoader;
13 import java.text.NumberFormat;
14 import java.util.ArrayList;
15 import java.util.Collections;
16 import java.util.HashMap;
17 import java.util.LinkedHashMap;
18 import java.util.List;
19 import java.util.Locale;
20 import java.util.Map;
21 import java.util.ResourceBundle;
22 import java.util.logging.Level;
23 import java.util.logging.Logger;
24 
25 import javax.swing.*;
26 import javax.swing.event.ListSelectionEvent;
27 import javax.swing.event.ListSelectionListener;
28 import javax.swing.event.MenuEvent;
29 import javax.swing.event.MenuListener;
30 
31 import xmipp.ij.commons.InputFieldsMessageDialog;
32 import xmipp.ij.commons.Tool;
33 import xmipp.ij.commons.XmippApplication;
34 import xmipp.ij.commons.XmippImageJ;
35 import xmipp.ij.commons.XmippUtil;
36 import xmipp.jni.Filename;
37 import xmipp.utils.ColorIcon;
38 import xmipp.utils.QuickHelpJDialog;
39 import xmipp.utils.XmippDialog;
40 import xmipp.utils.XmippMessage;
41 import xmipp.utils.XmippQuestionDialog;
42 import xmipp.utils.XmippResource;
43 import xmipp.utils.XmippWindowUtil;
44 import xmipp.viewer.particlepicker.extract.ExtractPickerJFrame;
45 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas;
46 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame;
47 import xmipp.viewer.particlepicker.training.model.Mode;
48 import xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker;
49 
50 public abstract class ParticlePickerJFrame extends JFrame implements ActionListener
51 {
52 
53  public static final int TOGGLE_LINEAR_MODE_KEY = KeyEvent.VK_L;
54  public static final int TOGGLE_ERASE_MODE_KEY = KeyEvent.VK_E;
55  public static final int NEXT_MICROGRAPH_KEY = KeyEvent.VK_R;
56  public static final int PREVIOUS_MICROGRAPH_KEY = KeyEvent.VK_W;
57  public static final int TOGGLE_MARKER_KEY = KeyEvent.VK_SPACE;
58  public static final int TOGGLE_NORMAL_MODE_KEY = KeyEvent.VK_P;
59  public static final int ERASE_ACTIVE = KeyEvent.VK_DELETE;
60  protected ParticlesDialog particlesdialog;
61 
62  protected JMenuItem ijmi;
63  protected JToggleButton circlechb;
64  protected JToggleButton rectanglechb;
65  protected JToggleButton centerchb;
66  protected JLabel shapelb;
67  protected JMenuItem savemi;
68  protected JMenuItem hcontentsmi;
69  protected JMenuItem pmi;
70  // protected JMenuItem importffilemi;
71  protected JMenuItem exportmi;
72  protected JMenu filtersmn;
73  protected String activefilter;
74 
75  // Particle size
76  protected JPanel sizepn;
77  protected JLabel sizelb;
78  protected JFormattedTextField sizetf;
79 
80  // Eraser size
81  protected JPanel eSizepn;
82  protected JLabel eSizelb;
83  protected JSpinner eSize;
84 
85  private List<JCheckBoxMenuItem> mifilters;
86  protected JMenu filemn;
87  protected JMenuItem importmi;
88  protected JButton colorbt;
89  protected Color color;
90  protected JPanel colorpn;
91  protected JButton resetbt;
92  protected JTable micrographstb;
93  protected ImportParticlesJDialog importpjd = null;
94  protected JMenuItem exitmi;
95  protected JLabel positionlb;
96  protected JToggleButton usezoombt;
97 
98  // MODES
99  protected ButtonGroup modesgrp; // buttons group
100  private JToggleButton normalPickingbt;// Linear picking
101  private JToggleButton linearPickingbt;// Linear picking
102  private JToggleButton eraserbt; // Erase button
103 
104  // Linear picking parameters
105  private JPanel steppn;
106  private JLabel steplb;
107  private JFormattedTextField steptf;
108 
109  private JMenuItem keyassistmi;
110  protected JMenu helpmn;
111  protected JButton savebt;
112  protected JButton saveandexitbt;
113  protected JToolBar tb;
114  protected ResourceBundle bundle;
115  protected String command;
116  protected JButton closebt;
117 
118  public ParticlePickerJFrame(ParticlePicker picker)
119  {
120  try {
121  File file = new File(Filename.getXmippPath("resources"));
122  URL[] urls = new URL[]{file.toURI().toURL()};
123  ClassLoader loader = new URLClassLoader(urls);
124  bundle = ResourceBundle.getBundle("Bundle", Locale.getDefault(), loader);
125  XmippApplication.addInstance(false);
126  setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
127  addWindowListener(new WindowAdapter()
128  {
129  public void windowClosing(WindowEvent winEvt)
130  {
131 
132  if (canExit()) close();
133 
134  }
135  });
136 
137  initMenuBar(picker);
138 
139  resetbt = XmippWindowUtil.getTextButton(bundle.getString("resetmic"), new ActionListener()
140  {
141 
142  @Override
143  public void actionPerformed(ActionEvent e)
144  {
145  String resetmsg = getResetMsg();
146  XmippQuestionDialog qd = new XmippQuestionDialog(ParticlePickerJFrame.this, resetmsg, false);
147  if (qd.showDialog())
148  resetMicrograph();
149  }
150  });
151 
152  // Create the text button
153  createZoomButton();
154 
155  savebt = XmippWindowUtil.getTextIconButton(bundle.getString("save"), "save.gif", new ActionListener()
156  {
157 
158  @Override
159  public void actionPerformed(ActionEvent arg0)
160  {
161  saveData(false);
162 
163  }
164  });
165 
166  saveandexitbt = XmippWindowUtil.getTextButton(bundle.getString("saveandexit"), new ActionListener()
167  {
168 
169  @Override
170  public void actionPerformed(ActionEvent e)
171  {
172  ParticlePicker picker = getParticlePicker();
173  if (picker.getMode() != Mode.ReadOnly)
174  picker.saveData();
175  if(picker instanceof SupervisedParticlePicker)
176  ((SupervisedParticlePicker)picker).getClassifier().setApplyChanges(true);
177 
178  if(picker.isScipionSave())
179  {
180  int count = picker.getParticlesCount();
181  if(count == 0)
182  {
183  XmippDialog.showInfo(ParticlePickerJFrame.this, XmippMessage.getEmptyFieldMsg("coordinates"));
184  return;
185  }
186  HashMap<String, String> msgfields = new HashMap<String, String>();
187  boolean createprot = picker.getPort() == null;
188  if(createprot)
189  msgfields.put("Run name:", "ProtUserCoordinates");
190 
191  String msg = String.format("<html>Are you sure you want to register a new set of Coordinates with <font color=red>%s</font> %s?", count, (count != 1)?"elements":"element");
192  InputFieldsMessageDialog dlg = new InputFieldsMessageDialog(ParticlePickerJFrame.this, "Question", msg);
193 
194  if (dlg.action == InputFieldsMessageDialog.OK_OPTION)
195  executeScipionSaveAndExit();
196 
197  }
198  else
199  close();
200 
201  }
202  });
203  closebt = XmippWindowUtil.getTextIconButton("Close", "fa-times.png", new ActionListener()
204  {
205 
206  @Override
207  public void actionPerformed(ActionEvent e)
208  {
209  if (canExit()) close();
210  }
211  });
212  if(picker.isScipionSave())
213  {
214  saveandexitbt.setText("Coordinates");
215  Image img = Toolkit.getDefaultToolkit().getImage(Filename.getXmippPath("resources" + File.separator + "fa-plus-circle.png"));
216  saveandexitbt.setIcon(new ImageIcon(img));
217  saveandexitbt.setToolTipText("Create Coordinates");
218  Color color = XmippWindowUtil.firebrick;
219  saveandexitbt.setBackground(color);
220  saveandexitbt.setForeground(Color.WHITE);
221 
222  }
223  micrographstb = new JTable();
224  micrographstb.getSelectionModel().addListSelectionListener(new MicrographsSelectionListener());
225  micrographstb.addMouseListener(new MouseListener()
226  {
227 
228  @Override
229  public void mouseReleased(MouseEvent arg0)
230  {
231  // TODO Auto-generated method stub
232 
233  }
234 
235  @Override
236  public void mousePressed(MouseEvent arg0)
237  {
238  // TODO Auto-generated method stub
239 
240  }
241 
242  @Override
243  public void mouseExited(MouseEvent arg0)
244  {
245  // TODO Auto-generated method stub
246 
247  }
248 
249  @Override
250  public void mouseEntered(MouseEvent arg0)
251  {
252  // TODO Auto-generated method stub
253 
254  }
255 
256  @Override
257  public void mouseClicked(MouseEvent arg0)
258  {
259  if (micrographstb.getSelectedRow() == -1)
260  return;
261  loadMicrograph();
262  }
263  });
264 
265  XmippWindowUtil.setScipionImageIcon(this);
266 
267  } catch (Exception ex) {
268  Logger.getLogger(ParticlePickerJFrame.class.getName()).log(Level.SEVERE, null, ex);
269  throw new IllegalArgumentException(ex);
270  }
271  }
272 
273  public void moveToNextMicrograph(){
274  int selectedRow = micrographstb.getSelectedRow();
275  selectedRow = selectedRow +1;
276  if (selectedRow < micrographstb.getRowCount()){
277  micrographstb.setRowSelectionInterval(selectedRow,selectedRow);
278  }
279  }
280 
281  public void moveToPreviousMicrograph(){
282  int selectedRow = micrographstb.getSelectedRow();
283  selectedRow = selectedRow -1;
284  if (selectedRow > -1){
285  micrographstb.setRowSelectionInterval(selectedRow,selectedRow);
286  }
287  }
288 
289  protected boolean canExit() {
290 
291  if (getParticlePicker().getParams().tmp && (getParticlePicker().isSaved() || getParticlePicker().isChanged()))
292  {
293  XmippQuestionDialog qd = new XmippQuestionDialog(ParticlePickerJFrame.this, "You are picking in a temporary folder. None of the saved or changed data will remain unless you export \"Coordinates\". Do you really want to exit?", false );
294  boolean exit = qd.showDialog();
295  if (!exit)
296  return false;
297 
298  }else if (getParticlePicker().isChanged())
299  {
300  XmippQuestionDialog qd = new XmippQuestionDialog(ParticlePickerJFrame.this, "Save changes before closing?");
301  boolean save = qd.showDialog();
302  if (save)
303  return saveData(true);
304  else if (qd.isCanceled())
305  return false;
306  }
307  return true;
308  }
309 
310  public void processSizeMouseWheelEvent(MouseWheelEvent e) {
311 
312  int notches = e.getWheelRotation();
313  increaseBoxSize(notches);
314  }
315 
316  protected class MicrographsSelectionListener implements ListSelectionListener
317  {
318 
319  @Override
320  public void valueChanged(ListSelectionEvent e)
321  {
322  if (e.getValueIsAdjusting())
323  return;
324 
325  if (micrographstb.getSelectedRow() == -1)
326  return;// Probably from fireTableDataChanged raised
327  loadMicrograph();
328  }
329  }
330 
331  protected abstract void loadMicrograph();
332 
333  public String getResetMsg()
334  {
335  return "Are you sure you want to remove all particles from micrograph?";
336  }
337 
338  private ParticlePickerJFrame getMyself(){
339  return this;
340  }
341  private void initMenuBar(ParticlePicker picker)
342  {
343  filemn = new JMenu(bundle.getString("file"));
344  helpmn = new JMenu(bundle.getString("help"));
345  savemi = new JMenuItem("Save", XmippResource.getIcon("save.gif"));
346  savemi.setMnemonic('S');
347  savemi.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, InputEvent.CTRL_DOWN_MASK));
348  savemi.addActionListener(new ActionListener()
349  {
350 
351  @Override
352  public void actionPerformed(ActionEvent e)
353  {
354  saveData(true);
355  }
356  });
357  filemn.add(savemi);
358  importmi = new JMenuItem("Import coordinates...", XmippResource.getIcon("import_wiz.gif"));
359  filemn.add(importmi);
360  if (picker.getMode() != Mode.Manual)
361  importmi.setEnabled(false);
362 
363  importmi.addActionListener(new ActionListener()
364  {
365  @Override
366  public void actionPerformed(ActionEvent e)
367  {
368  if (importpjd == null)
369  importpjd = new ImportParticlesJDialog(ParticlePickerJFrame.this);
370  importpjd.showDialog();
371 
372  }
373  });
374 
375  exitmi = new JMenuItem("Exit");
376  exitmi.addActionListener(new ActionListener()
377  {
378 
379  @Override
380  public void actionPerformed(ActionEvent arg0)
381  {
382  close();
383  }
384  });
385 
386  ijmi = new JMenuItem("ImageJ", XmippResource.getIcon("ij.gif"));
387  ijmi.setEnabled(picker.getMode() != Mode.ReadOnly);
388  ijmi.addActionListener(new ActionListener()
389  {
390 
391  @Override
392  public void actionPerformed(ActionEvent e)
393  {
394  XmippUtil.showImageJ(Tool.PICKER);
395  }
396  });
397 
398  hcontentsmi = new JMenuItem("Online help", XmippResource.getIcon("online_help.gif"));
399  hcontentsmi.addActionListener(new ActionListener()
400  {
401 
402  @Override
403  public void actionPerformed(ActionEvent e)
404  {
405  try
406  {
407  openHelpURl();
408 
409  }
410  catch (Exception ex)
411  {
412  showException(ex);
413 
414  }
415  }
416  });
417  helpmn.add(hcontentsmi);
418 
419  keyassistmi = new JMenuItem("Tips...", XmippResource.getIcon("bulb.png"));
420  keyassistmi.addActionListener(new ActionListener()
421  {
422 
423  private QuickHelpJDialog keyassistdlg;
424 
425  @Override
426  public void actionPerformed(ActionEvent e)
427  {
428  if (keyassistdlg == null)
429  keyassistdlg = new QuickHelpJDialog(ParticlePickerJFrame.this, false, "Tips", getKeyAssist());
430  keyassistdlg.setVisible(true);
431 
432  }
433  });
434  helpmn.add(keyassistmi);
435 
436  pmi = new JMenuItem("Particles", XmippResource.getIcon("table_view.gif"));
437  pmi.addActionListener(new ActionListener()
438  {
439 
440  @Override
441  public void actionPerformed(ActionEvent e)
442  {
443  loadParticles(false);
444  }
445  });
446 
447  mifilters = new ArrayList<JCheckBoxMenuItem>();
448  filtersmn = new JMenu(bundle.getString("filters"));
449  filtersmn.addMenuListener(new MenuListener()
450  {
451 
452  @Override
453  public void menuCanceled(MenuEvent arg0)
454  {
455  // TODO Auto-generated method stub
456 
457  }
458 
459  @Override
460  public void menuDeselected(MenuEvent arg0)
461  {
462  // TODO Auto-generated method stub
463 
464  }
465 
466  @Override
467  public void menuSelected(MenuEvent arg0)
468  {
469  boolean added;
470  for (JCheckBoxMenuItem mi : mifilters)
471  {
472  added = getParticlePicker().isFilterAdded(mi.getText());
473  mi.setSelected(added);
474  }
475 
476  }
477  });
478 
479  addFilterMenuItem(XmippImageJ.gaussianBlurFilter, true, picker);
480  addFilterMenuItem(ParticlePicker.xmippsmoothfilter, true, picker);
481  addFilterMenuItem(XmippImageJ.bandPassFilter, true, picker);
482  addFilterMenuItem(XmippImageJ.enhanceContrastFilter, true, picker);
483  addFilterMenuItem(XmippImageJ.brightnessContrastFilter, true, picker);
484  addFilterMenuItem(XmippImageJ.invertLUTFilter, true, picker);
485  addFilterMenuItem(XmippImageJ.substractBackgroundFilter, true, picker);
486  addFilterAppliedListener();
487  }
488 
489  protected boolean saveData(boolean notify) {
490  try {
491  getParticlePicker().saveData();
492  if (notify) showMessage("Data saved successfully");
493  setChanged(false);
494  return true;
495  } catch (Exception e1) {
496  XmippDialog.showException(getMyself(), e1);
497  return false;
498  }
499  }
500 
501  protected void addFilterAppliedListener() {
502 
503  Recorder.record = true;
504 
505  // detecting if a command is thrown by ImageJ
506 
507  ImagePlus.addImageListener(new ImageListener() {
508 
509  @Override
510  public void imageUpdated(ImagePlus imp) {
511  if(command != null)
512  {
513  getParticlePicker().updateFilters(command);
514  if(particlesdialog != null)
515  loadParticles(true);
516 
517  }
518  command = null;
519  }
520 
521  @Override
522  public void imageOpened(ImagePlus arg0) {
523 
524  }
525 
526  @Override
527  public void imageClosed(ImagePlus arg0) {
528  // TODO Auto-generated method stub
529 
530  }
531  });
532  }
533 
534  protected void openHelpURl()
535  {
536  XmippWindowUtil.openURI("https://github.com/I2PC/scipion/wiki/Picker");
537  }
538 
539  protected abstract void resetMicrograph();
540 
541  protected void enableEdition(boolean enable)
542  {
543  importmi.setEnabled(enable);
544  savemi.setEnabled(enable);
545  sizetf.setEnabled(enable);
546  colorbt.setEnabled(enable);
547  resetbt.setEnabled(enable);
548  savebt.setEnabled(enable);
549  eraserbt.setEnabled(enable);
550 
551  }
552 
553  private JCheckBoxMenuItem addFilterMenuItem(String command, boolean defaultlistener, ParticlePicker picker)
554  {
555  JCheckBoxMenuItem mi = new JCheckBoxMenuItem(command);
556  mifilters.add(mi);
557  mi.setSelected(picker.isFilterAdded(command));
558  if (defaultlistener)
559  mi.addActionListener(this);
560  filtersmn.add(mi);
561  //mi.setEnabled(picker.getMode() != Mode.ReadOnly);
562  return mi;
563  }
564 
565  @Override
566  public void actionPerformed(ActionEvent e)
567  {
568  try
569  {
570  JCheckBoxMenuItem item = (JCheckBoxMenuItem) e.getSource();
571  activefilter = item.getText();
572  if (item.isSelected())// filter added, will be registered by picker
573  // with options if needed
574  if (activefilter.equals(ParticlePicker.xmippsmoothfilter))
575  {
576  getParticlePicker().addFilter(ParticlePicker.xmippsmoothfilter, "xmipp");
577  reloadImage();
578  }
579  else
580  {
581  command = activefilter;
582  applyFilter(activefilter);
583 
584  }
585  else
586  {
587  // filter removed
588  getParticlePicker().removeFilter(activefilter);
589  reloadImage();
590  if(particlesdialog != null)
591  loadParticles(true);
592 
593  }
594  if(getParticlePicker().getMode() != Mode.ReadOnly)
595  getParticlePicker().saveConfig();
596  }
597  catch (Exception ex)
598  {
599 
600  ex.printStackTrace();
601  showException(ex);
602  }
603 
604  }
605 
606  public void applyFilter(String filter)
607  {
608  IJ.run(getMicrograph().getImagePlus(), filter, "");
609  }
610 
611  protected void reloadImage()
612  {
613  getCanvas().updateMicrograph();
614 
615  }
616 
617  public int getSide()
618  {
619  return 100;
620  }
621 
622  public abstract ParticlePickerCanvas getCanvas();
623 
624  public abstract ParticlesDialog initParticlesJDialog();
625 
626  public void loadParticles(boolean reset)
627  {
628  try
629  {
630  if(reset)
631  for (PickerParticle p : getAvailableParticles())
632  p.resetParticleCanvas();
633  if (particlesdialog == null)
634  particlesdialog = initParticlesJDialog();
635  else
636  {
637 
638  particlesdialog.loadParticles(false);
639  particlesdialog.setVisible(true);
640  }
641  }
642  catch (Exception ex)
643  {
644  showException(ex);
645  if (particlesdialog != null)
646  particlesdialog.close();
647  particlesdialog = null;
648  }
649 
650  }
651 
652  public void updateMicrographsModel()
653  {
654  updateMicrographsModel(false);
655 
656  }
657 
658  public abstract void updateMicrographsModel(boolean all);
659 
660  public ParticlesDialog getParticlesJDialog()
661  {
662  return particlesdialog;
663  }
664 
665  public abstract Micrograph getMicrograph();
666 
667  public abstract List<? extends PickerParticle> getAvailableParticles();
668 
669  public boolean isPickingAvailable(MouseEvent e)
670  {
671  if (getCanvas().getTool() != Tool.PICKER)
672  return false;
673  if (SwingUtilities.isRightMouseButton(e))
674  return false;
675  if (getParticlePicker().getMode() == Mode.ReadOnly ||
676  getParticlePicker().getMode() == Mode.Automatic)
677  return false;
678  if (e.isControlDown())
679  return false;
680  return true;
681  }
682 
683 
684 
685  public class ColorActionListener implements ActionListener
686  {
687  JColorChooser colorChooser;
688 
689  @Override
690  public void actionPerformed(ActionEvent e)
691  {
692  // Set up the dialog that the button brings up.
693  colorChooser = new JColorChooser();
694  colorChooser.setColor(getParticlePicker().getColor());
695  JDialog dialog = JColorChooser.createDialog(colorbt, "Pick a Color", true, // modal
696  colorChooser, new ActionListener()
697  {
698  @Override
699  public void actionPerformed(ActionEvent e)
700  {
701  updateColor(colorChooser.getColor());
702  getParticlePicker().setColor(colorChooser.getColor());
703  }
704  }, // OK button handler
705  null); // no CANCEL button handler
706  XmippWindowUtil.setLocation(0.5f, 0.5f, dialog);
707  dialog.setVisible(true);
708  }
709  }
710 
711  public void updateColor(Color color)
712  {
713  if (colorbt != null)
714  colorbt.setIcon(new ColorIcon(color));
715  getParticlePicker().setColor(color);
716  getCanvas().repaint();
717  getParticlePicker().saveConfig();
718  }
719 
720  protected void initShapePane()
721  {
722 
723  ShapeItemListener shapeListener = new ShapeItemListener();
724  shapelb = new JLabel("Shape:");
725  tb.add(shapelb);
726 
727  // Add shapes buttons
728  circlechb = addShapeButton("circle.png", shapeListener);
729  rectanglechb = addShapeButton("square.png", shapeListener);
730  centerchb = addShapeButton("plus.png", shapeListener);
731 
732  }
733  private JToggleButton addShapeButton(String iconName, ShapeItemListener listener){
734  Icon icon = XmippResource.getIcon(iconName);
735  JToggleButton button = new JToggleButton("", icon);
736  button.setSelected(true);
737  button.addItemListener(listener);
738  tb.add(button);
739 
740 
741  return button;
742  }
743 
744  private void createZoomButton(){
745 
746  usezoombt = new JToggleButton("-1", XmippResource.getIcon("zoom.png"));
747  usezoombt.setToolTipText("Keep zoom");
748  usezoombt.setFocusable(false);
749  usezoombt.setSelected(true);
750  usezoombt.addActionListener(new ActionListener()
751  {
752 
753  @Override
754  public void actionPerformed(ActionEvent e)
755  {
756  if(!usezoombt.isSelected())
757  getParticlePicker().setZoom(-1);
758  }
759  });
760  }
761 
762  private JToggleButton createModeButton(String iconName, int mnemonic, ItemListener itemListener, boolean selected){
763 
764  JToggleButton button = new JToggleButton("", XmippResource.getIcon(iconName));
765  button.setSelected(selected);
766  button.addItemListener(itemListener);
767  modesgrp.add(button);
768  //button.setMnemonic(mnemonic);
769  tb.add(button);
770 
771  return button;
772  }
773  public void initToolBar()
774  {
775  tb = new JToolBar();
776  tb.setFloatable(false);
777  tb.setBackground(this.color);
778 
779 
780  // To group modes buttons
781  modesgrp = new ButtonGroup();
782 
783  // Create an ItemListener to listen to mode changes
784  ItemListener changeListener = new ItemListener() {
785  @Override
786  public void itemStateChanged(ItemEvent itemEvent) {
787  showHideModeParameters();
788  }
789  };
790 
791  // Add the normal picking mode
792  normalPickingbt = createModeButton("picking.png",TOGGLE_NORMAL_MODE_KEY, changeListener, true);
793 
794  // If it's supervised picking.
795  if ((this instanceof SupervisedPickerJFrame))
796  {
797  // Linear picking mode
798  linearPickingbt = createModeButton("linearPicking.png",TOGGLE_LINEAR_MODE_KEY, changeListener, false);
799 
800  // Step pane
801  initStepPane();
802  }
803 
804  // Eraser modes
805  if (!(this instanceof ExtractPickerJFrame))
806  {
807  // Add eraser
808  eraserbt = createModeButton("eraser.png",TOGGLE_ERASE_MODE_KEY, changeListener, false);
809 
810  // Color pane
811  initColorPane(getParticlePicker().getColor());
812 
813  // Eraser size pane
814  initEraserSizePane();
815 
816  }
817 
818  tb.addSeparator();
819 
820  // Size pane
821  initSizePane();
822  tb.add(sizepn);
823 
824  // Shape pane
825  initShapePane();
826 
827  // Add color
828  if (colorbt != null) tb.add(colorpn);
829 
830  // Add step
831  if (steppn != null) tb.add(steppn);
832 
833  this.showHideModeParameters();
834 
835  }
836 
837  public boolean isEraserMode(MouseEvent e)
838  {
839  if (!eraseAvailable())
840  return false;
841 
842  boolean eraseHotKeyPressed = false;
843 
844  if (e != null) {
845  eraseHotKeyPressed = e.isShiftDown();
846  }
847 
848  return eraserbt.isSelected() || eraseHotKeyPressed;
849  }
850 
851  protected boolean eraseAvailable() {
852  return eraserbt != null;
853  }
854 
855  public void activateEraseMode(){
856  if (eraseAvailable()) {
857 
858  if (isEraserMode(null)) {
859  activateNormalMode();
860  } else {
861  eraserbt.setSelected(true);
862  setCanvasCursor();
863  showHideModeParameters();
864  }
865  }
866  }
867 
868  protected void setCanvasCursor(){
869  getCanvas().setCustomCursor();
870  }
871 
872  public boolean isLinearMode() {
873  if (linearModeAvailable()){
874  return linearPickingbt.isSelected();
875  } else {
876  return false;
877  }
878  }
879 
880  public boolean isNormalMode() {
881 
882  return normalPickingbt.isSelected();
883  }
884 
885  public void activateLinearMode(){
886  if (linearModeAvailable()) {
887 
888  if (isLinearMode()) {
889  activateNormalMode();
890  } else {
891  linearPickingbt.setSelected(true);
892  showHideModeParameters();
893  ((SupervisedPickerCanvas) getCanvas()).resetLinearPicking();
894  setCanvasCursor();
895  }
896  }
897  }
898 
899  public void activateNormalMode(){
900 
901  normalPickingbt.setSelected(true);
902  showHideModeParameters();
903  setCanvasCursor();
904 
905  }
906 
907  protected boolean linearModeAvailable() {
908  return linearPickingbt != null;
909  }
910 
911  public int getEraserSize(){
912  if (isEraserMode(null)){
913  return (Integer) eSize.getValue();
914  } else {
915  return 1;
916  }
917  }
918 
919  public void setEraserSize(int newSize){
920  if (newSize<1) newSize=1;
921  eSize.setValue(newSize);
922  }
923 
924  public int getStep(){
925  if (linearModeAvailable()){
926  return Integer.parseInt(steptf.getText());
927  } else {
928  return 1000;
929  }
930  }
931 
932  protected void showHideModeParameters(){
933 
934  boolean isEraseMode = isEraserMode(null);
935  boolean isLinearMode = isLinearMode();
936 
937  sizepn.setVisible(!isEraseMode);
938  eSizepn.setVisible(isEraseMode);
939  colorpn.setVisible(!isEraseMode);
940  if (linearModeAvailable()) steppn.setVisible(isLinearMode);
941 
942  // Shapes
943  shapelb.setVisible(!isEraseMode);
944  circlechb.setVisible(!isEraseMode);
945  centerchb.setVisible(!isEraseMode);
946  rectanglechb.setVisible(!isEraseMode);
947  }
948 
949  protected void displayZoom(double zoom)
950  {
951 
952  usezoombt.setText(String.format(Locale.US, "%.2f", zoom));
953  if(usezoombt.isSelected())
954  getParticlePicker().setZoom(zoom);
955  pack();
956  }
957 
958  class ShapeItemListener implements ItemListener
959  {
960  @Override
961  public void itemStateChanged(ItemEvent e)
962  {
963  changeShapes();
964  }
965  }
966 
967  public void changeShapes()
968  {
969  getCanvas().repaint();
970 
971  }
972 
973  public boolean isShapeSelected(Shape shape)
974  {
975  switch (shape)
976  {
977  case Rectangle:
978  return rectanglechb.isSelected();
979  case Circle:
980  return circlechb.isSelected();
981  case Center:
982  return centerchb.isSelected();
983  // case OnlyLast:
984  // return onlylastchb.isSelected();
985  }
986  return false;
987  }
988 
989  public abstract ParticlePicker getParticlePicker();
990 
991  public abstract void setChanged(boolean changed);
992 
993  protected void setTitle(){
994 
995  String title = "Xmipp Particle Picker - " + getParticlePicker().getMode();
996 
997  if (this.getParticlePicker().getParams().tmp){
998  title = title + " - in Temporal folder.";
999  }
1000  setTitle(title);
1001  }
1002  public void setSaved(boolean saved){
1003  };
1004 
1005  protected void initColorPane(Color color)
1006  {
1007  colorpn = new JPanel();
1008  colorpn.setOpaque(false);
1009  this.color = color;
1010  colorpn.add(new JLabel("Color:"));
1011  colorbt = new JButton();
1012  colorbt.setContentAreaFilled(false);
1013  colorbt.setFocusPainted(false);
1014  colorbt.setIcon(new ColorIcon(color));
1015  colorbt.setBorderPainted(false);
1016  colorbt.setMargin(new Insets(0, 0, 0, 0));
1017  colorbt.addActionListener(new ColorActionListener());
1018  colorpn.add(colorbt);
1019  }
1020 
1021  protected void initStepPane() {
1022  steppn = new JPanel();
1023  steppn.setOpaque(false);
1024 
1025  steplb = new JLabel("Step:");
1026  steppn.add(steplb);
1027 
1028 
1029  steptf = new JFormattedTextField(NumberFormat.getIntegerInstance());
1030  steptf.setColumns(3);
1031  steptf.setValue(100);
1032  steppn.add(steptf);
1033  }
1034 
1035  protected void initEraserSizePane()
1036  {
1037  eSizepn = new JPanel();
1038  eSizepn.setOpaque(false);
1039  int size = 100;
1040  eSizelb = new JLabel("Eraser size:");
1041  eSizepn.add(eSizelb);
1042  eSize = new JSpinner();
1043  JFormattedTextField text = getTextField(eSize);
1044  text.setColumns(5);
1045  eSize.setValue(size);
1046  eSizepn.add(eSize);
1047  // Default : hidden.
1048  eSizepn.setVisible(false);
1049  tb.add(eSizepn);
1050 
1051  }
1052 
1057  public JFormattedTextField getTextField(JSpinner spinner) {
1058  JComponent editor = spinner.getEditor();
1059  if (editor instanceof JSpinner.DefaultEditor) {
1060  return ((JSpinner.DefaultEditor)editor).getTextField();
1061  } else {
1062  System.err.println("Unexpected editor type: "
1063  + spinner.getEditor().getClass()
1064  + " isn't a descendant of DefaultEditor");
1065  return null;
1066  }
1067  }
1068 
1069  protected void initSizePane()
1070  {
1071  sizepn = new JPanel();
1072  sizepn.setOpaque(false);
1073  int size = getParticlePicker().getSize();
1074  sizelb = new JLabel("Size (px):");
1075  sizepn.add(sizelb);
1076  sizetf = new JFormattedTextField(NumberFormat.getIntegerInstance());
1077  sizetf.setColumns(4);
1078  sizetf.setValue(size);
1079  sizepn.add(sizetf);
1080  listenToFocusEventsOnSize();
1081  listenToChangeOnSize();
1082  // This is commented due to coredumps when rapid changes happen when pressing + or -
1083  //listenToKeysOnSize();
1084  listenToMouseOnSize();
1085  sizetf.setToolTipText("Use +, - or the mousewheel to quickly change the box size. Return will apply the size.");
1086 
1087  }
1088 
1089  private void listenToMouseOnSize() {
1090 
1091  sizetf.addMouseWheelListener(new MouseWheelListener() {
1092  @Override
1093  public void mouseWheelMoved(MouseWheelEvent mouseWheelEvent) {
1094 
1095  processSizeMouseWheelEvent(mouseWheelEvent);
1096 
1097  }
1098  });
1099  }
1100 
1101  private void listenToChangeOnSize() {
1102  sizetf.addActionListener(new ActionListener(){
1103 
1104  @Override
1105  public void actionPerformed(ActionEvent e) {
1106  // event from sizes
1107  readSizeFromTextField();
1108  }
1109  });
1110  }
1111 
1112  private void listenToFocusEventsOnSize() {
1113  sizetf.addFocusListener(new FocusListener()
1114  {
1115 
1116  @Override
1117  public void focusGained(FocusEvent fe) {
1118 
1119  sizetf.selectAll();
1120  }
1121 
1122  @Override
1123  public void focusLost(FocusEvent fe) {
1124  // event from sizes
1125  try {
1126  if(!fe.isTemporary())
1127  {
1128 
1129  sizetf.commitEdit();
1130  readSizeFromTextField();
1131  }
1132  } catch (Exception ex) {
1133  XmippDialog.showError(ParticlePickerJFrame.this, XmippMessage.getIllegalValueMsg("size", sizetf.getText()));
1134  Logger.getLogger(ParticlePickerJFrame.class.getName()).log(Level.SEVERE, null, ex);
1135  }
1136  }
1137  });
1138  }
1139 
1140  private void listenToKeysOnSize() {
1141 
1142  sizetf.addKeyListener(new KeyListener() {
1143  @Override
1144  public void keyTyped(KeyEvent keyEvent) {
1145  Character newValue = keyEvent.getKeyChar();
1146 
1147  if (newValue == "+".charAt(0)){
1148  increaseBoxSize(1);
1149 
1150  } else if (newValue == "-".charAt(0)){
1151 
1152  increaseBoxSize(-1);
1153  keyEvent.consume();
1154  }
1155 
1156  // if it's not a digit, do not let it pass
1157  if (!newValue.isDigit(newValue)) {
1158  keyEvent.consume();
1159  }
1160  }
1161 
1162  @Override
1163  public void keyPressed(KeyEvent keyEvent) {
1164 
1165  }
1166 
1167  @Override
1168  public void keyReleased(KeyEvent keyEvent) {
1169 
1170  }
1171 
1172  });
1173  }
1174 
1175  private void increaseBoxSize(int value){
1176 
1177  int size = ((Number) sizetf.getValue()).intValue();
1178  sizetf.setValue(size + value);
1179  readSizeFromTextField();
1180 
1181  }
1182 
1183  protected void readSizeFromTextField()
1184  {
1185 
1186  int size = ((Number) sizetf.getValue()).intValue();
1187  if (size == getParticlePicker().getSize())
1188  return;
1189 
1190  if (!getParticlePicker().isValidSize(ParticlePickerJFrame.this, size))
1191  {
1192 
1193  int prevsize = getParticlePicker().getSize();
1194  sizetf.setText(Integer.toString(prevsize));
1195  return;
1196  }
1197  updateSize(size);
1198 
1199  }
1200 
1201  public void updateSize(int size)
1202  {
1203 
1204  sizetf.setValue(size);
1205  sizetf.selectAll();
1206  if(getCanvas() != null)
1207  getCanvas().repaint();
1208  getParticlePicker().setSize(size);
1209  //updateMicrographsModel();
1210  if(particlesdialog != null)
1211  loadParticles(true);
1212  getParticlePicker().saveConfig();
1213  }
1214 
1216  public boolean showMessage(String message)
1217  {
1218  return XmippDialog.showInfo(this, message);
1219  }
1220 
1221  public boolean showException(Exception e)
1222  {
1223  return XmippDialog.showException(this, e);
1224  }
1225 
1226  public void close()
1227  {
1228  setVisible(false);
1229  dispose();
1230  if (getCanvas() != null)
1231  getCanvas().getIw().close();
1232  XmippApplication.removeInstance(false);
1233  }
1234 
1235  public abstract String importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty);
1236 
1237  public Map<Object, Object> getKeyAssist()
1238  {
1239  Map<Object, Object> map = Collections.synchronizedMap(new LinkedHashMap<Object, Object>());
1240  map.put("Shift + scroll up / ctrl + left click", "Zoom in");
1241  map.put("Shift + scroll down / ctrl + right click", "Zoom out");
1242  map.put("Right click + mouse move", "Moves image previously expanded");
1243  map.put("Left click", "Adds or selects a particle. In erase mode, deletes or disables selected particles");
1244  map.put("Shift + left click", "Deletes or disables selected particle");
1245  map.put("Left click + mouse move", "Moves selected particle. In erase mode, deletes or disables particles");
1246  map.put("Left", "Moves selected particle to the left");
1247  map.put("Right", "Moves selected particle to the right");
1248  map.put("Up", "Moves selected particle up");
1249  map.put("Down", "Moves selected particle down");
1250  map.put((char)TOGGLE_ERASE_MODE_KEY, "Toggle between erase and picking");
1251  map.put((char)NEXT_MICROGRAPH_KEY, "Select Next Micrograph");
1252  map.put((char)PREVIOUS_MICROGRAPH_KEY, "Select Previous Micrograph");
1253  map.put("Space bar", "hide/show particle markers.");
1254 
1255  if (linearModeAvailable()) {
1256 
1257  map.put((char)TOGGLE_LINEAR_MODE_KEY, "Toggle between normal picking and linear picking mode");
1258  map.put((char)SupervisedPickerCanvas.POLIGONAL_MODE_KEY + " (continuous)", "While in linear picking mode, linear picking will be continuous (polygonal mode).");
1259  map.put("ESCAPE", "Will reset the linear picking canceling the pending line");
1260  }
1261 
1262  return map;
1263  }
1264 
1265  protected void executeScipionSaveAndExit()
1266  {
1267  getCanvas().setEnabled(false);
1268  XmippWindowUtil.blockGUI(ParticlePickerJFrame.this, "Creating set ...");
1269  new Thread(new Runnable() {
1270 
1271  @Override
1272  public void run() {
1273 
1274  try {
1275  String cmd = String.format("run function registerCoords '%s'", getParticlePicker().getOutputDir());
1276  XmippWindowUtil.runCommand(cmd, getParticlePicker().getParams().port);
1277  XmippWindowUtil.releaseGUI(ParticlePickerJFrame.this.getRootPane());
1278  getCanvas().setEnabled(true);
1279 
1280  close();
1281 
1282  } catch (Exception ex) {
1283  ex.printStackTrace();
1284  throw new IllegalArgumentException(ex.getMessage());
1285  }
1286 
1287  }
1288  }).start();
1289  }
1290 
1291 }
1292 
1293 class NoneSelectedButtonGroup extends ButtonGroup {
1294 
1295  @Override
1296  public void setSelected(ButtonModel model, boolean selected) {
1297 
1298  if (selected) {
1299 
1300  super.setSelected(model, selected);
1301 
1302  } else {
1303 
1304  clearSelection();
1305  }
1306  }
1307 }
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static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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abstract List<? extends PickerParticle > getAvailableParticles()
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static final String bandPassFilter
Definition: XmippImageJ.java:11
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static final String brightnessContrastFilter
Definition: XmippImageJ.java:15
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static final Color firebrick
Definition: XmippWindowUtil.java:57
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static final String substractBackgroundFilter
Definition: XmippImageJ.java:13
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Definition: XmippImageJ.java:16
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Definition: XmippDialog.java:217
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Definition: XmippUtil.java:28
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Definition: XmippWindowUtil.java:242
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abstract ParticlesDialog initParticlesJDialog()
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Definition: XmippDialog.java:199
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Definition: XmippWindowUtil.java:389
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static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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Definition: XmippWindowUtil.java:140
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Definition: XmippWindowUtil.java:342
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JFormattedTextField getTextField(JSpinner spinner)
Definition: ParticlePickerJFrame.java:1057
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Definition: ParticlePicker.java:398
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Definition: XmippWindowUtil.java:134
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boolean showError(String message)
Definition: XmippDialog.java:211
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Definition: XmippMessage.java:66
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static void openURI(String uri)
Definition: XmippWindowUtil.java:190
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Definition: XmippApplication.java:28
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Definition: XmippApplication.java:18
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static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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static final String gaussianBlurFilter
Definition: XmippImageJ.java:14
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static final String enhanceContrastFilter
Definition: XmippImageJ.java:17
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.viewer.particlepicker;
8 
9 import java.util.logging.Level;
10 import java.util.logging.Logger;
11 import org.apache.commons.cli.BasicParser;
12 import org.apache.commons.cli.CommandLine;
13 import org.apache.commons.cli.Options;
14 import org.apache.commons.cli.ParseException;
15 import xmipp.viewer.particlepicker.training.model.Mode;
16 
21 public class ParticlePickerParams {
22 
23  private Options options;
24 
25  public final static String SCIPIONOPT = "scipion";
26  public final static String INPUTOPT = "input";
27  public final static String OUTPUTOPT = "output";
28  public final static String MODEOPT = "mode";
29  public final static String THREADSOPT = "threads";
30  public final static String FASTOPT = "fast";
31  public final static String INCOREOPT = "incore";
32  public final static String CLASSIFIER = "classifier";
33  public final static String TMP = "tmp";
34  private CommandLine cmdLine;
35 
36 
37  public String inputfile;
38  public String outputdir;
39  public Integer port;
40  public Mode mode;
41  public Integer threads = 1;
42  public boolean fast;
43  public boolean incore;
44  public String classifierProperties;
45  public boolean tmp;
46 
47  public ParticlePickerParams(Mode mode)
48  {
49  this.mode = mode;
50  }
51 
52  public ParticlePickerParams(String[] args)
53  {
54  try {
55  defineArgs();
56  processArgs(args);
57  } catch (ParseException ex) {
58  Logger.getLogger(ParticlePickerParams.class.getName()).log(Level.SEVERE, null, ex);
59  }
60  }
61 
62  public void defineArgs() {
63  options = new Options();
64  options.addOption(INPUTOPT, true, "");
65  options.addOption(OUTPUTOPT, true, "");
66  options.addOption(MODEOPT, true, "");
67  options.addOption(THREADSOPT, true, "");
68  options.addOption(FASTOPT, true, "");
69  options.addOption(INCOREOPT, true, "");
70  options.addOption(SCIPIONOPT, true, "");
71  options.addOption(CLASSIFIER, true, "");
72  options.addOption(TMP,true, "Warns about loosing data. Coordinates mus be generated.");
73  }
74 
75  public void processArgs(String args[]) throws ParseException {
76 
77  String[] cmdargs;
78  BasicParser parser = new BasicParser();
79  cmdLine = parser.parse(options, args);
80  inputfile = cmdLine.getOptionValue(INPUTOPT);
81  outputdir = cmdLine.getOptionValue(OUTPUTOPT);
82  mode = Mode.Manual;
83  if(cmdLine.hasOption(MODEOPT))
84  {
85  String str = cmdLine.getOptionValue(MODEOPT);
86  mode = Mode.getMode(str);
87  if(mode != Mode.Review && mode != Mode.ReadOnly && mode != Mode.Automatic)
88  throw new IllegalArgumentException("Only modes Automatic, Review, ReadOnly can be specified from the command line");
89  }
90  if (cmdLine.hasOption(THREADSOPT))
91  threads = Integer.parseInt(cmdLine.getOptionValue(THREADSOPT));
92  if (cmdLine.hasOption(FASTOPT))
93  fast = Boolean.parseBoolean(cmdLine.getOptionValue(FASTOPT));
94  if (cmdLine.hasOption(INCOREOPT))
95  incore = Boolean.parseBoolean(cmdLine.getOptionValue(INCOREOPT));
96 
97 
98  if (cmdLine.hasOption(SCIPIONOPT)) {
99  cmdargs = cmdLine.getOptionValues(SCIPIONOPT);
100  if(cmdargs != null)
101  port = Integer.parseInt(cmdargs[0]);
102  }
103  if (cmdLine.hasOption(CLASSIFIER)) {
104  classifierProperties = cmdLine.getOptionValue(CLASSIFIER);
105 
106  }
107  if (cmdLine.hasOption(TMP)) {
108  tmp = Boolean.parseBoolean(cmdLine.getOptionValue(TMP));
109 
110  }
111 
112 
113  }
114 
115 
116  public boolean isScipion()
117  {
118  return cmdLine.hasOption(SCIPIONOPT);
119  }
120 
121 }
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1 package xmipp.viewer.particlepicker;
2 
3 import ij.plugin.frame.Recorder;
4 
5 import java.awt.Color;
6 import java.io.File;
7 import java.io.FilenameFilter;
8 import java.lang.reflect.Field;
9 import java.util.ArrayList;
10 import java.util.HashMap;
11 import java.util.List;
12 import java.util.Locale;
13 import java.util.logging.Level;
14 import java.util.logging.Logger;
15 
16 import javax.swing.JFrame;
17 
18 import xmipp.ij.commons.IJCommand;
19 import xmipp.ij.commons.XmippImageJ;
20 import xmipp.jni.Filename;
21 import xmipp.jni.MDLabel;
22 import xmipp.jni.MetaData;
23 import xmipp.jni.Program;
24 import xmipp.utils.XmippMessage;
25 import xmipp.viewer.particlepicker.training.model.Mode;
26 
34 public abstract class ParticlePicker {
35 
36  protected String macrosfile;
37  protected static Logger logger;
38  protected String outputdir = ".";
39  protected boolean changed;
40  protected boolean saved;
41  protected Mode mode;
42  protected List<IJCommand> filters;
43  protected String selfile;
44 
45  protected String configfile;
46 
47 
48  public static final String xmippsmoothfilter = "Xmipp Smooth Filter";
49  public static final String particlesAutoBlock = "particles_auto";
50 
51  protected Color color;
52  protected int size;
53 
54  public static final int sizemax = 2000;
55  protected String block;
56 
57  protected static Color[] colors = new Color[]{Color.GREEN, Color.BLUE, Color.CYAN, Color.MAGENTA, Color.ORANGE, Color.PINK, Color.YELLOW};
58 
59  protected static int nextcolor;
60  public final HashMap<Format, String> emextensions;
61  protected ParticlePickerParams params;
62  protected static ParticlePicker picker;
63  protected double zoom = -1.f;
64  private boolean showDeleted = false;
65 
66  public boolean isShowDeleted() {
67  return showDeleted;
68  }
69 
70  public void setShowDeleted(boolean showDeleted) {
71  this.showDeleted = showDeleted;
72  }
73  public void toggleShowDeleted(){
74  this.showDeleted = ! this.showDeleted;
75  }
76 
77  public double getZoom()
78  {
79  return zoom;
80  }
81 
82  public void setZoom(double zoom)
83  {
84  this.zoom = zoom;
85  }
86 
87 
88  public static Color getNextColor() {
89  Color next = colors[nextcolor];
90  nextcolor++;
91  if (nextcolor == colors.length) {
92  nextcolor = 0;
93  }
94  return next;
95  }
96 
97  public static String getParticlesBlock(Format f, String file) {
98  String blockname = getParticlesBlockName(f);
99  if (f == null) {
100  return null;
101  }
102  return blockname + "@" + file;
103 
104  }
105 
106  public static String getParticlesBlockName(Format f) {
107  if (f == Format.Xmipp301) {
108  return "particles";
109  }
110  if (f == Format.Xmipp30) {
111  return "DefaultFamily";
112  }
113  return null;
114  }
115 
116  public static String getParticlesBlock(String file) {
117  return getParticlesBlock(Format.Xmipp301, file);
118 
119  }
120 
121  public ParticlePickerParams getParams()
122  {
123  return params;
124  }
125 
126 
127  public String getParticlesAutoBlock(String file) {
128  return particlesAutoBlock + "@" + file;
129  }
130 
131  public String getParticlesBlock(Micrograph m) {
132  return getParticlesBlock(getOutputPath(m.getPosFile()));
133 
134  }
135 
136  public String getParticlesAutoBlock(Micrograph m) {
137  return getParticlesAutoBlock(getOutputPath(m.getPosFile()));
138  }
139 
140  public ParticlePicker(String selfile, ParticlePickerParams params) {
141  this(null, selfile, ".", params);
142  }
143 
144  public ParticlePicker(String selfile, String outputdir, ParticlePickerParams params) {
145  this(null, selfile, outputdir, params);
146  }
147 
148  public ParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params) {
149 
150  this.params = params;
151  this.block = block;
152  this.outputdir = outputdir;
153  if(!new File(outputdir).isDirectory())
154  throw new IllegalArgumentException(XmippMessage.getInvalidDirectoryMsg(outputdir));
155  this.selfile = selfile;
156  this.mode = params.mode;
157  this.configfile = getOutputPath("config.xmd");
158  picker = this;
159  filters = new ArrayList<IJCommand>();
160  loadEmptyMicrographs();
161  loadConfig();
162  emextensions = new HashMap<Format, String>();
163  emextensions.put(Format.Xmipp, ".pos");
164  emextensions.put(Format.Xmipp24, ".pos");
165  emextensions.put(Format.Xmipp30, ".pos");
166  emextensions.put(Format.Xmipp301, ".pos");
167  emextensions.put(Format.Relion, ".star");
168  emextensions.put(Format.Eman, ".box");
169 
170  }
171 
172  public void loadConfig() {
173 
174  try {
175  String file = configfile;
176  filters.clear();
177  Micrograph m = getMicrographs().get(0);
178  boolean existsConfig = new File(file).exists();
179  color = getNextColor();
180  if (!existsConfig) {
181  size = getDefaultSize();
182  setMicrograph(m);
183 
184  }
185  else
186  {
187  String mname;
188  int rgb;
189  MetaData md = new MetaData("properties@" + file);
190  long id = md.firstObject();
191  if(md.containsLabel(MDLabel.MDL_MICROGRAPH))
192  {
193  mname = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
194  m = getMicrograph(mname);
195  if(m == null)
196  m = getMicrographs().get(0);
197  }
198  setMicrograph(m);
199  if(md.containsLabel(MDLabel.MDL_COLOR))
200  {
201  rgb = md.getValueInt(MDLabel.MDL_COLOR, id);
202  color = new Color(rgb);
203  }
204  size = md.getValueInt(MDLabel.MDL_PICKING_PARTICLE_SIZE, id);
205  md.destroy();
206  String command, options;
207  if (MetaData.containsBlock(file, "filters")) {
208  md = new MetaData("filters@" + file);
209  long[] ids = md.findObjects();
210  for (long filterid : ids) {
211  command = IJCommand.getString(md.getValueString(MDLabel.MDL_MACRO_CMD, filterid));
212  options = IJCommand.getString(md.getValueString(MDLabel.MDL_MACRO_CMD_ARGS, filterid));
213  if (options.equals("NULL")) {
214  options = "";
215  }
216  filters.add(new IJCommand(command, options));
217  }
218  md.destroy();
219  }
220  }
221  if (!existsConfig || (existsConfig && !MetaData.containsBlock(file, "filters")))
222  {
223  filters.add(new IJCommand(XmippImageJ.gaussianBlurFilter, "sigma=2"));
224  filters.add(new IJCommand(XmippImageJ.enhanceContrastFilter, "saturated=0.4"));
225  saveConfig();
226  }
227 
228  } catch (Exception e) {
229  getLogger().log(Level.SEVERE, e.getMessage(), e);
230  throw new IllegalArgumentException(e.getMessage());
231  }
232 
233  }
234 
235  public synchronized void saveConfig() {
236  try {
237  MetaData md;
238  String file = configfile;
239  md = new MetaData();
240  long id = md.addObject();
241  saveConfig(md, id);
242  md.write("properties@" + file);
243  md.destroy();
244  String cmd, options;
245  md = new MetaData();
246  for (IJCommand f : filters) {
247  id = md.addObject();
248  cmd = f.getMdCommand();
249  md.setValueString(MDLabel.MDL_MACRO_CMD, cmd, id);
250  options = f.getMdOptions();
251  md.setValueString(MDLabel.MDL_MACRO_CMD_ARGS, options, id);
252  }
253  md.writeBlock("filters@" + file);
254  md.destroy();
255 
256 
257  } catch (Exception e) {
258  getLogger().log(Level.SEVERE, e.getMessage(), e);
259  throw new IllegalArgumentException(e.getMessage());
260  }
261 
262  }
263 
264  protected void saveConfig(MetaData md, long id) {
265  Micrograph m = getMicrograph();
266  md.setValueString(MDLabel.MDL_MICROGRAPH, m.getName(), id);
267  md.setValueInt(MDLabel.MDL_COLOR, getColor().getRGB(), id);
268  md.setValueInt(MDLabel.MDL_PICKING_PARTICLE_SIZE, getSize(), id);
269  }
270 
271  public Format detectFileFormat(String path) {
272  if(!new File(path).exists())
273  return Format.None;
274  if (path.endsWith(emextensions.get(Format.Xmipp)))
275  {
276  if(MetaData.isPlainPos(path) )
277  return Format.Xmipp24;
278  if (MetaData.containsBlock(path, getParticlesBlockName(Format.Xmipp30))) {
279  return Format.Xmipp30;
280  }
281  return Format.Xmipp301;
282  }
283  else if (path.endsWith(emextensions.get(Format.Eman))) {
284  return Format.Eman;
285  }
286  else if (path.endsWith(emextensions.get(Format.Relion)))
287  return Format.Relion;
288 
289  return Format.None;
290  }
291 
292 
293 
294 
295  public Format detectFormat(String path, String preffix, StringBuffer suffix) {
296  Format f;
297  if(suffix.length() == 0)
298  for(String ext: emextensions.values())
299  {
300  suffix.setLength(0);
301  suffix.append(ext);
302  f = detectFormat(path, preffix, suffix);
303  if(f != Format.None)
304  return f;
305  }
306  else
307  {
308  String file;
309  for (Micrograph m : getMicrographs())
310  {
311  file = Filename.join(path, preffix + m.getName() + suffix);
312  f = detectFileFormat(file);
313  if(f != Format.None)
314  return f;
315  }
316  }
317  return Format.None;
318  }
319 
320  public String getExportFile(String path) {
321  String particlesfile;
322  File folderToScan = new File(path);
323  File[] listOfFiles = folderToScan.listFiles();
324 
325  //Checking file with exported particles
326  for (int i = 0; i < listOfFiles.length; i++) {
327  if (listOfFiles[i].isFile()) {
328  particlesfile = listOfFiles[i].getName();
329  if (particlesfile.endsWith("extract_list.xmd")) {
330  return Filename.join(path, particlesfile);
331  }
332  }
333  }
334  return null;
335  }
336 
337 
338  public String getPosFileFromXmipp24Project(String projectdir, String mname) {
339  String suffix = ".raw.Common.pos";
340  return String.format("%1$s%2$sPreprocessing%2$s%3$s%2$s%3$s%4$s", projectdir, File.separator, mname, suffix);
341  }
342 
343  public abstract void loadEmptyMicrographs();
344 
345 
346 
347 
348  public void updateFilters(String command) {
349  if (command != null) {
350  String options = "";
351  if (Recorder.getCommandOptions() != null) {
352  options = Recorder.getCommandOptions();
353  }
354  //boolean isavailable = availableFilters.contains(command);
355  boolean isadded = isFilterAdded(command);
356  if (!isadded) {
357  addFilter(command, options);
358  } else if (!(options == null || options.equals(""))) {
359  setFilterOptions(command, options);
360  }
361  saveConfig();
362  }
363  }
364 
365  void removeFilter(String filter) {
366  for (IJCommand f : filters) {
367  if (f.getCommand().equals(filter)) {
368  filters.remove(f);
369  saveConfig();
370  break;
371  }
372  }
373  }// function removeFilter
374 
375  public boolean isFilterAdded(String filter) {
376  for (IJCommand f : filters) {
377  if (f.getCommand().equals(filter)) {
378  return true;
379  }
380  }
381  return false;
382  }// function isFilterSelected
383 
384 
385  public String getMicrographsSelFile() {
386  return selfile;
387  }
388 
389  public void setFilterOptions(String command, String options)
390  {
391  for (IJCommand f : filters) {
392  if (f.getCommand().equals(command)) {
393  f.setOptions(options);
394  }
395  }
396  }
397 
398  public void addFilter(String command, String options) {
399  IJCommand f = new IJCommand(command, options);
400  filters.add(f);
401  }
402 
403  public List<IJCommand> getFilters() {
404  return filters;
405  }
406 
407  public void setChanged(boolean changed) {
408  this.changed = changed;
409  }
410 
411  public boolean isChanged() {
412  return changed;
413  }
414 
415  public boolean isSaved() {
416  return saved;
417  }
418 
419  public void setSaved(boolean saved) {
420  this.saved = saved;
421  }
422 
423  public Mode getMode() {
424  return mode;
425  }
426 
427  public static Logger getLogger() {
428  try {
429  if (logger == null) {
430  // FileHandler fh = new FileHandler("PPicker.log", true);
431  // fh.setFormatter(new SimpleFormatter());
432  logger = Logger.getLogger("PPickerLogger");
433  // logger.addHandler(fh);
434  }
435  return logger;
436  } catch (Exception e) {
437  // TODO Auto-generated catch block
438  e.printStackTrace();
439  }
440  return null;
441  }
442 
443  public String getOutputPath(String file) {
444  return outputdir + File.separator + file;
445  }
446 
447  public String getOutputDir() {
448  return outputdir;
449  }
450 
451  public abstract List<? extends Micrograph> getMicrographs();
452 
453  public int getMicrographIndex() {
454  return getMicrographs().indexOf(getMicrograph());
455  }
456 
457  public String getTemplatesFile(String name) {
458  return getOutputPath(name + "_templates.stk");
459  }
460 
461  public Mode validateState(Mode state) {
462 
463  if (mode == Mode.Review && state != Mode.Review) {
464  setChanged(true);
465  return Mode.Review;
466  }
467  if (mode == Mode.Manual && !(state == Mode.Manual || state == Mode.Available)) {
468  throw new IllegalArgumentException(String.format("Can not use %s mode on this data", mode));
469  }
470  if (mode == Mode.Supervised && state == Mode.Review) {
471  throw new IllegalArgumentException(String.format("Can not use %s mode on this data", mode));
472  }
473  return state;
474 
475  }// function validateState
476 
477  public void saveData() {
478  saveConfig();
479  //saveData(getMicrograph());
480  //setChanged(false);
481  }// function saveData
482 
483  public abstract void saveData(Micrograph m);
484 
485  public Micrograph getMicrograph(String name) {
486  for (Micrograph m : getMicrographs()) {
487  if (m.getName().equalsIgnoreCase(name)) {
488  return m;
489  }
490  }
491  return null;
492  }
493 
497  public void fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty) {
498 
499  if (f == Format.Auto) {
500  f = detectFileFormat(path);
501  }
502  String blockname;
503  switch (f) {
504  case Xmipp24:
505  md.readPlain(path, "xcoor ycoor");
506  break;
507  case Xmipp30:
508  blockname = getParticlesBlockName(f); //only used with Xmipp
509  if (MetaData.containsBlock(path, blockname)) {
510  md.read(getParticlesBlock(f, path));
511  }
512  break;
513  case Xmipp301:
514  fillParticlesMdFromXmipp301File(path, m, md);
515  break;
516  case Eman:
517  fillParticlesMdFromEmanFile(path, m, md, scale);
518  break;
519  case Relion:
520  fillParticlesMdFromRelionFile(path, m, md);
521 
522  break;
523  default:
524  md.clear();
525  }
526  if (scale != 1.f) {
527  String command = String.format(Locale.ENGLISH, "xcoor=xcoor*%f,ycoor=ycoor*%f", scale, scale);
528  md.operate(command);
529  }
530  int width = (int) (m.getWidth() / scale);// original width
531  int height = (int) (m.getHeigth() / scale);// original height
532  if (invertx) {
533  md.operate(String.format("xcoor=%d-xcoor", width));
534  }
535  if (inverty) {
536  md.operate(String.format("ycoor=%d-ycoor", height));
537  }
538 
539 
540  }// function importParticlesFromFile
541 
542  public void fillParticlesMdFromXmipp301File(String file, Micrograph m, MetaData md) {
543 
544  String blockname = getParticlesBlockName(Format.Xmipp301); //only used with Xmipp
545  if (MetaData.containsBlock(file, blockname)) {
546  md.read(getParticlesBlock(Format.Xmipp301, file));
547  }
548  if (MetaData.containsBlock(file, particlesAutoBlock)) {
549  MetaData mdAuto = new MetaData();
550  mdAuto.read(getParticlesAutoBlock(file));
551  mdAuto.removeDisabled();
552  md.unionAll(mdAuto);
553  mdAuto.destroy();
554  }
555 
556  }
557 
558  public void fillParticlesMdFromRelionFile(String file, Micrograph m, MetaData md) {
559  MetaData relionmd = new MetaData(file);
560  if(!relionmd.containsLabel(MDLabel.RLN_IMAGE_COORD_X))
561  throw new IllegalArgumentException(String.format("File %s format is not supported", file));
562  long[] ids = relionmd.findObjects();
563  int xcoor, ycoor;
564  long id;
565  for(int i = 0; i < ids.length; i++ )
566  {
567  xcoor = (int)relionmd.getValueDouble(MDLabel.RLN_IMAGE_COORD_X, ids[i]);
568  ycoor = (int)relionmd.getValueDouble(MDLabel.RLN_IMAGE_COORD_Y, ids[i]);
569  id = md.addObject();
570  md.setValueInt(MDLabel.MDL_XCOOR, xcoor, id);
571  md.setValueInt(MDLabel.MDL_YCOOR, ycoor, id);
572  }
573  relionmd.destroy();
574 
575  }
576 
577  public void fillParticlesMdFromEmanFile(String file, Micrograph m, MetaData md, float scale) {
578  // inverty = true;
579  md.readPlain(file, "xcoor ycoor particleSize");
580  //System.err.format("After readPlain: md.size: %d\n", md.size());
581 
582  long fid = md.firstObject();
583  int size = md.getValueInt(MDLabel.MDL_PICKING_PARTICLE_SIZE, fid);
584 
585  int half = size / 2;
586  //System.err.format("Operate string: %s\n", String.format("xcoor=xcoor+%d,ycoor=ycoor+%d", half, half));
587  md.operate(String.format("xcoor=xcoor+%d,ycoor=ycoor+%d", half, half));
588 
589  setSize(Math.round(size * scale));
590  }// function fillParticlesMdFromEmanFile
591 
592  public void runXmippProgram(String program, String args) {
593  try {
594  Program.runByName(program, args);
595  } catch (Exception e) {
596  getLogger().log(Level.SEVERE, e.getMessage(), e);
597  throw new IllegalArgumentException(e);
598  }
599  }
600 
601  public abstract Micrograph getMicrograph();
602 
603  public abstract void setMicrograph(Micrograph m);
604 
605  public abstract boolean isValidSize(JFrame parent, int size);
606 
607  public int getSize() {
608  return size;
609  }
610 
611  public void setSize(int size) {
612 
613  this.size = size;
614  }
615 
616  public Color getColor() {
617  return color;
618  }
619 
620  public void setColor(Color color) {
621  this.color = color;
622  }
623 
624  public static Color getColor(String name) {
625  Color color;
626  try {
627  Field field = Class.forName("java.awt.Color").getField(name);
628  color = (Color) field.get(null);// static field, null for parameter
629  } catch (Exception e) {
630  color = null; // Not defined
631  }
632  return color;
633  }
634 
635  public static int getDefaultSize() {
636  return 100;
637  }
638 
639  public int getRadius() {
640  return size / 2;
641  }
642 
643  public void importSize(String path, Format f, double scale)
644  {
645  if(f == Format.Xmipp301)
646  {
647  String configfile = String.format("%s%s%s", path, File.separator, "config.xmd");
648  if(new File(configfile).exists())
649  {
650  MetaData configmd = new MetaData(configfile);
651  int size = configmd.getValueInt(MDLabel.MDL_PICKING_PARTICLE_SIZE, configmd.firstObject());
652  size = (int)(size * scale);
653  setSize(size);
654  saveConfig();
655  configmd.destroy();
656  }
657  }
658  }
659 
660  public static File[] getCoordsFiles(String folder)
661  {
662  return new File(folder).listFiles(new FilenameFilter() {
663  public boolean accept(File dir, String name) {
664  String lowercasename = name.toLowerCase();
665  return lowercasename.endsWith(".pos") || lowercasename.endsWith(".box");
666  }
667  });
668  }
669 
670  public boolean isScipionSave()
671  {
672  if(params == null)
673  return false;
674  return params.port != null && mode != Mode.ReadOnly;
675  }
676 
677 
678  public abstract int getParticlesCount();
679 
680 
681 
682  public static ParticlePicker getPicker()
683  {
684  return picker;
685  }
686 
687  public Integer getPort()
688  {
689  return params.port;
690  }
691 
692 
693 
694 
695 }
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromEmanFile
void fillParticlesMdFromEmanFile(String file, Micrograph m, MetaData md, float scale)
Definition: ParticlePicker.java:577
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xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromXmipp301File
void fillParticlesMdFromXmipp301File(String file, Micrograph m, MetaData md)
Definition: ParticlePicker.java:542
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xmipp.jni.MetaData.addObject
native long addObject()
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xmipp.jni.MetaData.setValueString
native boolean setValueString(int label, String value, long objId)
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xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(String file)
Definition: ParticlePicker.java:116
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xmipp.viewer.particlepicker.ParticlePicker.detectFormat
Format detectFormat(String path, String preffix, StringBuffer suffix)
Definition: ParticlePicker.java:295
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xmipp.jni.MDLabel.MDL_MACRO_CMD
static final int MDL_MACRO_CMD
< Number which will multiply all features (double)
Definition: MDLabel.java:280
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xmipp.jni.Filename.join
static String join(String... paths)
Definition: Filename.java:473
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xmipp.jni.MetaData.write
native void write(String filename)
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xmipp.viewer.particlepicker.ParticlePicker.setMicrograph
abstract void setMicrograph(Micrograph m)
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xmipp.jni.MetaData.clear
native void clear()
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xmipp.viewer.particlepicker.ParticlePicker.runXmippProgram
void runXmippProgram(String program, String args)
Definition: ParticlePicker.java:592
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xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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xmipp.viewer.particlepicker.ParticlePicker.getMicrographs
abstract List<? extends Micrograph > getMicrographs()
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xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MetaData.writeBlock
native void writeBlock(String filename)
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xmipp.jni.MetaData.read
final void read(String filename)
Definition: MetaData.java:125
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xmipp.viewer.particlepicker.Micrograph.getName
static String getName(String file, int level)
Definition: Micrograph.java:140
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xmipp.viewer.particlepicker.ParticlePicker.ParticlePicker
ParticlePicker(String selfile, String outputdir, ParticlePickerParams params)
Definition: ParticlePicker.java:144
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xmipp.viewer.particlepicker.ParticlePicker.setFilterOptions
void setFilterOptions(String command, String options)
Definition: ParticlePicker.java:389
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xmipp.jni.MetaData.removeDisabled
native void removeDisabled()
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xmipp.viewer.particlepicker.ParticlePicker.ParticlePicker
ParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params)
Definition: ParticlePicker.java:148
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromRelionFile
void fillParticlesMdFromRelionFile(String file, Micrograph m, MetaData md)
Definition: ParticlePicker.java:558
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xmipp.jni.MDLabel.MDL_MACRO_CMD_ARGS
static final int MDL_MACRO_CMD_ARGS
Definition: MDLabel.java:281
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MetaData.containsBlock
static boolean containsBlock(String file, String block)
Definition: MetaData.java:230
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xmipp.jni.MetaData.unionAll
native void unionAll(MetaData mdIn)
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xmipp.viewer.particlepicker.ParticlePicker.emextensions
final HashMap< Format, String > emextensions
Definition: ParticlePicker.java:60
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.viewer.particlepicker.ParticlePicker.isValidSize
abstract boolean isValidSize(JFrame parent, int size)
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.viewer.particlepicker.ParticlePicker.getCoordsFiles
static File [] getCoordsFiles(String folder)
Definition: ParticlePicker.java:660
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xmipp.jni.MDLabel.RLN_IMAGE_COORD_X
static final int RLN_IMAGE_COORD_X
Definition: MDLabel.java:483
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.jni.MetaData.readPlain
native void readPlain(String file, String columns)
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xmipp.viewer.particlepicker.ParticlePicker.getPosFileFromXmipp24Project
String getPosFileFromXmipp24Project(String projectdir, String mname)
Definition: ParticlePicker.java:338
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xmipp.jni.MetaData.isPlainPos
static boolean isPlainPos(String file)
Definition: MetaData.java:653
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.jni.MetaData.firstObject
native long firstObject()
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xmipp.jni.MDLabel.RLN_IMAGE_COORD_Y
static final int RLN_IMAGE_COORD_Y
Definition: MDLabel.java:484
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xmipp.viewer.particlepicker.ParticlePicker.ParticlePicker
ParticlePicker(String selfile, ParticlePickerParams params)
Definition: ParticlePicker.java:140
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xmipp.viewer.particlepicker.ParticlePicker.addFilter
void addFilter(String command, String options)
Definition: ParticlePicker.java:398
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xmipp.jni.MetaData.operate
native void operate(String operateStr)
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xmipp.jni.MDLabel.MDL_COLOR
static final int MDL_COLOR
Definition: MDLabel.java:282
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xmipp.jni.Program.runByName
static native int runByName(String progName, String args)
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xmipp.utils.XmippMessage.getInvalidDirectoryMsg
static String getInvalidDirectoryMsg(String outputdir)
Definition: XmippMessage.java:89
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xmipp.ij.commons.IJCommand.getString
static String getString(String mdstring)
Definition: IJCommand.java:42
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xmipp.viewer.particlepicker.ParticlePicker.importSize
void importSize(String path, Format f, double scale)
Definition: ParticlePicker.java:643
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xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.jni.MDLabel.MDL_PICKING_PARTICLE_SIZE
static final int MDL_PICKING_PARTICLE_SIZE
Definition: MDLabel.java:287
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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xmipp.ij.commons.XmippImageJ.gaussianBlurFilter
static final String gaussianBlurFilter
Definition: XmippImageJ.java:14
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromFile
void fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
Definition: ParticlePicker.java:497
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xmipp.ij.commons.XmippImageJ.enhanceContrastFilter
static final String enhanceContrastFilter
Definition: XmippImageJ.java:17
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class  xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask
 
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package  xmipp.viewer.particlepicker.training.model
 
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 import javax.swing.SwingWorker;
4 import xmipp.viewer.particlepicker.training.gui.TemplatesJDialog;
5 
6 public class ParticleToTemplatesTask extends SwingWorker<String, Object>
7 {
8 
9  private static TemplatesJDialog dialog;
10  private ManualParticle particle;
11 
12 
13  public ParticleToTemplatesTask(ManualParticle particle)
14  {
15  this.particle = particle;
16  }
17 
18  public static void setTemplatesDialog(TemplatesJDialog d)
19  {
20  dialog = d;
21  }
22 
23  @Override
24  protected String doInBackground() throws Exception
25  {
26  try
27  {
28 
29  SupervisedParticlePicker picker = (SupervisedParticlePicker)particle.getParticlePicker();
30  if (particle.getMicrograph().fits(particle.getX(), particle.getY(), picker.getSize()))
31  picker.addParticleToTemplates(particle);
32 
33  }
34  catch (Exception e)
35  {
36  throw new IllegalArgumentException(e);
37  }
38 
39  return "";
40  }
41 
42  @Override
43  protected void done() {
44  if(dialog != null && dialog.isVisible())
45  dialog.loadTemplates(true);
46  }
47 
48 }
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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1 package xmipp.jni;
2 
3 import java.awt.Point;
4 
5 
6 
7 public class Particle implements Comparable<Particle> {
8  protected int x;
9  protected int y;
10  protected double cost;
11 
12  public Particle(int x, int y)
13  {
14  this.x = x;
15  this.y = y;
16  }
17 
18  public Particle(int x, int y, double cost)
19  {
20  this.x = x;
21  this.y = y;
22  this.cost = cost;
23  }
24 
25 
26  public int getX() {
27  return x;
28  }
29 
30  public void setX(int x) {
31  this.x = x;
32  }
33 
34  public int getY() {
35  return y;
36  }
37 
38  public void setY(int y) {
39  this.y = y;
40  }
41 
42  public double getCost()
43  {
44  return cost;
45  }
46 
47  public void setCost(double cost)
48  {
49  this.cost = cost;
50 
51  }
52 
53 
54 
55  public boolean contains(int x2, int y2, int size )
56  {
57  int radius = size/2;
58  if(x2 < x - radius || x2 > x + radius)
59  return false;
60  if(y2 < y - radius || y2 > y + radius)
61  return false;
62  return true;
63  }
64 
65  public void setPosition(int x, int y) {
66  this.x = x;
67  this.y = y;
68  }
69 
70  public Point getPosition() {
71  return new Point(x, y);
72 
73  }
74 
75  public String toString()
76  {
77  return String.format("x = %s; y = %s cost = %.2f", x, y, cost);
78  }
79 
80 
81  @Override
82  public int compareTo(Particle p) {
83  if(p.x > x)
84  return 1;
85  if(p.x == x)
86  {
87  if(p.y > y)
88  return 1;
89  if(p.y == y)
90  return 0;
91  return -1;
92  }
93  return -1;
94  }
95 }
xmipp.jni.Particle.setCost
void setCost(double cost)
Definition: Particle.java:47
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xmipp.jni.Particle.setX
void setX(int x)
Definition: Particle.java:30
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void setPosition(int x, int y)
Definition: Particle.java:65
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Particle(int x, int y, double cost)
Definition: Particle.java:18
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xmipp.jni.Particle.toString
String toString()
Definition: Particle.java:75
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xmipp.jni.Particle.Particle
Particle(int x, int y)
Definition: Particle.java:12
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xmipp.jni.Particle.getPosition
Point getPosition()
Definition: Particle.java:70
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xmipp.jni.Particle.contains
boolean contains(int x2, int y2, int size)
Definition: Particle.java:55
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xmipp.jni.Particle.compareTo
int compareTo(Particle p)
Definition: Particle.java:82
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xmipp.jni.Particle.getCost
double getCost()
Definition: Particle.java:42
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xmipp.jni.Particle.setY
void setY(int y)
Definition: Particle.java:38
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class  xmipp.viewer.particlepicker.ParticlesDialog
 
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package  xmipp.viewer.particlepicker
 
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1 package xmipp.viewer.particlepicker;
2 
3 import java.awt.BorderLayout;
4 import java.awt.Dialog;
5 import java.awt.Dimension;
6 import java.awt.GridBagConstraints;
7 import java.awt.GridBagLayout;
8 import java.awt.Panel;
9 import java.awt.ScrollPane;
10 import java.awt.event.ComponentEvent;
11 import java.awt.event.WindowAdapter;
12 import java.awt.event.WindowEvent;
13 import java.util.List;
14 import xmipp.utils.XmippMessage;
15 import xmipp.utils.XmippWindowUtil;
16 
17 public class ParticlesDialog extends Dialog
18 {
19 
20  protected ParticlePickerJFrame frame;
21  protected Panel particlespn;
22  protected ScrollPane sp;
23  protected GridBagConstraints constraints;
24  protected int width, height, rows, columns, side;
25  public static final int maxHeight = (int)(0.9 * XmippWindowUtil.getScreenRectangle().height);
26  public static final int minWidth = 600;
27 
28  public ParticlesDialog(ParticlePickerJFrame frame)
29  {
30  super(frame);
31  this.frame = frame;
32  initComponents();
33 
34  addWindowListener(new WindowAdapter()
35  {
36  public void windowClosing(WindowEvent winEvt)
37  {
38  resetParticlesDialog();
39  close();
40  }
41 
42  });
43  }
44 
45  protected void resetParticlesDialog()
46  {
47  frame.particlesdialog = null;
48 
49  }
50 
51  public void loadParticles(boolean resize)
52  {
53 
54  List<? extends PickerParticle> particles = frame.getAvailableParticles();
55  side = frame.getSide();
56 
57  if (side == 0)
58  throw new IllegalArgumentException(XmippMessage.getOutOfBoundsMsg("side"));
59 
60  if (particles.isEmpty())
61  {
62  particlespn.removeAll();
63  width = minWidth;
64  height = maxHeight;
65  sp.setPreferredSize(new Dimension(width, height));
66  pack();
67  return;
68  }
69 
70  if (resize) // first time or keep size
71  {
72  columns = Math.min(minWidth, particles.size() * side) / side;
73  rows = (int) Math.ceil(particles.size() / (float) columns);
74  width = side * columns + 20;
75  height = Math.min(side * rows, maxHeight);
76 
77  }
78  else//size changed by user
79  {
80  Dimension d = sp.getSize();
81  width = (int) d.getWidth();
82  height = (int)d.getHeight();
83  columns = width / side;
84  rows = (int) Math.ceil((particles.size() / (float) columns));
85 
86  }
87  sp.setPreferredSize(new Dimension(width, height));
88  particlespn.removeAll();
89 
90  particles = frame.getAvailableParticles();
91  int index = 0;
92  ParticleCanvas c;
93  PickerParticle p;
94  for (int i = 0; i < rows; i++)
95  for (int j = 0; j < columns; j++, index++)
96  {
97 
98  if (index == particles.size())
99  break;
100  p = particles.get(index);
101  c = p.getParticleCanvas(frame);
102 
103  particlespn.add(c, XmippWindowUtil.getConstraints(constraints, j, i, 1));
104  }
105  // particlespn.revalidate();
106  sp.getVAdjustable().setValue(sp.getVAdjustable().getMaximum());
107  sp.getHAdjustable().setValue(sp.getHAdjustable().getMaximum());
108  pack();
109 
110  }
111 
112 
113 
114  private void initComponents()
115  {
116 
117  setTitle("Particles");
118  setLayout(new BorderLayout());
119  constraints = new GridBagConstraints();
120  sp = new ScrollPane(ScrollPane.SCROLLBARS_AS_NEEDED);
121 
122  particlespn = new Panel(new GridBagLayout());
123  sp.add(particlespn);
124  add(sp, BorderLayout.CENTER);
125  loadParticles(true);
126  XmippWindowUtil.setLocation(0.6f, 0, this);
127  setVisible(true);
128  setAlwaysOnTop(true);
129  sp.addComponentListener(new java.awt.event.ComponentAdapter()
130  {
131  public void componentResized(ComponentEvent e)
132  {
133  loadParticles(false);
134  }
135  });
136 
137  }
138 
139  public void close()
140  {
141  setVisible(false);
142  dispose();
143 
144  }
145 
146 
147 
148 }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.getAvailableParticles
abstract List<? extends PickerParticle > getAvailableParticles()
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xmipp.viewer.particlepicker.ParticlesDialog.ParticlesDialog
ParticlesDialog(ParticlePickerJFrame frame)
Definition: ParticlesDialog.java:28
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xmipp.utils.XmippMessage.getOutOfBoundsMsg
static String getOutOfBoundsMsg(Object o)
Definition: XmippMessage.java:56
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xmipp.viewer.particlepicker.PickerParticle.getParticleCanvas
ParticleCanvas getParticleCanvas(ParticlePickerJFrame frame)
Definition: PickerParticle.java:38
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xmipp.utils.XmippWindowUtil.getScreenRectangle
static Rectangle getScreenRectangle()
Definition: XmippWindowUtil.java:82
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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class  xmipp.viewer.particlepicker.PickerParticle
 
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package  xmipp.viewer.particlepicker
 
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1 package xmipp.viewer.particlepicker;
2 
3 import xmipp.jni.Particle;
4 
5 public class PickerParticle extends Particle
6 {
7 
8  private ParticleCanvas canvas;
9  protected Micrograph micrograph;
10 
11  public PickerParticle(int x, int y, Micrograph m)
12  {
13  super(x, y);
14  this.micrograph = m;
15  // TODO Auto-generated constructor stub
16  }
17 
18  public PickerParticle(int x, int y, Micrograph m, double cost)
19  {
20  super(x, y, cost);
21  this.micrograph = m;
22  // TODO Auto-generated constructor stub
23  }
24 
25  public int getX0(int size)
26  {
27  int radius = size/2;
28  return getX() - radius;
29  }
30 
31  public int getY0(int size)
32  {
33  int radius = size/2;
34  return getY() - radius;
35  }
36 
37 
38  public ParticleCanvas getParticleCanvas(ParticlePickerJFrame frame)
39  {
40  if(canvas == null)
41  canvas = new ParticleCanvas(this, frame);
42  return canvas;
43  }
44 
45  public void resetParticleCanvas()
46  {
47  canvas = null;
48  }
49 
50 
51  public Micrograph getMicrograph() {
52  return micrograph;
53  }
54 
55 
56  public void setMicrograph(Micrograph micrograph) {
57  this.micrograph = micrograph;
58  }
59 
60 }
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PickerParticle(int x, int y, Micrograph m, double cost)
Definition: PickerParticle.java:18
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xmipp.viewer.particlepicker.PickerParticle.setMicrograph
void setMicrograph(Micrograph micrograph)
Definition: PickerParticle.java:56
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ParticleCanvas getParticleCanvas(ParticlePickerJFrame frame)
Definition: PickerParticle.java:38
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xmipp.viewer.particlepicker.PickerParticle.PickerParticle
PickerParticle(int x, int y, Micrograph m)
Definition: PickerParticle.java:11
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class  xmipp.jni.PickingClassifier
 
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package  xmipp.jni
 
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1 package xmipp.jni;
2 
3 
4 public class PickingClassifier extends Classifier
5 {
6 
7  // pointer to AutoParticlePicking2 class in C++ space. Needed by native library.
8  long peer;
9 
10  // Initialize library.
11  static
12  {
13  System.loadLibrary("XmippJNI");
14  }
15 
16  public PickingClassifier(int particlesize, String output, MDRow[] mics) throws Exception {
17  create(particlesize, output, mics);
18  }
19 
20  private native void create(int particle_size, String output, MDRow[] mics);
21 
22  public native void destroy();
23 
24  public synchronized native Particle[] autopick(String micrograph, int percent);
25 
26  public synchronized native void correct(MDRow[] manualRows, MDRow[] automaticRows);
27 
28  public synchronized native void train(MDRow[] micrographs, int x, int y, int width, int height);
29 
30  public synchronized native void setSize(int psize);
31 
32  public native int getParticlesThreshold();
33 
34 
35 
36  // Should be called by GarbageCollector before destroying
37  @Override
38  @SuppressWarnings("FinalizeDeclaration")
39  protected void finalize() throws Throwable {
40  super.finalize();
41  destroy();
42  }
43 
44  @Override
45  public boolean needsTraining()
46  {
47  return true;
48  }
49 
50  @Override
51  public int getTrainingParticlesMinimum()
52  {
53  // TODO Auto-generated method stub
54  return 15;
55  }
56 
57 }
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native int getParticlesThreshold()
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synchronized native void correct(MDRow[] manualRows, MDRow[] automaticRows)
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PickingClassifier(int particlesize, String output, MDRow[] mics)
Definition: PickingClassifier.java:16
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xmipp.jni.PickingClassifier.setSize
synchronized native void setSize(int psize)
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synchronized native Particle [] autopick(String micrograph, int percent)
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class  xmipp.viewer.windows.PlotJDialog
 
class  xmipp.viewer.windows.PlotJDialog.ColumnsTableModel
 
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package  xmipp.viewer.windows
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import java.awt.Color;
29 import java.awt.Component;
30 import java.awt.Dimension;
31 import java.awt.GridBagConstraints;
32 import java.awt.GridBagLayout;
33 import java.awt.Insets;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.util.ArrayList;
37 import java.util.Arrays;
38 import java.util.HashMap;
39 import java.util.List;
40 
41 import javax.swing.BorderFactory;
42 import javax.swing.DefaultCellEditor;
43 import javax.swing.JComboBox;
44 import javax.swing.JFrame;
45 import javax.swing.JLabel;
46 import javax.swing.JOptionPane;
47 import javax.swing.JPanel;
48 import javax.swing.JScrollPane;
49 import javax.swing.JTable;
50 import javax.swing.JTextField;
51 import javax.swing.ListSelectionModel;
52 import javax.swing.table.AbstractTableModel;
53 import javax.swing.table.TableColumn;
54 
55 import xmipp.jni.Filename;
56 import xmipp.jni.MetaData;
57 import xmipp.utils.ColorEditor;
58 import xmipp.utils.ColorRenderer;
59 import xmipp.utils.Params;
60 import xmipp.utils.ScipionParams;
61 import xmipp.utils.XmippDialog;
62 import xmipp.utils.XmippMessage;
63 import xmipp.utils.XmippWindowUtil;
64 import xmipp.viewer.models.ColumnInfo;
65 import xmipp.viewer.models.GalleryData;
66 import xmipp.viewer.models.ImageGalleryTableModel;
67 import xmipp.viewer.scipion.ScipionGalleryData;
68 import xmipp.viewer.scipion.ScipionGalleryJFrame;
69 
70 public class PlotJDialog extends XmippDialog
71 {
72  private static final long serialVersionUID = 1L;
73  private JTable tableColumns;
74  private HashMap<ColumnInfo, ColumnInfo.ColumnExtraInfo> rowsExtra;
75  private ColumnsTableModel model;
76  private JTextField tfTitle, tfXLabel, tfYLabel, tfBins;
77  private JComboBox plotTypecb;
78  private JComboBox jcbXAxis;
79  private List<ColumnInfo> rows;
80  // This will be used for check for results from the dialog
81  boolean fireEvent = true;
82  GridBagConstraints gbc = new GridBagConstraints();
83  ImageGalleryTableModel gallery;
84  JPanel panelEntries;
85  String[] COLORS = { "0000CC", "009900", "CC0000", "000000", "FF6600", "FFFF00", "00CCFF" };
86  String[] plotTypes = new String[]{"Plot", "Histogram", "Scatter"};
87  private JLabel binslb;
88 
89  public PlotJDialog(GalleryJFrame parent) {
90  super(parent, "Plot columns", false);
91 
92  rows = new ArrayList<ColumnInfo>();
93  rowsExtra = new HashMap<ColumnInfo, ColumnInfo.ColumnExtraInfo>();
94  int i = 0;
95  for (ColumnInfo ci : parent.getData().getLabelsInfo())
96  if (ci.type == MetaData.LABEL_INT || ci.type == MetaData.LABEL_DOUBLE) {// int or double
97 
98  rows.add(ci);
99  rowsExtra.put(ci, ci.new ColumnExtraInfo(COLORS[i % COLORS.length]));
100  ++i;
101  }
102  this.gallery = parent.gallery;
103  btnOkText = "Plot";
104  closeOnAction = false;
105  initComponents();
106  }// constructor ColumnsJDialog
107 
108  private void addPair(String text, Component c, int row) {
109  addPair(text, c, row, 0);
110  }
111 
112  private void addPair(String text, Component c, int row, int column) {
113  JLabel label = new JLabel(text);
114  gbc.anchor = GridBagConstraints.EAST;
115  panelEntries.add(label, XmippWindowUtil.getConstraints(gbc, column, row));
116  gbc.anchor = GridBagConstraints.WEST;
117  panelEntries.add(c, XmippWindowUtil.getConstraints(gbc, column + 1, row));
118  }
119 
120  protected void createEntries() {
121  tfTitle = new JTextField(20);
122  tfXLabel = new JTextField(20);
123  tfYLabel = new JTextField(20);
124 
125  JPanel plotPanel = new JPanel();
126  plotTypecb = new JComboBox(plotTypes);
127  plotTypecb.addActionListener(new ActionListener() {
128 
129  @Override
130  public void actionPerformed(ActionEvent ae) {
131  binslb.setVisible(isHistogram());
132  tfBins.setVisible(isHistogram());
133 
134  validate();
135  pack();
136  }
137  });
138  plotPanel.add(plotTypecb);
139  binslb = new JLabel("Bins");
140  binslb.setVisible(false);
141  tfBins = new JTextField(10);
142  tfBins.setText("50");
143  tfBins.setVisible(false);
144  plotPanel.add(binslb);
145  plotPanel.add(tfBins);
146  panelEntries = new JPanel(new GridBagLayout());
147  addPair("Title:", tfTitle, 0);
148  addPair("X label:", tfXLabel, 1);
149  addPair("Y label:", tfYLabel, 2);
150  addPair("Type:", plotPanel, 3);
151  jcbXAxis = new JComboBox();
152  jcbXAxis.addItem("");
153  for (ColumnInfo ci : rows)
154  jcbXAxis.addItem(ci.labelName);
155  addPair("X Axis:", jcbXAxis, 5);
156  jcbXAxis.addActionListener(new ActionListener() {
157 
158  @Override
159  public void actionPerformed(ActionEvent ae) {
160  tfXLabel.setText(jcbXAxis.getSelectedItem().toString());
161  }
162  });
163  }
164 
165  public boolean isHistogram()
166  {
167  return plotTypecb.getSelectedIndex() == 1;
168  }
169 
170  @Override
171  protected void createContent(JPanel panel) {
172  setResizable(false);
173  panel.setLayout(new GridBagLayout());
174  gbc.anchor = GridBagConstraints.EAST;
175  gbc.insets = new Insets(5, 5, 5, 5);
176 
177  JPanel groupstbpn = new JPanel();
178  JScrollPane sp = new JScrollPane();
179  groupstbpn.setBorder(BorderFactory.createTitledBorder("Labels"));
180  groupstbpn.add(sp);
181  sp.setOpaque(true);
182  model = new ColumnsTableModel();
183  tableColumns = new JTable(model);
184  tableColumns.getColumnModel().getColumn(0).setPreferredWidth(250);
185  tableColumns.setPreferredScrollableViewportSize(new Dimension(450, 200));
186  sp.setViewportView(tableColumns);
187  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
188  createEntries();
189  panel.add(panelEntries, XmippWindowUtil.getConstraints(gbc, 1, 0));
190 
191  tableColumns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
192  tableColumns.setDefaultRenderer(Color.class, new ColorRenderer());
193  tableColumns.setDefaultEditor(Color.class, new ColorEditor());
194  setComboEditor(3, "solid", "dashed", "dotted");
195  setComboEditor(4, "none", ".", ",", "o", "v", "^", "<", ">", "1", "2",
196  "3", "4", "s", "p", "h", "H", "+", "x", "D", "d", "|", "_");
197  }// function initComponents
198 
199  private void setComboEditor(int col, String... args) {
200  TableColumn column = tableColumns.getColumnModel().getColumn(col);
201  JComboBox cb = new JComboBox(args);
202  column.setCellEditor(new DefaultCellEditor(cb));
203  }
204 
205  @Override
206  public void handleCancel() {
207  closeOnAction = true;
208  }
209 
210  @Override
211  public void handleOk() {
212 
213  if(plotTypecb.getSelectedItem().equals("Histogram") && tfBins.getText().isEmpty())
214  {
215  XmippDialog.showError((JFrame)parent, XmippMessage.getEmptyFieldMsg("Bins"));
216  return;
217  }
218 
219  String labels = "";
220  String colors = "";
221  String styles = "";
222  String markers = "";
223  Boolean checked = false;
224 
225  int plots = 0;
226  ColumnInfo plotci = null;
227  for (ColumnInfo ci: rows) {
228  ColumnInfo.ColumnExtraInfo cei = rowsExtra.get(ci);
229  if (cei.plot) {
230  plots ++;
231  labels += ci.labelName + " ";
232  colors += "#" + cei.color + " ";
233  styles += cei.linestyle + " ";
234  markers += cei.marker + " ";
235  checked = true;
236  plotci = ci;
237  }
238  }
239  String ylabel = tfYLabel.getText().trim();
240  if(plots == 1 && ylabel.isEmpty())
241  ylabel = plotci.labelName;
242 
243  if (!checked)
244  {
245  XmippDialog.showError((JFrame)parent, XmippMessage.getEmptyFieldMsg("Label"));
246  return;
247  }
248 
249  try {
250 
251  String[] argsBasic;
252  Params params = gallery.data.parameters;
253  GalleryData data = gallery.data;
254  String orderColumn = "id";
255  String orderDirection = "ASC";
256  String[] sortby = data.getSortBy();
257  if(sortby != null)
258  {
259  orderColumn = sortby[0];
260  orderDirection = sortby[1];
261  }
262  if(params.port != null)
263  {
264  String command = String.format("run function schedulePlot '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' %s %s",
265  data.getFileName(), data.getPreffix(), plotTypecb.getSelectedItem(),
266  labels, colors, styles, markers, getXColumn(), ylabel, getXLabel(), getPlotTitle(), getBins(), orderColumn, orderDirection);
267 
268  XmippWindowUtil.runCommand(command, params.port);
269  }
270  else
271  {
272  String pwplot = "python -m pyworkflow.apps.pw_plot";
273  String cmd = String.format("%s --file %s --type %s --columns \"%s\" --orderColumn %s --orderDir %s --colors \"%s\" --styles \"%s\" --markers \"%s\""
274  , pwplot, data.getFileName(), plotTypecb.getSelectedItem(), labels, orderColumn, orderDirection, colors, styles, markers);
275  if(!data.getPreffix().isEmpty())
276  cmd += " --block " + data.getPreffix();
277 
278  if(!getXColumn().isEmpty())
279  cmd += " --xcolumn " + getXColumn();
280  if(!data.getPreffix().isEmpty())
281  cmd += " --block " + data.getPreffix();
282  if(plotTypecb.getSelectedItem().equals("Histogram"))
283  cmd += " --bins " + getBins();
284  if(!getPlotTitle().isEmpty())
285  cmd += " --title " + getPlotTitle();
286  if(!getXLabel().isEmpty())
287  cmd += " --xtitle " + getXLabel();
288  if(!ylabel.isEmpty())
289  cmd += " --ytitle " + ylabel;
290  String output = XmippWindowUtil.executeCommand(cmd, false);
291  }
292 
293  } catch (Exception e) {
294  e.printStackTrace();
295  }
296  }
297 
298  public String getXColumn()
299  {
300  if (jcbXAxis.getSelectedIndex() != 0)
301  return jcbXAxis.getSelectedItem().toString();
302  return "";
303  }
304 
305  public String getXLabel()
306  {
307  return tfXLabel.getText().trim();
308  }
309 
310 
311 
312  public String getPlotTitle() {
313  return tfTitle.getText();
314  }
315 
316  public String getBins() {
317  if(tfBins.isVisible())
318  return tfBins.getText();
319  return "";
320  }
321 
322  class ColumnsTableModel extends AbstractTableModel {
323  private static final long serialVersionUID = 1L;
324 
325  private String[] columns = { "Label", "Plot", "Color", "Line style",
326  "Marker" };
327 
328  @Override
329  public Class getColumnClass(int column) {
330  switch (column) {
331  case 0:
332  case 3:
333  case 4:
334  return String.class;
335  case 1:
336  return Boolean.class;
337  case 2:
338  return Color.class;
339  default:
340  return null;
341  }
342  }
343 
344  @Override
345  public Object getValueAt(int row, int column) {
346  ColumnInfo ci = rows.get(row);
347  ColumnInfo.ColumnExtraInfo cei = rowsExtra.get(ci);
348  switch (column) {
349  case 0:
350  return ci.labelName;
351  case 1:
352  return cei.plot;
353  case 2:
354  return ColorEditor.stringToColor(cei.color);
355  case 3:
356  return cei.linestyle;
357  case 4:
358  return cei.marker;
359  }
360  return null;
361  }
362 
363  @Override
364  public void setValueAt(Object value, int row, int column) {
365  /* We will use labelName to store Color and comments to store marker */
366  ColumnInfo ci = rows.get(row);
367  ColumnInfo.ColumnExtraInfo cei = rowsExtra.get(ci);
368  switch (column) {
369  case 1:
370  cei.plot = (Boolean) value;
371 
372  break;
373  case 2:
374  cei.color = ColorEditor.colorToString((Color) value);
375  break;
376  case 3:
377  cei.linestyle = (String) value;
378  break;
379  case 4:
380  cei.marker = (String) value;
381  break;
382  }
383  }
384 
385  @Override
386  public String getColumnName(int columnIndex) {
387  return columns[columnIndex];
388  }
389 
390  @Override
391  public int getColumnCount() {
392  return columns.length;
393  }
394 
395  @Override
396  public int getRowCount() {
397  return rows.size();
398  // return frame.getParticlePicker().getFamilies().size();
399  }
400 
401  @Override
402  public boolean isCellEditable(int row, int column) {
403  switch (column) {
404  case 0:
405  return false;
406  default:
407  return true;
408 
409  }
410  }
411 
412  }// class ColumnsTableModel
413 
414 }// class ColumnsJDialog
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xmipp.jni.MetaData.LABEL_DOUBLE
static final int LABEL_DOUBLE
Definition: MetaData.java:47
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xmipp.viewer.models.GalleryData.getLabelsInfo
List< ColumnInfo > getLabelsInfo()
Definition: GalleryData.java:1495
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static Color stringToColor(String input)
Definition: ColorEditor.java:99
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xmipp.utils.XmippWindowUtil.executeCommand
static String executeCommand(String[] command, boolean wait)
Definition: XmippWindowUtil.java:276
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xmipp.jni.MetaData.LABEL_INT
static final int LABEL_INT
Definition: MetaData.java:45
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xmipp.utils.ColorEditor.colorToString
static String colorToString(Color c)
Definition: ColorEditor.java:109
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xmipp.viewer.windows.PlotJDialog.PlotJDialog
PlotJDialog(GalleryJFrame parent)
Definition: PlotJDialog.java:89
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void actionPerformed(ActionEvent evt)
Definition: XmippDialog.java:163
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xmipp.utils.XmippWindowUtil.runCommand
static void runCommand(String command, Integer port)
Definition: XmippWindowUtil.java:342
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xmipp.viewer.windows.PlotJDialog.createContent
void createContent(JPanel panel)
Definition: PlotJDialog.java:171
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boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.utils.XmippMessage.getEmptyFieldMsg
static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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1 package xmipp.ij.commons;
2 
3 import java.awt.event.ActionEvent;
4 import java.awt.event.ActionListener;
5 
6 import javax.swing.Timer;
7 
8 public class PollTimer extends Timer
9 {
10  private final XmippIJWindow xp;
11  private static final int PERIOD = 5000; // repeat every 5 seconds
12 
13  public PollTimer(final XmippIJWindow xp)
14  {
15  super(PERIOD, new ActionListener()
16  {
17 
18  @Override
19  public void actionPerformed(ActionEvent e)
20  {
21  xp.loadData();
22  }
23  });
24  this.xp = xp;
25  }
26 }
xmipp.ij.commons.PollTimer.PollTimer
PollTimer(final XmippIJWindow xp)
Definition: PollTimer.java:13
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1 package xmipp.jni;
2 
3 public class ProgTomographAlignment
4 {
5  //Load the native library
6  static
7  {
8  System.loadLibrary("XmippJNI");
9  storeIds();
10  }
11  // hold pointer to Image class in C++ space
12  private long peer;
13  // Catching some ids
14  private static native void storeIds();
15  // Functions to create objects.
16  protected native void create();
17 
18  public native void setInputFilename(String name);
19  public native void setRoot(String name);
20  public native void produceSideInfo();
21  public native void run();
22  public native void writeTransformations(String name);
23  public native int getIteration();
24 
25  // destructor
26  private synchronized native void destroy();
27 
28  // non-native functions
29  // constructor
30  public ProgTomographAlignment()
31  {
32  create();
33  }
34 
35  // Should be called by GarbageCollector before destroying
36  @Override
37  protected void finalize() throws Throwable
38  {
39  super.finalize();
40  destroy();
41  }
42 
43 
44 
45 }
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xmipp.jni.ProgTomographAlignment.setInputFilename
native void setInputFilename(String name)
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xmipp.jni.ProgTomographAlignment.setRoot
native void setRoot(String name)
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1 package xmipp.jni;
2 
6 public class Program {
7  public static native int runByName(String progName, String args) throws Exception;
8 }
xmipp.jni.Program.runByName
static native int runByName(String progName, String args)
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1 package xmipp.jni;
2 
3 public class Projection {
4 
5  /*public static native void projectVolume(ImageGeneric volume, ImageGeneric projection,
6  double rot, double tilt, double psi) throws Exception;*/
7 
8  public static native void projectVolume(ImageGeneric volume, ImageGeneric projection,
9  double matrix[]) throws Exception;
10 
11  public static native double entropyOtsuSegmentation(ImageGeneric volume, double percentile, boolean binarize) throws Exception;
12 
13 // public static native double[] eulerDirection2Angles(double vector[]) throws Exception;
14  public static native double[] eulerMatrix2Angles(double matrix[]) throws Exception;
15 }
xmipp.jni.Projection.projectVolume
static native void projectVolume(ImageGeneric volume, ImageGeneric projection, double matrix[])
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xmipp.jni.Projection.eulerMatrix2Angles
static native double [] eulerMatrix2Angles(double matrix[])
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xmipp.jni.Projection.entropyOtsuSegmentation
static native double entropyOtsuSegmentation(ImageGeneric volume, double percentile, boolean binarize)
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1 package xmipp.utils;
2 
3 
4 import java.awt.Frame;
5 import java.awt.GridBagConstraints;
6 import java.awt.GridBagLayout;
7 import java.awt.Insets;
8 import java.awt.event.ActionEvent;
9 import java.awt.event.ActionListener;
10 import java.util.Map;
11 
12 import javax.swing.JButton;
13 import javax.swing.JDialog;
14 
15 
16 
17 public class QuickHelpJDialog extends JDialog
18 {
19 
20  protected JButton okbt;
21  protected QuickHelpPane helppn;
22  protected String helptitle;
23  protected Map<Object, Object> helpmap;
24  protected final boolean editmap;
25 
26  public QuickHelpJDialog(Frame window, boolean modal, String helptitle, Map<Object, Object> map)
27  {
28  this(window, modal, helptitle, map, false);
29  }
30 
31  public QuickHelpJDialog(Frame window, boolean modal, String helptitle, Map<Object, Object> map, boolean editmap)
32  {
33  super(window, modal);
34  this.helpmap = map;
35  this.helptitle = helptitle;
36  this.editmap = editmap;
37  initComponents();
38  }
39 
40  private void initComponents()
41  {
42  setIconImage(XmippResource.getIcon("xmipp_logo.png").getImage());
43  setResizable(false);
44  setDefaultCloseOperation(HIDE_ON_CLOSE);
45  setTitle(helptitle);
46  GridBagConstraints constraints = new GridBagConstraints();
47  constraints.insets = new Insets(5, 5, 5, 5);
48  setLayout(new GridBagLayout());
49  helppn = new QuickHelpPane( helptitle, helpmap, editmap);
50  add(helppn, XmippWindowUtil.getConstraints(constraints, 0, 0, 1));
51  okbt = XmippWindowUtil.getTextButton("Ok", new ActionListener()
52  {
53 
54  @Override
55  public void actionPerformed(ActionEvent e)
56  {
57  setVisible(false);
58 
59  }
60  });
61  add(okbt, XmippWindowUtil.getConstraints(constraints, 0, 1));
62  pack();
63  XmippWindowUtil.setLocation(0.5f, 0.5f, this);
64  }
65 
66 
67 
68 }
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xmipp.utils.QuickHelpJDialog.QuickHelpJDialog
QuickHelpJDialog(Frame window, boolean modal, String helptitle, Map< Object, Object > map)
Definition: QuickHelpJDialog.java:26
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xmipp.utils.XmippResource.getIcon
static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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xmipp.utils.XmippWindowUtil.getTextButton
static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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xmipp.utils.QuickHelpJDialog.helpmap
Map< Object, Object > helpmap
Definition: QuickHelpJDialog.java:23
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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xmipp.utils.QuickHelpJDialog.QuickHelpJDialog
QuickHelpJDialog(Frame window, boolean modal, String helptitle, Map< Object, Object > map, boolean editmap)
Definition: QuickHelpJDialog.java:31
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class  xmipp.utils.QuickHelpPane
 
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package  xmipp.utils
 
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1 package xmipp.utils;
2 
3 
4 
5 import java.awt.Dimension;
6 import java.util.Map;
7 import javax.swing.BorderFactory;
8 import javax.swing.JButton;
9 import javax.swing.JPanel;
10 import javax.swing.JScrollPane;
11 import javax.swing.JTable;
12 import javax.swing.table.AbstractTableModel;
13 
14 
15 
16 
17 public class QuickHelpPane extends JPanel
18 {
19  protected JPanel buttonspn;
20  protected String title;
21  protected JTable helptb;
22  protected Map<Object, Object> helpmap;
23  protected Object[] keys;
24  protected final boolean editmap;
25 
26  public QuickHelpPane(String title, Map<Object, Object> helpmap)
27  {
28  this(title, helpmap, false);
29  }
30 
31  public QuickHelpPane(String title, Map<Object, Object> helpmap, boolean editmap)
32  {
33 
34  this.helpmap = helpmap;
35  this.editmap = editmap;
36  if(helpmap.size() == 0)
37  throw new IllegalArgumentException("There is no help information available");
38  keys = helpmap.keySet().toArray();
39  this.title = title;
40  initComponents();
41  }
42 
43  protected void initComponents()
44  {
45 // setBorder(BorderFactory.createTitledBorder(title));
46 
47  JScrollPane sp = new JScrollPane();
48  add(sp);
49  sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
50  sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
51  initHelpTable();
52  sp.setViewportView(helptb);
53  int height = Math.min(600, helptb.getRowHeight() * helpmap.size() + 5);
54  sp.setPreferredSize(new Dimension(800, height));
55  setVisible(true);
56  }
57 
58  protected void initHelpTable()
59  {
60  helptb = new JTable();
61  helptb.setShowHorizontalLines(false);
62  helptb.setTableHeader(null);
63 // int lines = 2;
64 // helptb.setRowHeight( helptb.getRowHeight() * lines);
65  helptb.setModel(new AbstractTableModel()
66  {
67 
68  @Override
69  public Object getValueAt(int row, int column)
70  {
71  Object key = keys[row];
72  if(column == 0)
73  return key;
74  return helpmap.get(key);
75 
76  }
77 
78  @Override
79  public boolean isCellEditable(int row, int column)
80  {
81  if(column == 0)
82  return false;
83  return editmap;
84  }
85 
86  @Override
87  public Class getColumnClass(int column)
88  {
89  return String.class;
90  }
91 
92  @Override
93  public int getRowCount()
94  {
95  return helpmap.size();
96  }
97 
98  @Override
99  public int getColumnCount()
100  {
101  return 2;
102  }
103 
104  @Override
105  public void setValueAt(Object value, int row, int column)
106  {
107  helpmap.put(keys[row], value);
108  }
109 
110 
111  });
112  helptb.setDefaultRenderer(String.class, new MultilineCellRenderer());
113  helptb.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
114  helptb.getColumnModel().getColumn(0).setPreferredWidth(250);
115  helptb.getColumnModel().getColumn(1).setPreferredWidth(550);
116 
117  }
118 
119  void addButton(JButton bt)
120  {
121  buttonspn.add(bt);
122  }
123 
124 
125 }
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Map< Object, Object > helpmap
Definition: QuickHelpPane.java:22
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QuickHelpPane(String title, Map< Object, Object > helpmap)
Definition: QuickHelpPane.java:26
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xmipp.utils.QuickHelpPane.QuickHelpPane
QuickHelpPane(String title, Map< Object, Object > helpmap, boolean editmap)
Definition: QuickHelpPane.java:31
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1 # Xmipp
2 
3 Welcome to Xmipp API Documentation. Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.
4 
5 * Java modules documentation
6 
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class  Red_And_Blue
 
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Red_And_Blue.java
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1 import java.awt.*;
2 import ij.*;
3 import ij.gui.*;
4 import ij.process.*;
5 import ij.plugin.PlugIn;
6 
8 public class Red_And_Blue implements PlugIn {
9 
10  public void run(String arg) {
11  long start = System.currentTimeMillis();
12  int w = 400, h = 400;
13  ImageProcessor ip = new ColorProcessor(w, h);
14  int[] pixels = (int[])ip.getPixels();
15  int i = 0;
16  for (int y = 0; y < h; y++) {
17  int red = (y * 255) / (h - 1);
18  for (int x = 0; x < w; x++) {
19  int blue = (x * 255) / (w - 1);
20  pixels[i++] = (255 << 24) | (red << 16) | blue;
21  }
22  }
23  new ImagePlus("Red and Blue", ip).show();
24  IJ.showStatus(""+(System.currentTimeMillis()-start));
25  }
26 
27 }
28 
Red_And_Blue.run
void run(String arg)
Definition: Red_And_Blue.java:10
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Definition: Red_And_Blue.java:8
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class  xmipp.viewer.RowHeaderRenderer
 
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package  xmipp.viewer
 
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1 package xmipp.viewer;
2 
3 import java.awt.Component;
4 import javax.swing.BorderFactory;
5 import javax.swing.JLabel;
6 import javax.swing.JList;
7 import javax.swing.ListCellRenderer;
8 import javax.swing.UIManager;
9 import javax.swing.border.Border;
10 
11 public class RowHeaderRenderer extends JLabel implements ListCellRenderer {
12 
13  protected Border border;
14 
15  public RowHeaderRenderer() {
16  super();
17 
18  setOpaque(true);
19 
20  border = BorderFactory.createCompoundBorder(
21  UIManager.getBorder("TableHeader.cellBorder"),
22  BorderFactory.createEmptyBorder(0, 0, 0, 2));
23 
24  // Border to show the entire label and with the same look and feel as
25  // columns.
26  setBorder(border);
27  }
28 
29  public Component getListCellRendererComponent(JList list, Object value,
30  int index, boolean selected, boolean hasFocus) {
31 
32  setEnabled(list.isEnabled());
33 
34  setFont(list.getFont());
35  setText(value.toString());
36 
37  return this;
38  }
39 }
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Component getListCellRendererComponent(JList list, Object value, int index, boolean selected, boolean hasFocus)
Definition: RowHeaderRenderer.java:29
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class  xmipp.viewer.windows.SaveImagesJDialog
 
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package  xmipp.viewer.windows
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import javax.swing.JPanel;
29 import javax.swing.JLabel;
30 import javax.swing.JTextField;
31 import xmipp.jni.MetaData;
32 import xmipp.utils.XmippWindowUtil;
33 import xmipp.viewer.models.ImageGalleryTableModel;
34 
35 public class SaveImagesJDialog extends SaveJDialog {
36  private static final long serialVersionUID = 1L;
37  ImageGalleryTableModel gallery;
38  JPanel panelButtons;
39  JTextField textField;
40  MetaData imagesMd;
41 
42  public SaveImagesJDialog(GalleryJFrame parent, String proposedFileName) {
43  super(parent, proposedFileName, true);
44  }// constructor ColumnsJDialog
45 
46  @Override
47  protected void initComponents(){
48  this.gallery = ((GalleryJFrame)parent).gallery;
49  this.btnOkText = "Save Images";
50  super.initComponents();
51  }
52 
53  @Override
54  protected void createContent(JPanel panel) {
55  super.createContent(panel);
56 
57  imagesMd = gallery.data.getClassesImages(gallery.getSelection());
58  String text = String.format("<html>You are about to save <font color='red'>%d</font> images from <font color='red'>%d</font> classes.",
59  imagesMd.size(), gallery.getSelectionCount());
60  panel.add(new JLabel(text), XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
61  }// function initComponents
62 
63  @Override
64  protected void fillMdOptions(){
65  // Just to avoid adding some metadata options.
66  // this dialog will override the existing file
67  }
68 
69  @Override
70  public void handleOk() {
71  imagesMd.write(getMdFilename());
72  imagesMd.destroy();
73  }// function actionPerformed
74 
75  @Override
76  public void handleCancel(){
77  imagesMd.destroy();
78  }
79 }// class ColumnsJDialog
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MetaData getClassesImages(boolean[] selection)
Definition: GalleryData.java:1098
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SaveImagesJDialog(GalleryJFrame parent, String proposedFileName)
Definition: SaveImagesJDialog.java:42
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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class  xmipp.viewer.windows.SaveJDialog
 
class  xmipp.viewer.windows.SaveJDialog.BrowseField
 
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.windows;
27 
28 import java.awt.Dimension;
29 import java.awt.GridBagConstraints;
30 import java.awt.GridBagLayout;
31 import java.awt.event.ActionEvent;
32 import java.io.File;
33 
34 import javax.swing.BorderFactory;
35 import javax.swing.ButtonGroup;
36 import javax.swing.JButton;
37 import javax.swing.JCheckBox;
38 import javax.swing.JComboBox;
39 import javax.swing.JLabel;
40 import javax.swing.JPanel;
41 import javax.swing.JRadioButton;
42 import javax.swing.JTextField;
43 
44 import xmipp.jni.Filename;
45 import xmipp.jni.MDLabel;
46 import xmipp.jni.MetaData;
47 import xmipp.utils.XmippDialog;
48 import xmipp.utils.XmippFileChooser;
49 import xmipp.utils.XmippWindowUtil;
50 import xmipp.viewer.models.ColumnInfo;
51 import xmipp.viewer.models.GalleryData;
52 
53 public class SaveJDialog extends XmippDialog
54 {
55  protected static final long serialVersionUID = 1L;
56  protected JPanel group;
57  protected GridBagConstraints gbc;
58 
59  protected XmippFileChooser fc;
60  protected JCheckBox chbMd;
61 // protected JCheckBox chbImg;
62  // protected JButton btnBrowseMd;
63  // protected JTextField tbMd;
64  // protected JTextField tbImg;
65  // protected JButton btnBrowseImg;
66  protected BrowseField browseMd;
67  protected BrowseField browseImg;
68  protected JComboBox cbExtension;
69  protected JComboBox cbLabel;
70 // protected JRadioButton rbStack;
71  protected JRadioButton rbIndependent;
72  protected JRadioButton rbMdOverride;
73  protected JRadioButton rbMdAppend;
74 // protected JPanel panelImg;
75  protected JPanel panelMd;
76  protected GalleryData data;
77  private String block;
78  private JCheckBox chbDiscard;
79  private boolean isselection;
80  private String filename;
81 
82  public SaveJDialog(GalleryJFrame parent, String file, boolean isselection)
83  {
84  super(parent, "Save", true);
85  this.isselection = isselection;
86  this.filename = file;
87  initComponents();
88  setMdFilename(file);
89  }// constructor SaveJDialog
90 
91  public SaveJDialog(GalleryJFrame parent)
92  {
93  this(parent, null, false);
94  }// constructor SaveJDialog
95 
96  @Override
97  protected void createContent(JPanel panel)
98  {
99  this.data = ((GalleryJFrame) parent).getData();
100  //setMinimumSize(new Dimension(500, 300));
101  setResizable(false);
102  panel.setLayout(new GridBagLayout());
103  gbc = new GridBagConstraints();
104  gbc.ipadx = 5;
105  gbc.ipady = 5;
106  gbc.weightx = 1.0;
107  gbc.weighty = 1.0;
108  // gbc.insets = new Insets(5, 5, 5, 5);
109  // gbc.weightx = 1.0;
110  // gbc.weighty = 1.0;
111  gbc.anchor = GridBagConstraints.NORTHWEST;
112  File initial;
113  if (filename != null)
114  initial = new File(Filename.getFilename(filename));
115  else
116  initial = new File(System.getProperty("user.dir"));
117  fc = new XmippFileChooser(initial);
118 
119  group = new JPanel(new GridBagLayout());
120  group.setBorder(BorderFactory.createTitledBorder("Save options"));
121 
122  // Checkbox to save metadata
123  // chbMd = new JCheckBox("Save metadata", true);
124  // chbMd.addActionListener(this);
125  group.add(new JLabel("Metadata path:"), XmippWindowUtil.getConstraints(gbc, 0, 0));
126 
127  createMdOptions();
128  group.add(panelMd, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
129 
130  // Checkbox to save images
131 // chbImg = new JCheckBox("Save images", false);
132 // chbImg.addActionListener(this);
133 // group.add(chbImg, XmippWindowUtil.getConstraints(gbc, 0, 2));
134 
135  //createImageOptions();
136  //group.add(panelImg, XmippWindowUtil.getConstraints(gbc, 0, 3, 2));
137 
138  gbc.anchor = GridBagConstraints.PAGE_START;
139  panel.add(group, XmippWindowUtil.getConstraints(gbc, 0, 0, 2));
140  // Change default Ok text button
141  btnOkText = "Save";
142  pack();
143  }// function initComponents
144 
145  protected JPanel createBrowse(BrowseField browse)
146  {
147  JPanel panel = new JPanel();
148  browse.tb = new JTextField(30);
149  panel.add(browse.tb);
150  browse.btn = XmippWindowUtil.getIconButton("folderopen.gif", this);
151  panel.add(browse.btn);
152  return panel;
153  }
154 
155  protected void createMdOptions()
156  {
157  GridBagConstraints gbc = new GridBagConstraints();
158  // Metadata options panel
159  panelMd = new JPanel(new GridBagLayout());
160  // panelMd.setBackground(Color.blue);
161  browseMd = new BrowseField();
162  JPanel panelBrowse = createBrowse(browseMd);
163  panelMd.add(panelBrowse, XmippWindowUtil.getConstraints(gbc, 0, 0, 3));
164  fillMdOptions();
165  }
166 
167  protected void fillMdOptions(){
168  chbDiscard = new JCheckBox("Save Active Metadata Only", false);
169  if(!isselection)
170  panelMd.add(chbDiscard, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
171  rbMdOverride = new JRadioButton("Overwrite file");
172  panelMd.add(rbMdOverride, XmippWindowUtil.getConstraints(gbc, 0, 2));
173  gbc.anchor = GridBagConstraints.WEST;
174  rbMdAppend = new JRadioButton("Replace/Append", true);
175  panelMd.add(rbMdAppend, XmippWindowUtil.getConstraints(gbc, 1, 2));
176  ButtonGroup group = new ButtonGroup();
177  group.add(rbMdOverride);
178  group.add(rbMdAppend);
179  }
180 
181  public boolean isOverwrite()
182  {
183  return rbMdOverride.isSelected();
184  }
185 
186 // protected void createImageOptions()
187 // {
188 // GridBagConstraints gbc = new GridBagConstraints();
189 // // gbc.insets = new Insets(0, 0, 0, 5);
190 // // Image options panel
191 // panelImg = new JPanel(new GridBagLayout());
192 // // panelImg.setBackground(Color.red);
193 // panelImg.setVisible(false);
194 // gbc.anchor = GridBagConstraints.EAST;
195 // panelImg.add(new JLabel("Label "), XmippWindowUtil.getConstraints(gbc, 0, 0));
196 // cbLabel = new JComboBox();
197 // for (ColumnInfo ci : data.labels)
198 // if (ci.allowRender)
199 // cbLabel.addItem(ci.labelName);
200 // gbc.anchor = GridBagConstraints.WEST;
201 // panelImg.add(cbLabel, XmippWindowUtil.getConstraints(gbc, 1, 0));
202 // browseImg = new BrowseField();
203 // JPanel panelBrowse = createBrowse(browseImg);
204 // panelImg.add(new JLabel("Output stack filename:"), XmippWindowUtil.getConstraints(gbc, 0, 1, 5));
205 // panelImg.add(panelBrowse, XmippWindowUtil.getConstraints(gbc, 0, 2, 5));
206 // rbStack = new JRadioButton("Stack", true);
207 // panelImg.add(rbStack, XmippWindowUtil.getConstraints(gbc, 2, 0));
208 // rbIndependent = new JRadioButton("Separate images");
209 // // gbc.anchor = GridBagConstraints.WEST;
210 // panelImg.add(rbIndependent, XmippWindowUtil.getConstraints(gbc, 3, 0));
211 // ButtonGroup group = new ButtonGroup();
212 // group.add(rbStack);
213 // group.add(rbIndependent);
214 // }// function createImageOptions
215 
217  public void setInitialValues()
218  {
219  browseMd.tb.setText("");
220 // browseImg.tb.setText("");
221  rbMdAppend.setSelected(true);
222 // chbImg.setSelected(false);
223 // rbStack.setSelected(true);
224 
225  }
226 
227  @Override
228  public void handleActionPerformed(ActionEvent evt)
229  {
230  Object obj = evt.getSource();
231  // Handle open button action.
232  if (obj == browseMd.btn)
233  browseFile(browseMd.tb);
234  else if (obj == browseImg.btn)
235  browseFile(browseImg.tb);
236 // else if (obj == chbImg)
237 // panelImg.setVisible(chbImg.isSelected());
238  else if (obj == chbMd)
239  panelMd.setVisible(chbMd.isSelected());
240 
241  }
242 
243  private void browseFile(JTextField tb)
244  {
245  int returnVal = fc.showOpenDialog(this);
246 
247  if (returnVal == XmippFileChooser.APPROVE_OPTION)
248  {
249  File file = fc.getSelectedFile();
250  String text = (block == null)? file.getPath(): block + "@" + file.getPath();
251  tb.setText(text);
252  }
253  }
254 
255  public class BrowseField
256  {
257  public JTextField tb;
258  public JButton btn;
259  }
260 
262  public String getMdFilename()
263  {
264  return browseMd.tb.getText();
265  }
266 
267  public void setMdFilename(String file)
268  {
269  if (file != null)
270  {
271  if (file.contains("@"))
272  block = file.substring(0, file.lastIndexOf("@"));
273  browseMd.tb.setText(file);
274  }
275  else
276  {
277  block = null;
278  browseMd.tb.setText("");
279  }
280 
281  }
282 
283  public boolean isAppendMode()
284  {
285  return rbMdAppend.isSelected();
286  }
287 
288  public void setAppendMode(boolean value)
289  {
290  rbMdAppend.setSelected(value);
291  }
292 
293  public boolean doSaveImages()
294  {
295  return false;
296  //return chbImg.isSelected();
297  }
298 
299  public boolean isOutputIndependent()
300  {
301  return rbIndependent.isSelected();
302  }
303 
304  public String getOutput()
305  {
306  return browseImg.tb.getText();
307  }
308 
309  public int getImageLabel()
310  {
311  try
312  {
313  return MetaData.str2Label(cbLabel.getSelectedItem().toString());
314  }
315  catch (Exception e)
316  {
317  e.printStackTrace();
318  return MDLabel.MDL_UNDEFINED;
319  }
320  }
321 
322  public boolean saveActiveMetadataOnly()
323  {
324  return chbDiscard.isSelected();
325  }
326 }// class SaveJDialog
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xmipp.viewer.windows.SaveJDialog.handleActionPerformed
void handleActionPerformed(ActionEvent evt)
Definition: SaveJDialog.java:228
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xmipp.viewer.windows.SaveJDialog.setAppendMode
void setAppendMode(boolean value)
Definition: SaveJDialog.java:288
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xmipp.jni.MetaData.str2Label
static native int str2Label(String labelName)
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xmipp.viewer.windows.SaveJDialog.serialVersionUID
static final long serialVersionUID
Definition: SaveJDialog.java:55
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xmipp.viewer.windows.SaveJDialog.SaveJDialog
SaveJDialog(GalleryJFrame parent, String file, boolean isselection)
Definition: SaveJDialog.java:82
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xmipp.jni.MDLabel.MDL_UNDEFINED
static final int MDL_UNDEFINED
Definition: MDLabel.java:4
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xmipp.viewer.windows.SaveJDialog.SaveJDialog
SaveJDialog(GalleryJFrame parent)
Definition: SaveJDialog.java:91
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xmipp.jni.Filename.getFilename
static String getFilename(String filename)
Definition: Filename.java:302
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xmipp.viewer.windows.SaveJDialog.createBrowse
JPanel createBrowse(BrowseField browse)
Definition: SaveJDialog.java:145
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xmipp.utils.XmippWindowUtil.getIconButton
static JButton getIconButton(String icon, ActionListener listener)
Definition: XmippWindowUtil.java:124
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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xmipp.viewer.windows.SaveJDialog.createContent
void createContent(JPanel panel)
Definition: SaveJDialog.java:97
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class  xmipp.viewer.scipion.ScipionGalleryData
 
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package  xmipp.viewer.scipion
 
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ScipionGalleryData.java
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 package xmipp.viewer.scipion;
7 
8 import xmipp.utils.ScipionParams;
9 
10 import java.io.File;
11 import java.sql.SQLException;
12 import java.util.List;
13 import java.util.logging.Level;
14 import java.util.logging.Logger;
15 
16 import xmipp.ij.commons.Geometry;
17 import xmipp.jni.EllipseCTF;
18 import xmipp.jni.Filename;
19 import xmipp.jni.ImageGeneric;
20 import xmipp.jni.MDLabel;
21 import xmipp.jni.MetaData;
22 import xmipp.utils.Params;
23 import xmipp.utils.XmippWindowUtil;
24 import xmipp.viewer.models.ClassInfo;
25 import xmipp.viewer.models.ColumnInfo;
26 import xmipp.viewer.models.GalleryData;
27 import xmipp.viewer.scipion.ScipionMetaData.EMObject;
28 
33 public class ScipionGalleryData extends GalleryData {
34 
35  public ScipionGalleryData(ScipionGalleryJFrame window, String fn, Params parameters) {
36  this(window, parameters, new ScipionMetaData(fn));
37  }
38 
39  public ScipionGalleryData(ScipionGalleryJFrame window, Params parameters, ScipionMetaData md) {
40  super(window, parameters, md);
41  }
42 
43  public void setFileName(String file) {
44  if (file.contains("@")) {
45  int sep = file.lastIndexOf("@");
46  selectedBlock = file.substring(0, sep);
47  filename = file.substring(sep + 1);
48  }
49  filename = file;
50  mdBlocks = ((ScipionMetaData)md).getBlocks();
51  selectedBlock = mdBlocks[0];
52 
53  }
54 
55 
56  @Override
57  public ColumnInfo initColumnInfo(int label)
58  {
59  return ((ScipionMetaData)md).getColumnInfo(label);
60  }
61 
62  public String getValueFromLabel(int index, int label) {
63  return ((ScipionMetaData) md).getValueFromLabel(index, label);
64  }
65 
66 
67 
68 
72  @Override
73  public ScipionMetaData getSelectionMd(boolean[] selection) {
74  return null;//metadata operations are not used in scipion
75  }
76 
80  public MetaData getClassesImages() {
81  return null;
82  }
83 
84 
85 
89  public MetaData getClassImages(int index) {
90  try {
91  long id = ids[index];
92  ScipionMetaData childmd = ((ScipionMetaData) md).getEMObject(id).childmd;
93  return childmd;
94  } catch (Exception e) {
95  e.printStackTrace();
96  }
97  return null;
98  }
99 
100  public String getLabel(long objId, int label) {
101  try {
102  if (isClassification) {
103  ScipionMetaData.EMObject emo = ((ScipionMetaData) md).getEMObject(objId);
104  return String.format("Class %s (%d images)", emo.getId(), emo.childmd.size());
105  } else {
106  return md.getValueString(label, objId);
107  }
108  } catch (Exception e) {
109  e.printStackTrace();
110  }
111  return null;
112  }
113 
114  public void readMd() {
115  hasMdChanges = false;
116  hasClassesChanges = false;
117  md = getMetaData(selectedBlock);
118  }
119 
120  public MetaData getMetaData(String block) {
121  if (md.getBlock().equals(block)) {
122  return md;
123  }
124  ScipionMetaData child = ((ScipionMetaData) md).getChild(block);
125  if (child != null) {
126  return child;
127  }
128  ScipionMetaData parent = ((ScipionMetaData) md).getParent();
129  if (parent.getBlock().equals(selectedBlock))// from child to parent
130  {
131  return parent;
132  }
133  return parent.getChild(selectedBlock);
134 
135  }
136 
137  public ScipionMetaData getScipionMetaData(){
138  return (ScipionMetaData) md;
139  }
140 
144  public ClassInfo getItemClassInfo(int index) {
145  return null;
146  }
147 
151  private void setItemClassInfo(long id, ClassInfo cli) {
152 
153  }
154 
158  public void setItemClass(int index, ClassInfo cli) {
159 
160  }
161 
162  public ClassInfo getClassInfo(int classNumber) {
163  return null;
164  }
165 
170  public void updateClassesInfo() {
171 
172  }// function upateClassesInfo
173 
177  public void loadClassesInfo() {
178 
179  }// function loadClassesInfo
180 
181  public MetaData[] getClassesMd() {
182  return null;
183  }
184 
188  public void addClass(ClassInfo ci) {
189 
190  }
191 
195  public void removeClass(int classNumber) {
196 
197  }
198 
199  public boolean hasClasses()//for Scipion usage only
200  {
201  return mdBlocks.length > 1 && ((ScipionMetaData) md).getSetType().contains("SetOfClasses");
202  }
203 
204  public boolean hasMicrographParticles() {
205  return false;//fixme?? cannot open picker from sqlite
206  }
207 
208  public List<ScipionMetaData.EMObject> getEMObjects() {
209  return ((ScipionMetaData)md).getEMObjects();
210  }
211 
215  public boolean isFile(ColumnInfo ci) {
216  return ci.labelName.contains("filename") || ci.labelName.equals("_psdFile");
217  }
218 
219  public boolean isImageFile(ColumnInfo ci) {
220  return ci.allowRender;
221  }
222 
223 
224  public void overwrite(String path, boolean[] selection) throws SQLException {
225  ((ScipionMetaData) md).overwrite(filename, path, selection);
226  }
227 
228 
229 
230  public String getPreffix() {
231  return ((ScipionMetaData) md).getPreffix();
232  }
233 
234  @Override
235  public void removeCTF(int row) {
236  ScipionMetaData.EMObject emo = ((ScipionMetaData) md).getEMObjects().get(row);
237  emo.setLabel("");
238  emo.setComment("");
239  super.removeCTF(row);
240  window.fireTableRowsUpdated(row, row);
241  }
242 
243  public String createSortFile(String psdFile, int row) {
244  return null;
245  }
246 
247  @Override
248  public void recalculateCTF(int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn) {
249 
250  ScipionMetaData.EMObject emo;
251  long id;
252  if(isEnabled(row))
253  {
254  for(int i = 0; i <selection.length; i ++ )
255  if(selection[i] && isEnabled(i))
256  {
257  id = ids[i];
258  emo = ((ScipionMetaData) md).getEMObject(id);
259  md.putCTF(id, ellipseCTF);
260  emo.setLabel("(recalculate ctf)");
261  emo.setComment(ellipseCTF.toString());
262  window.fireTableRowsUpdated(i, i);
263  }
264  }
265 
266  }
267 
268  public ColumnInfo getGeoMatrixColumn(ColumnInfo ci)
269  {
270  return ((ScipionMetaData)md).getGeoMatrixColumn(ci);
271  }
272 
273  public Geometry getGeometry(long id, ColumnInfo ci)
274  {
275  return getGeometry(id, "2D", ci);
276  }
277 
278  public Geometry getGeometry(long id, String type, ColumnInfo ci)
279  {
280  if (!containsGeometryInfo(type))
281  return null;
282  ScipionMetaData.EMObject emo = ((ScipionMetaData)md).getEMObject(id);
283  ColumnInfo column = getGeoMatrixColumn(ci);
284 
285  String matrix = (String)emo.getValue(column);
286  return new Geometry(matrix);
287  }
288 
289  public int getEnabledCount() {
290  return ((ScipionMetaData)md).getEnabledCount();
291  }
292 
296  @Override
297  public void setEnabled(int index, boolean isenabled) {
298  try {
299  if (!isVolumeMode()) { // slices in a volume are always enabled
300  getEMObjects().get(index).setEnabled(isenabled);
301  hasMdChanges = true;
302  if(!isenabled && isRecalculateCTF(index))
303  removeCTF(index);
304  }
305  } catch (Exception e) {
306  e.printStackTrace();
307  }
308  }
309 
310  public boolean hasMdChanges()
311  {
312  return ((ScipionMetaData)md).isChanged();
313  }
314 
318  public boolean isEnabled(int index) {
319  try {
320  if (isVolumeMode()) {
321  return true;
322  }
323  return getEMObjects().get(index).isEnabled();
324  } catch (Exception e) {
325  e.printStackTrace();
326  }
327  return true;
328  }
329 
330  public String getValueFromCol(int index, ColumnInfo ci) {
331  try {
332  return getEMObjects().get(index).getValueString(ci);
333  } catch (Exception e) {
334  e.printStackTrace();
335  }
336  return null;
337  }
338 
339  public void setValueToCol(int index, ColumnInfo ci, String value) {
340  try {
341  getEMObjects().get(index).setValue(ci, value);
342  setMdChanges(true);
343 
344  } catch (Exception e) {
345  e.printStackTrace();
346  }
347  }
348 
349  public void loadSelection(String selectedPath) {
350  ((ScipionMetaData)md).loadSelection(selectedPath);
351 
352  }
353 
354 
355  public String getExtraPath()
356  {
357  if(filename == null)
358  return null;
359  String dir = new File(filename).getParent();
360  if(dir == null)
361  return null;
362  return Filename.join(dir, "extra");
363  }
364 
368  public boolean checkifIsClassificationMd() {
369  return ((ScipionMetaData)md).isClassificationMd();
370  }
371 
372  public void runObjectCommand(int index, String objectCommand) {
373  try {
374  ScipionParams params = (ScipionParams)parameters;
375  String command = String.format("run function runObjectCommand '%s' %s %s", objectCommand, params.inputid, getId(index));
376  XmippWindowUtil.runCommand(command, params.port);
377 // String[] cmd = new String[]{params.python, params.getObjectCmdScript(), String.format("'%s'", objectCommand), params.projectid, params.other, String.valueOf(getId(index))};
378 // XmippWindowUtil.executeCommand(cmd, false);
379  } catch (Exception ex) {
380  Logger.getLogger(GalleryData.class.getName()).log(Level.SEVERE, null, ex);
381  }
382  }
383 
384 
385 
386  public MetaData getImagesMd(boolean[] selection, boolean selected) {
387 
388  MetaData imagesmd = new MetaData();
389  int index = 0;
390  String imagepath;
391  EMObject emo;
392  long imageid;
393  String matrix;
394 
395  for (long id : md.findObjects()) {
396  if (isEnabled(index) && (!selected ||selection[index])) {
397 
398  imagepath = md.getValueString(getRenderLabel(), id, true);
399  if (imagepath != null && ImageGeneric.exists(imagepath)) {
400  imageid = imagesmd.addObject();
401  imagesmd.setValueString(MDLabel.MDL_IMAGE, imagepath, imageid);
402  if (useGeo())
403  {
404  emo = ((ScipionMetaData)md).getEMObject(id);
405  matrix = String.format("'%s'", emo.getValueString(getGeoMatrixColumn(ciFirstRender)));
406  imagesmd.setValueString(MDLabel.MDL_TRANSFORM_MATRIX, matrix, imageid);//copy geo info in mdRow
407  }
408 
409  }
410  }
411  index++;
412  }
413  return imagesmd;
414  }
415 
416  public String getChimeraProjectionCmd(int row) {
417  int label = getRenderLabel();
418  ColumnInfo ci = getColumnInfo(label);
419  Geometry geo = getGeometry(ids[row], "3D", ci);
420  if(geo == null)
421  geo = getGeometry(ids[row], "Projection", ci);
422  String command = String.format("rotate_matrix '%s'", geo.getMatrix());
423  return command;
424  }
425 
426 
427 
428 
429 
430 }
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xmipp.jni.MetaData.addObject
native long addObject()
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xmipp.jni.MetaData.setValueString
native boolean setValueString(int label, String value, long objId)
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xmipp.jni.MDLabel.MDL_TRANSFORM_MATRIX
static final int MDL_TRANSFORM_MATRIX
< Name for a Metadata file (std::string)
Definition: MDLabel.java:394
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xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
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xmipp.jni.Filename.join
static String join(String... paths)
Definition: Filename.java:473
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xmipp.viewer.scipion.ScipionGalleryData.setValueToCol
void setValueToCol(int index, ColumnInfo ci, String value)
Definition: ScipionGalleryData.java:339
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xmipp.viewer.windows.GalleryJFrame.fireTableRowsUpdated
void fireTableRowsUpdated(int from, int to)
Definition: GalleryJFrame.java:502
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xmipp.viewer.scipion.ScipionGalleryData.createSortFile
String createSortFile(String psdFile, int row)
Definition: ScipionGalleryData.java:243
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xmipp.jni.ImageGeneric.exists
static boolean exists(String imagepath)
Definition: ImageGeneric.java:291
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xmipp.viewer.scipion.ScipionMetaData.getChild
ScipionMetaData getChild(String block)
Definition: ScipionMetaData.java:471
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.viewer.scipion.ScipionGalleryData.getLabel
String getLabel(long objId, int label)
Definition: ScipionGalleryData.java:100
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xmipp.viewer.models.GalleryData.getColumnInfo
ColumnInfo getColumnInfo(String labelName)
Definition: GalleryData.java:477
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xmipp.viewer.scipion.ScipionGalleryData.getImagesMd
MetaData getImagesMd(boolean[] selection, boolean selected)
Definition: ScipionGalleryData.java:386
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xmipp.viewer.scipion.ScipionGalleryData.getGeometry
Geometry getGeometry(long id, String type, ColumnInfo ci)
Definition: ScipionGalleryData.java:278
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xmipp.viewer.scipion.ScipionGalleryData.getValueFromCol
String getValueFromCol(int index, ColumnInfo ci)
Definition: ScipionGalleryData.java:330
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.viewer.scipion.ScipionGalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: ScipionGalleryData.java:273
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xmipp.jni.MetaData.putCTF
void putCTF(long id, EllipseCTF ellipseCTF)
Definition: MetaData.java:694
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xmipp.jni.MDLabel.MDL_IMAGE
static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
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xmipp.utils.XmippWindowUtil.runCommand
static void runCommand(String command, Integer port)
Definition: XmippWindowUtil.java:342
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xmipp.viewer.scipion.ScipionGalleryData.ScipionGalleryData
ScipionGalleryData(ScipionGalleryJFrame window, String fn, Params parameters)
Definition: ScipionGalleryData.java:35
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xmipp.viewer.scipion.ScipionGalleryData.overwrite
void overwrite(String path, boolean[] selection)
Definition: ScipionGalleryData.java:224
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xmipp.viewer.scipion.ScipionGalleryData.getEMObjects
List< ScipionMetaData.EMObject > getEMObjects()
Definition: ScipionGalleryData.java:208
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xmipp.viewer.scipion.ScipionGalleryData.recalculateCTF
void recalculateCTF(int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)
Definition: ScipionGalleryData.java:248
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xmipp.viewer.scipion.ScipionGalleryData.setEnabled
void setEnabled(int index, boolean isenabled)
Definition: ScipionGalleryData.java:297
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xmipp.viewer.scipion.ScipionGalleryData.getSelectionMd
ScipionMetaData getSelectionMd(boolean[] selection)
Definition: ScipionGalleryData.java:73
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xmipp.viewer.scipion.ScipionGalleryData.ScipionGalleryData
ScipionGalleryData(ScipionGalleryJFrame window, Params parameters, ScipionMetaData md)
Definition: ScipionGalleryData.java:39
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xmipp.viewer.scipion.ScipionGalleryData.runObjectCommand
void runObjectCommand(int index, String objectCommand)
Definition: ScipionGalleryData.java:372
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xmipp.viewer.scipion.ScipionGalleryData.getValueFromLabel
String getValueFromLabel(int index, int label)
Definition: ScipionGalleryData.java:62
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xmipp.viewer.scipion.ScipionGalleryData.setItemClass
void setItemClass(int index, ClassInfo cli)
Definition: ScipionGalleryData.java:158
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class  xmipp.viewer.scipion.ScipionGalleryJFrame
 
class  xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenu
 
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package  xmipp.viewer.scipion
 
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 package xmipp.viewer.scipion;
7 
8 import xmipp.ij.commons.InputFieldsMessageDialog;
9 import xmipp.utils.ScipionParams;
10 import java.awt.Color;
11 import java.awt.Image;
12 import java.awt.event.ActionEvent;
13 import java.awt.event.ActionListener;
14 import java.io.File;
15 import java.lang.reflect.InvocationTargetException;
16 import java.sql.SQLException;
17 import java.util.HashMap;
18 import java.util.logging.Level;
19 import java.util.logging.Logger;
20 import javax.swing.Icon;
21 import javax.swing.JButton;
22 import javax.swing.SwingUtilities;
23 import xmipp.ij.commons.XmippApplication;
24 import xmipp.jni.MetaData;
25 import xmipp.utils.XmippDialog;
26 import xmipp.utils.XmippFileChooser;
27 import xmipp.utils.XmippResource;
28 import xmipp.utils.XmippWindowUtil;
29 import xmipp.viewer.windows.GalleryJFrame;
30 
35 public class ScipionGalleryJFrame extends GalleryJFrame {
36 
37  private static Logger logger = Logger.getLogger(ScipionGalleryJFrame.class.getName());
38 
39  private String type;
40  private Integer port;
41  private JButton cmdbutton;
42  private String sqlitefile;
43  private JButton classcmdbutton;
44  private String inputid;
45  private HashMap<String, String> msgfields;
46  private final String runNameKey = "Run name:";
47  private String other;
48  private JButton representativesbt;
49  private InputFieldsMessageDialog dlg;
50  private JButton createvolbt;
51  private String setType;
52  private boolean recalculateCTF;
53 
54  private static final String runProtCreateSubset = "run protocol ProtUserSubSet inputObject=%s sqliteFile='%s','%s' outputClassName=%s other='%s' label='%s'";
55 
56 
57  public ScipionGalleryJFrame(ScipionGalleryData data) {
58  super(data);
59  readScipionParams((ScipionParams)data.parameters);
60 
61  }
62 
63 
64 
65  protected void readScipionParams(ScipionParams parameters)
66  {
67  try {
68  setType = ((ScipionMetaData)data.getMd()).getSetType();
69  type = data.hasClasses()? "Particles": setType.replace("SetOf", "");
70  port = parameters.port;
71  inputid = parameters.inputid;
72  sqlitefile = data.getTmpFile("_state");
73  msgfields = new HashMap<String, String>();
74  msgfields.put(runNameKey, "create subset");
75  other = parameters.other;
76  recalculateCTF = parameters.recalculateCTF;
77  initComponents();
78  } catch (Exception ex) {
79  logger.log(Level.SEVERE, null, ex);
80  throw new IllegalArgumentException(ex.getMessage());
81  }
82  }
83 
84  protected void initComponents() {
85  Icon icon = XmippResource.getIcon("fa-times.png");
86  JButton closebt = new JButton("Close", icon);
87  closebt.addActionListener(new ActionListener() {
88 
89  @Override
90  public void actionPerformed(ActionEvent ae) {
91  close();
92  }
93  });
94 
95  buttonspn.add(closebt);
96  if(!XmippApplication.isScipion())
97  return;
98 
99  if (type != null) {
100  if(!data.isCTFMd()) {
101  if (other.equals("deepCons")) {
102  cmdbutton = XmippWindowUtil.getScipionIconButton("Create Coordinates");
103  cmdbutton.addActionListener(new ActionListener() {
104  @Override
105  public void actionPerformed(ActionEvent ae) {
106  createCoordSubsetFromImages();
107  }
108  });
109  }
110  else
111  {
112  cmdbutton = XmippWindowUtil.getScipionIconButton("Create " + type);
113  cmdbutton.addActionListener(new ActionListener() {
114  @Override
115  public void actionPerformed(ActionEvent ae) {
116  createSimpleSubset();
117  }
118  });
119  }
120  buttonspn.add(cmdbutton);
121  }
122  if(data.hasClasses())
123  {
124  classcmdbutton = XmippWindowUtil.getScipionIconButton("Create Classes");
125  classcmdbutton.addActionListener(new ActionListener() {
126 
127  @Override
128  public void actionPerformed(ActionEvent ae) {
129  createSubsetFromClasses();
130 
131  }
132  });
133 
134  String repText = setType.equals("SetOfClasses2D") ? "Create Averages": "Create Volumes";
135  representativesbt = XmippWindowUtil.getScipionIconButton(repText);
136  representativesbt.addActionListener(new ActionListener() {
137 
138  @Override
139  public void actionPerformed(ActionEvent ae) {
140  createRepresentativesSubset();
141 
142  }
143  });
144 
145  buttonspn.add(representativesbt);
146  buttonspn.add(classcmdbutton);
147  }
148 
149 
150  if(data.isCTFMd())
151  {
152  if (recalculateCTF) {
153  icon = XmippResource.getIcon("fa-cogs.png");
154  JButton recalculatectfbt = XmippWindowUtil.getScipionIconButton("Recalculate CTFs");
155  recalculatectfbt.addActionListener(new ActionListener() {
156 
157  @Override
158  public void actionPerformed(ActionEvent ae) {
159  if (!data.hasRecalculateCTF()) {
160  XmippDialog.showError(ScipionGalleryJFrame.this, "There are no ctfs to recalculate");
161  return;
162  }
163  String command = String.format("run function recalculateCTF %s %s", inputid, sqlitefile);
164  runCommand(command, "Recalculating CTF", false);
165  }
166  });
167  recalculatectfbt.setIcon(icon);
168  buttonspn.add(recalculatectfbt);
169  }
170 
171  JButton ctfsubsetbt = XmippWindowUtil.getScipionIconButton("Create Micrographs");
172  ctfsubsetbt.addActionListener(new ActionListener() {
173 
174  @Override
175  public void actionPerformed(ActionEvent ae) {
176  if (confirmCreate("Micrographs"))
177  {
178  String command = String.format(runProtCreateSubset,
179  inputid, sqlitefile, "", "SetOfMicrographs", other, getRunLabel());
180  runCommand(command, "Creating set ...");
181  }
182  }
183  });
184  buttonspn.add(ctfsubsetbt);
185 
186  }
187  if(setType.equals("SetOfVolumes") || setType.equals("SetOfClasses3D"))
188  {
189  createvolbt = XmippWindowUtil.getScipionIconButton("Create Volume");
190  createvolbt.addActionListener(new ActionListener() {
191 
192  @Override
193  public void actionPerformed(ActionEvent ae) {
194  createVolume();
195  }
196  });
197  buttonspn.add(createvolbt);
198  createvolbt.setVisible(!data.isTableMode());
199  }
200 
201 
202  if (!SwingUtilities.isEventDispatchThread()) {
203 
204  Runnable pack = new Runnable() {
205  @Override
206  public void run() {
207  ScipionGalleryJFrame.this.pack();
208  }
209  };
210 
211  try {
212  SwingUtilities.invokeAndWait(pack);
213  } catch (Exception e) {
214 
215  logger.log(Level.WARNING, "ScipionGalleryJFrame.pack threw an exception: " + e.getMessage());
216  }
217  } else {
218  pack();
219  }
220 
221  enableActions();
222  jcbBlocks.addActionListener(new ActionListener() {
223 
224  @Override
225  public void actionPerformed(ActionEvent ae) {
226  enableActions();
227  }
228  });
229  }
230  }
231 
232 
233  protected void createVolume()
234  {
235  msgfields.put(runNameKey, "ProtRegisterVolume");
236  dlg = new InputFieldsMessageDialog(ScipionGalleryJFrame.this, "Question", "Are you sure you want to register volume in scipion?", msgfields);
237  int create = dlg.action;
238  if (create == InputFieldsMessageDialog.OK_OPTION);
239  {
240  String command = String.format(runProtCreateSubset,
241  inputid, sqlitefile, "", setType, data.getSelVolId().toString() + ",Volume", getRunLabel());
242  runCommand(command, "Creating volume ...");
243  }
244  }
245 
246  public String getRunLabel()
247  {
248  return dlg.getFieldValue(runNameKey);
249  }
250 
251  public String getDBPreffix()
252  {
253  return ((ScipionGalleryData)data).getPreffix();
254  }
255 
256  protected void createSimpleSubset()
257  {
258  int size = 0;
259 
260  if(data.hasClasses())
261  {
262  boolean[] selection = gallery.getSelection();
263  for(ScipionMetaData.EMObject emo: ((ScipionGalleryData)data).getEMObjects())
264  {
265  if(gallery.hasSelection() && !data.hasDisabled())
266  {
267  if(selection[emo.index] && emo.childmd != null)
268  size += emo.childmd.getEnabledCount();
269  }
270  else if(emo.isEnabled() && emo.childmd != null)
271  size += emo.childmd.getEnabledCount();
272  }
273  }
274  else if (gallery.hasSelection() && !data.hasDisabled())
275  size = gallery.getSelectionCount();
276  else
277  size = data.getEnabledCount();
278 
279  if (confirmCreate(type, size))
280  {
281  String command = String.format(runProtCreateSubset,
282  inputid, sqlitefile, data.getPreffix(), String.format("SetOf%s", type), other, getRunLabel());
283  runCommand(command, "Creating set ...");
284  }
285  }
286 
287  protected void createCoordSubsetFromImages()
288  {
289  int size = 0;
290 
291  if(data.hasClasses())
292  {
293  boolean[] selection = gallery.getSelection();
294  for(ScipionMetaData.EMObject emo: ((ScipionGalleryData)data).getEMObjects())
295  {
296  if(gallery.hasSelection() && !data.hasDisabled())
297  {
298  if(selection[emo.index] && emo.childmd != null)
299  size += emo.childmd.getEnabledCount();
300  }
301  else if(emo.isEnabled() && emo.childmd != null)
302  size += emo.childmd.getEnabledCount();
303  }
304  }
305  else if (gallery.hasSelection() && !data.hasDisabled())
306  size = gallery.getSelectionCount();
307  else
308  size = data.getEnabledCount();
309 
310  if (confirmCreate("Coordinates", size))
311  {
312  String runProtDeepConsSubset = "run protocol XmippProtDeepConsSubSet inputObject=%s sqliteFile='%s','%s' outputClassName=%s other='%s' label='%s'";
313  String command = String.format(runProtDeepConsSubset,
314  inputid, sqlitefile, data.getPreffix(),
315  String.format("SetOfCoordinates"), other, getRunLabel());
316  runCommand(command, "Creating set ...");
317  }
318  }
319 
320  protected void createSubsetFromClasses()
321  {
322  if (confirmCreate("Classes")) {
323  String command = String.format(runProtCreateSubset,
324  inputid, sqlitefile, "", setType , other, getRunLabel());
325  runCommand(command, "Creating set ...");
326  }
327  }
328 
329  protected void createRepresentativesSubset()
330  {
331  if (confirmCreate("Representatives")) {
332  String output = setType.equals("SetOfClasses2D")? "SetOfAverages,Representatives":"SetOfVolumes,Representatives";
333  String command = String.format(runProtCreateSubset, inputid, sqlitefile, "", output , other, getRunLabel());
334  runCommand(command, "Creating set ...");
335  }
336  }
337 
338  public boolean confirmCreate(String output)
339  {
340  int size;
341  if(!data.hasDisabled())
342  {
343  size = gallery.hasSelection()? gallery.getSelectionCount(): data.size();
344  }
345  else
346  size = data.getEnabledCount();
347  return confirmCreate(output, size);
348  }
349 
350  public boolean confirmCreate(String output, int size)
351  {
352  String msg = String.format("<html>Are you sure you want to create a new set of %s with <font color=red>%s</font> %s?", output, size, (size == 1)?"element":"elements");
353  dlg = new InputFieldsMessageDialog(ScipionGalleryJFrame.this, "Question", msg, msgfields);
354  return dlg.action == InputFieldsMessageDialog.OK_OPTION;
355  }
356 
357  public void reloadTableData(boolean changed)
358  {
359  super.reloadTableData(changed, gallery.getSelection());
360  enableActions();
361  }
362 
363  protected void enableActions() {
364  boolean isenabled = !data.isVolumeMode();
365  Color color = isenabled ? XmippWindowUtil.firebrick : XmippWindowUtil.lightgrey;
366  Color forecolor = isenabled ? Color.WHITE : Color.GRAY;
367  if(cmdbutton != null)
368  {
369  cmdbutton.setVisible(isenabled);
370  cmdbutton.setBackground(color);
371  cmdbutton.setForeground(forecolor);
372  }
373  if(classcmdbutton != null)
374  {
375  isenabled = data.hasClasses() && !data.isVolumeMode();
376  color = isenabled? XmippWindowUtil.firebrick: XmippWindowUtil.lightgrey;
377  forecolor = isenabled? Color.WHITE: Color.GRAY;
378  classcmdbutton.setVisible( isenabled);
379  classcmdbutton.setBackground(color);
380  classcmdbutton.setForeground(forecolor);
381  representativesbt.setVisible( isenabled);
382  representativesbt.setBackground(color);
383  representativesbt.setForeground(forecolor);
384  }
385  }
386 
387  @Override
388  protected void changeView()
389  {
390  super.changeView();
391 
392  if(setType.equals("SetOfVolumes") || setType.equals("SetOfClasses3D"))
393  {
394 
395  // It will be null when invoked as a stand alone viewer.
396  if (cmdbutton != null){
397  cmdbutton.setVisible(data.isTableMode());
398  createvolbt.setVisible(!data.isTableMode());
399  }
400  }
401  }
402 
403  public boolean proceedWithChanges()
404  {
405  return true;
406  }
407 
408  protected void runCommand(final String command, String msg)
409  {
410  runCommand(command, msg, gallery.hasSelection() && !data.hasDisabled());
411  }
412 
413  protected void runCommand(final String command, String msg, boolean useSelection)
414  {
415  try {
416  boolean[] selection = null;
417 
418  if(useSelection)
419  selection = gallery.getSelection();
420  ((ScipionGalleryData)data).overwrite(sqlitefile, selection);
421  XmippWindowUtil.runCommand(command, port);
422  //close(false);
423  } catch (SQLException ex) {
424  logger.log(Level.SEVERE, null, ex);
425  }
426  }
430  @Override
431  public void openMetadata(final MetaData md)
432  {
433  try
434  {
435  SwingUtilities.invokeLater(new Runnable() {
436 
437  @Override
438  public void run() {
439  new ScipionGalleryJFrame(new ScipionGalleryData(ScipionGalleryJFrame.this, ((ScipionParams)data.parameters).getScipionParams(), (ScipionMetaData)md));
440  }
441  });
442 
443  }
444  catch(Exception e)
445  {
446  XmippDialog.showError(this, e.getMessage());
447  }
448  }
449 
450  protected void initGalleryMenu() {
451  menu = new ScipionGalleryMenu();
452 
453  }
454 
455  protected class ScipionGalleryMenu extends GalleryMenu//To customize showj menu for scipion
456  {
457 
458  @Override
459  protected void handleActionPerformed(ActionEvent evt)
460  {
461  super.handleActionPerformed(evt);
462  String cmd = evt.getActionCommand();
463  try
464  {
465  if (cmd.equals(FILE_LOAD_SEL))
466  {
467  fc.setApproveButtonText("Open");
468  fc.setDialogTitle("Load a status file");
469  fc.setApproveButtonToolTipText("Choose a file with state data");
470 
471  if (fc.showOpenDialog(ScipionGalleryJFrame.this) != XmippFileChooser.CANCEL_OPTION)
472  loadSelection(fc.getSelectedPath());
473  }
474  if (cmd.equals(FILE_SAVE_SEL))
475  {
476  fc.setSelectedFile(new File(sqlitefile));
477  fc.setDialogTitle("Save state");
478  fc.setApproveButtonToolTipText("Choose where to save the status");
479  fc.setApproveButtonText("Save");
480  if (fc.showOpenDialog(ScipionGalleryJFrame.this) != XmippFileChooser.CANCEL_OPTION)
481  saveSelection(fc.getSelectedPath());
482  }
483  }
484  catch (Exception e)
485  {
486  showException(e);
487  }
488  }
489 
490  protected void loadSelection(String path) {
491 
492  ((ScipionGalleryData)data).loadSelection(path);
493  reloadTableData();
494 
495  }
496 
497  protected void saveSelection(String path) {
498  try {
499 // boolean[] selection = null;
500 // if(gallery.hasSelection() && !data.hasDisabled())
501 // selection = gallery.getSelection();
502 // ((ScipionGalleryData)data).overwrite(path, selection);
503 
504  ScipionGalleryData sgData = (ScipionGalleryData)data;
505 
506  if (sgData.getScipionMetaData().getParent() != null) {
507  sgData.getScipionMetaData().getParent().overwrite(getFilename(), path, null);
508  } else {
509  sgData.overwrite(path, null);
510  }
511  } catch (SQLException ex) {
512  logger.log(Level.SEVERE, null, ex);
513  }
514  }
515 
516  @Override
517  public void addExtraMenuItems()
518  {
519  addItem(FILE_LOAD_SEL, "Load state ...");
520  addItem(FILE_SAVE_SEL, "Save state ...", "save_as.gif");
521 
522  }
523  }
524 
525 
526 
527 }
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xmipp.utils.XmippWindowUtil.lightgrey
static final Color lightgrey
Definition: XmippWindowUtil.java:58
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xmipp.viewer.scipion.ScipionMetaData.overwrite
void overwrite(String src, String path, boolean[] selection)
Definition: ScipionMetaData.java:634
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xmipp.utils.XmippWindowUtil.firebrick
static final Color firebrick
Definition: XmippWindowUtil.java:57
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xmipp.viewer.scipion.ScipionGalleryJFrame.confirmCreate
boolean confirmCreate(String output, int size)
Definition: ScipionGalleryJFrame.java:350
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xmipp.utils.XmippMenuCreator.addItem
JMenuItem addItem(String key, String text, String... values)
Definition: XmippMenuCreator.java:56
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xmipp.viewer.scipion.ScipionGalleryJFrame.runCommand
void runCommand(final String command, String msg, boolean useSelection)
Definition: ScipionGalleryJFrame.java:413
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xmipp.utils.XmippWindowUtil.getScipionIconButton
static JButton getScipionIconButton(String text)
Definition: XmippWindowUtil.java:156
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xmipp.utils.XmippResource.getIcon
static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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xmipp.utils.Params.recalculateCTF
boolean recalculateCTF
Definition: Params.java:93
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xmipp.utils.XmippWindowUtil.runCommand
static void runCommand(String command, Integer port)
Definition: XmippWindowUtil.java:342
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xmipp.viewer.scipion.ScipionGalleryData.overwrite
void overwrite(String path, boolean[] selection)
Definition: ScipionGalleryData.java:224
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xmipp.viewer.scipion.ScipionGalleryJFrame.readScipionParams
void readScipionParams(ScipionParams parameters)
Definition: ScipionGalleryJFrame.java:65
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.viewer.models.GalleryData.getTmpFile
String getTmpFile(String suffix)
Definition: GalleryData.java:158
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xmipp.viewer.models.GalleryData.getMd
MetaData getMd(List< Long > ids)
Definition: GalleryData.java:1626
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xmipp.viewer.scipion.ScipionGalleryJFrame.runCommand
void runCommand(final String command, String msg)
Definition: ScipionGalleryJFrame.java:408
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class  xmipp.viewer.scipion.ScipionMetaData
 
class  xmipp.viewer.scipion.ScipionMetaData.EMObject
 
class  xmipp.viewer.scipion.ScipionMetaData.EMObjectComparator
 
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package  xmipp.viewer.scipion
 
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Xmipp -  v20.07 -
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ScipionMetaData.java
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 package xmipp.viewer.scipion;
7 
8 import ij.IJ;
9 import ij.ImagePlus;
10 
11 import java.io.File;
12 import java.io.IOException;
13 import java.sql.Connection;
14 import java.sql.DriverManager;
15 import java.sql.PreparedStatement;
16 import java.sql.ResultSet;
17 import java.sql.SQLException;
18 import java.sql.Statement;
19 import java.util.*;
20 import java.util.logging.Level;
21 import java.util.logging.Logger;
22 
23 import org.sqlite.SQLiteConfig;
24 import xmipp.ij.commons.ImagePlusFromFile;
25 import xmipp.ij.commons.XmippUtil;
26 import xmipp.jni.CTFDescription;
27 import xmipp.jni.EllipseCTF;
28 import xmipp.jni.Filename;
29 import xmipp.jni.MetaData;
30 import xmipp.utils.StopWatch;
31 import xmipp.viewer.models.ColumnInfo;
32 
37 public class ScipionMetaData extends MetaData {
38 
39  protected List<ColumnInfo> columns;
40  protected List<EMObject> emobjects;
41  protected ScipionMetaData parent;
42  protected boolean haschilds;
43  protected int labelscount = 0;
44  protected ColumnInfo idci, labelci, commentci, enabledci;
45  protected String preffix = "";
46  protected String[] blocks;
47  protected int enableds;
48  protected Boolean checkTmp;
49  protected HashMap<String, String> properties;
50  protected HashMap <Long, EMObject> idsmap;
51  protected String self;
52 
53 
54  public ScipionMetaData(String dbfile) {
55 
56  this.filename = dbfile;
57  columns = new ArrayList<ColumnInfo>();
58  emobjects = new ArrayList<EMObject>();
59  loadData();
60  if (isClassificationMd()) {
61  String preffix;
62  haschilds = true;
63  List<String> childblocks = new ArrayList<String>();
64  for (EMObject emo : emobjects) {
65  if((Integer)emo.getValue("_size") != 0)
66  {
67  preffix = String.format("Class%03d_", emo.getId());
68  emo.childmd = new ScipionMetaData(dbfile, preffix);
69  emo.childmd.setParent(this);
70  childblocks.add(emo.childmd.getBlock());
71  }
72  }
73  blocks = new String[childblocks.size() + 1];
74  blocks[0] = getBlock();
75  for (int i = 0; i < childblocks.size(); i++) {
76  blocks[i + 1] = childblocks.get(i);
77 
78  }
79  }
80  else
81  blocks = new String[]{getBlock()};
82 
83  }
84 
85  public ScipionMetaData(String dbfile, String preffix) {
86 
87  this.filename = dbfile;
88  columns = new ArrayList<ColumnInfo>();
89  emobjects = new ArrayList<EMObject>();
90  this.preffix = preffix;
91  loadData();
92  blocks = new String[]{getBlock()};
93 
94  }
95 
96  public void loadData() {
97  Connection c = null;
98  Statement stmt = null;
99  try {
100  String query;
101 // c = etConnection(filename);
102  c = getConnectionReadOnly(filename);
103  stmt = c.createStatement();
104  ResultSet rs;
105  if (preffix == null || preffix.equals(""))
106  {
107  query = "SELECT name FROM sqlite_master WHERE type='table' AND name='Properties';";
108  rs = stmt.executeQuery(query);
109  boolean exists = rs.next();
110  if(exists)
111  {
112  properties = new HashMap<String, String>();
113  String key, value;
114  query = "SELECT * FROM Properties;";
115  rs = stmt.executeQuery(query);
116 
117  while (rs.next()) {
118  key = rs.getString("key");
119  value = rs.getString("value");
120  properties.put(key, value);
121  }
122  }
123  }
124  String name, alias, clsname;
125  int type;
126  boolean allowRender;
127  ColumnInfo ci;
128 
129  name = alias = "enabled";
130  labelscount++;
131  enabledci = new ColumnInfo(labelscount, name, alias, MetaData.LABEL_INT, false, true);
132  columns.add(enabledci);
133 
134  name = alias = "id";
135  labelscount++;
136  idci = new ColumnInfo(labelscount, name, alias, MetaData.LABEL_INT, false, false);
137  columns.add(idci);
138 
139  name = alias = "label";
140  labelscount++;
141  labelci = new ColumnInfo(labelscount, name, alias, MetaData.LABEL_STRING, false, false);
142  columns.add(labelci);
143 
144  name = alias = "comment";
145  labelscount++;
146  commentci = new ColumnInfo(labelscount, name, alias, MetaData.LABEL_STRING, false, false);
147  columns.add(commentci);
148 
149 
150 
151  loadValues(c);
152 
153 
154  query = String.format("SELECT * FROM %sClasses;", preffix);
155  rs = stmt.executeQuery(query);
156  while (rs.next()) {
157  name = rs.getString("label_property");
158  alias = rs.getString("column_name");
159  clsname = rs.getString("class_name");
160  if(name.equals("self"))
161  {
162  self = clsname;
163  continue;
164  }
165 
166  type = getTypeMapping(clsname);
167  if(type == -1)
168  continue;//complex object is empty, unless is matrix
169  labelscount++;
170  allowRender = isImage(name);
171  ci = new ColumnInfo(labelscount, name, alias, type, allowRender, false);
172  columns.add(ci);
173  }
174 
175 
176  rs.close();
177  stmt.close();
178  c.close();
179  StopWatch.getInstance().printElapsedTime("loaded data");
180  } catch (Exception e) {
181  throw new IllegalArgumentException(e);
182 
183 
184  }
185  }
186 
187  protected void loadValues(Connection c)
188  {
189  try {
190  idsmap = new HashMap<Long, EMObject>();
191  Statement stmt = c.createStatement();
192  ResultSet rs;
193  EMObject emo;
194  String alias;
195 
196  String query = String.format("SELECT id, label, comment, enabled FROM %sObjects;", preffix);
197  rs = stmt.executeQuery(query);
198  Object value;
199  int index = 0;
200  while (rs.next()) {
201  emo = new EMObject(index, this);
202  for (ColumnInfo column : columns) {
203  alias = column.comment;
204  switch (column.type) {
205 
206  case MetaData.LABEL_INT:
207  value = rs.getInt(alias);
208  break;
209  case MetaData.LABEL_DOUBLE:
210  value = rs.getFloat(alias);
211  break;
212  default:
213  value = rs.getString(alias);
214  }
215  emo.values.put(column, value);
216  }
217  emobjects.add(emo);
218  idsmap.put(emo.getId(), emo);
219  if(emo.isEnabled())
220  enableds ++;
221  else
222  emo.changed = true;
223  index ++;
224  }
225  } catch (SQLException ex) {
226  throw new IllegalArgumentException(ex);
227 
228  }
229  }
230 
231  public void setParent(ScipionMetaData md) {
232  this.parent = md;
233  }
234 
235  public String[] getBlocks() {
236  return blocks;
237 
238  }
239 
240 
241  public String getBlock() {
242  String setType = getSetType();
243  if(setType.isEmpty())
244  setType = "noname";
245  String block = setType.replace("SetOf", "");
246 
247  if (preffix == null) {
248  return block;
249  }
250  return preffix + block;
251  }
252 
253 
254 
255  public List<EMObject> getEMObjects() {
256  return emobjects;
257  }
258 
259  public EMObject getEMObject(long id) {
260  return idsmap.get(id);
261  }
262 
263  public synchronized String getValueFromLabel(int index, int label) {
264  if (index >= size()) {
265  return null;
266  }
267  EMObject emo = emobjects.get(index);
268  Object value = emo.getValue(getColumnInfo(label));
269  if (value == null) {
270  return null;
271  }
272  return value.toString();
273  }
274 
275  public ColumnInfo getColumnInfo(int label) {
276 
277  for (ColumnInfo ci : columns) {
278  if (ci.label == label) {
279  return ci;
280  }
281  }
282  return null;
283  }
284 
285  public ColumnInfo getColumnInfo(String labelName) {
286  for (ColumnInfo ci : columns) {
287  if (ci.labelName.equals(labelName)) {
288  return ci;
289  }
290  }
291  return null;
292  }
293 
294 
295  public void add(EMObject emo) {
296  emobjects.add(emo);
297  if (emo.childmd != null) {
298  haschilds = true;
299  }
300  }
301 
302 
303 
304 
305  public long[] findObjects() {
306  long[] ids = new long[emobjects.size()];
307  for (int i = 0; i < ids.length; i++) {
308  ids[i] = emobjects.get(i).getId();
309  }
310  return ids;
311 
312  }
313 
314  public int[] getActiveLabels() {
315  int[] labels = new int[columns.size()];
316  for (int i = 0; i < labels.length; i++) {
317  labels[i] = columns.get(i).label;
318  }
319  return labels;
320  }
321 
322  @Override
323  public boolean containsLabel(int label) {
324  for (int i = 0; i < columns.size(); i++) {
325  if (columns.get(i).label == label) {
326  return true;
327  }
328  }
329  return false;
330  }
331 
332  @Override
333  public boolean setEnabled(boolean isenabled, long id) {
334  EMObject emo = getEMObject(id);
335  emo.setEnabled(isenabled);
336  return true;
337  }
338 
339  @Override
340  public boolean getEnabled(long id) {
341  EMObject emo = getEMObject(id);
342  return emo.isEnabled();
343 
344  }
345 
346  public List<ColumnInfo> getColumnsInfo() {
347  return columns;
348  }
349 
350  public boolean isImage(String label) {
351  String setType = getSetType();
352  if (setType == null)
353  return false;
354  if(label.contains("_filename"))
355  {
356  String indexLabel = label.replace("_filename", "_index");
357  if(getColumnInfo(indexLabel) != null)
358  return true;
359  }
360  if (setType.equals("SetOfMicrographs") || setType.equals("SetOfParticles") || setType.equals("SetOfVolumes")) {
361  if (label.equals("_filename")) {
362  return true;
363  }
364  } else if (setType.equals("SetOfCTF")) {
365  if (label.equals("_micObj._filename") || label.equals("_psdFile") || label.equals("_xmipp_enhanced_psd")
366  ||label.equals("_xmipp_ctfmodel_quadrant") ||label.equals("_xmipp_ctfmodel_halfplane")) {
367  return true;
368  }
369  } else if (setType.equals("SetOfClasses2D") || setType.equals("SetOfClasses3D")) {
370  if (label.equals("_representative._filename")) {
371  return true;
372  }
373  }
374  return false;
375  }
376 
377  public static boolean hasIndex(String self) {
378  if (self.equals("Particle")) {
379  return true;
380  }
381  return false;
382  }
383 
384  public boolean isColumnFormat() {
385  return true;
386  }
387 
388  public synchronized Object getValueObject(int label, long id) {
389  EMObject emo = getEMObject(id);
390  ColumnInfo c = getColumnInfo(label);
391  if (c != null) {
392  return emo.getValue(c);
393  }
394  return null;
395  }
396 
397  public int getValueInt(int label, long id) {
398  Object value = getValueObject(label, id);
399  if (value != null) {
400  return (Integer) value;
401  }
402  return Integer.MIN_VALUE;
403  }
404 
405  public double getValueDouble(int label, long id) {
406  Object value = getValueObject(label, id);
407  if (value != null) {
408  return (Float) value;
409  }
410  return Double.NaN;
411  }
412 
413  public String getValueString(int label, long id) {
414  Object value = getValueObject(label, id);
415  if (value == null)
416  return "";
417  if (value instanceof Float)
418  return String.format("%.2f", value);
419  return value.toString();
420  }
421 
422 
423  @Override
424  public int size() {
425  return emobjects.size();
426  }
427 
428  @Override
429  public boolean setValueString(int label, String value, long id) {
430  return setValueObject(label, value, id);
431  }
432 
433  @Override
434  public boolean setValueDouble(int label, double value, long id) {
435  return setValueObject(label, new Double(value).floatValue(), id);
436  }
437 
438  @Override
439  public boolean setValueInt(int label, int value, long id) {
440  return setValueObject(label, value, id);
441  }
442 
443  public boolean setValueObject(int label, Object value, long id) {
444  EMObject emo = getEMObject(id);
445  ColumnInfo ci = getColumnInfo(label);
446  emo.setValue(ci, value);
447  return true;
448  }
449 
450  @Override
451  public void importObjects(MetaData md, long[] ids) {
452  ScipionMetaData smd = (ScipionMetaData) md;
453  EMObject emo;
454  for (int i = 0; i < ids.length; i++) {
455  emo = smd.getEMObject(ids[i]);
456  add(emo);
457  }
458  }
459 
460  public void unionAll(MetaData md) {
461  emobjects.addAll(((ScipionMetaData) md).getEMObjects());
462  }
463 
464  public void destroy() {
465  }
466 
467  public ScipionMetaData getParent() {
468  return parent;
469  }
470 
471  public ScipionMetaData getChild(String block) {
472  if (!haschilds) {
473  return null;
474  }
475  for (EMObject emo : emobjects) {
476  if (emo.childmd != null && emo.childmd.getBlock().equals(block))//from parent to child
477  {
478  return emo.childmd;
479  }
480  }
481  return null;
482  }
483 
484  public void write(String path) {
485  new File(path).delete();//overwrite file
486  if (path.contains("@")) {
487  writeBlock(path.substring(path.lastIndexOf("@") + 1));
488  return;
489  }
490  if (parent != null) {
491  parent.write(path);//this will write parent and siblings
492  return;
493  }
494  writeBlock(path);
495  if (haschilds) {
496  for (EMObject emo : emobjects) {
497  if (emo.childmd != null) {
498  emo.childmd.writeBlock(path);
499  }
500  }
501  }
502  }
503 
504 
505 
506  public void writeBlock(String path) {
507  //Might fail if some fixed column was added
508 
509  Connection c = null;
510  Statement stmt = null;
511  try {
512 
513  c = getConnection(path);
514  c.setAutoCommit(false);
515  stmt = c.createStatement();
516 
517  String sql = String.format("DROP TABLE IF EXISTS %1$sClasses; CREATE TABLE %1$sClasses(\n"
518  + "id INTEGER PRIMARY KEY AUTOINCREMENT,\n"
519  + " label_property TEXT UNIQUE,\n"
520  + " column_name TEXT UNIQUE,\n"
521  + " class_name TEXT DEFAULT NULL\n"
522  + " )", preffix);
523  stmt.executeUpdate(sql);
524 
525  String line = ", (%s, \'%s\', \'%s\', \'%s\')";
526  ColumnInfo ci;
527  String createcols = "", cols = "", type;
528  for (int i = 0; i < columns.size(); i++) {
529  ci = columns.get(i);
530  type = getTypeMapping(ci.type);
531  sql += String.format(line, i + 2, ci.labelName, ci.comment, type);
532  createcols += String.format("%s %s DEFAULT NULL,", ci.comment, type);
533  cols += String.format("%s,", ci.comment);
534  }
535  stmt.executeUpdate(sql);
536  createcols = createcols.substring(0, createcols.length() - 1);
537  cols = cols.substring(0, cols.length() - 1);
538  sql = String.format("DROP TABLE IF EXISTS %1$sObjects; CREATE TABLE %1$sObjects(\n"
539  + " %2$s)", preffix, createcols);
540 
541  stmt.executeUpdate(sql);
542  if (size() == 0) {
543  return;
544  }
545  sql = String.format("INSERT INTO %sObjects(%s) VALUES ", preffix, cols);
546  Object value;
547  for (EMObject emo : emobjects) {
548  sql += "(";
549  for (ColumnInfo column : columns) {
550  value = emo.getValue(column);
551  if (value != null) {
552  if (column.type == MetaData.LABEL_STRING) {
553 
554  String str = (String) value;
555  if (str.contains("@")) {
556  str = str.substring(str.lastIndexOf("@") + 1);
557  }
558  value = str;
559  sql += String.format("'%s',", value);
560  } else {
561  sql += String.format("%s,", value);
562  }
563  } else {
564  sql += "NULL,";
565  }
566  }
567  sql = sql.substring(0, sql.length() - 1) + "),";
568  }
569  sql = sql.substring(0, sql.length() - 1);
570  stmt.executeUpdate(sql);
571  c.commit();
572  stmt.close();
573  c.close();
574 
575  } catch (Exception e) {
576  e.printStackTrace();
577 
578  }
579  }
580 
581  public static String getTypeMapping(int type) {
582  if (type == MetaData.LABEL_INT) {
583  return "Integer";
584  }
585  if (type == MetaData.LABEL_DOUBLE) {
586  return "Float";
587  }
588  return "String";
589  }
590 
591  public static int getTypeMapping(String type) {
592  if (type.equals("Integer")) {
593  return MetaData.LABEL_INT;
594  }
595  if (type.equals("Float")) {
596  return MetaData.LABEL_DOUBLE;
597  }
598  if(type.equals("Boolean"))
599  return MetaData.LABEL_INT;
600 
601  if(type.equals("String") || type.equals("Matrix") || type.equals("CsvList"))
602  return MetaData.LABEL_STRING;
603  return -1;
604  }
605 
606  public String getPreffix() {
607  return preffix;
608  }
609 
610  public void print() {
611  System.out.println(toString());
612  }
613 
614  public double[] getStatistics(boolean applyGeo) {
615  return null;
616  }
617 
618  public void sort(int sortLabel, boolean ascending) {
619  ColumnInfo ci = getColumnInfo(sortLabel);
620  try {
621  loadNeighborhoodValues(0, ci, size());
622  } catch (SQLException ex) {
623  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
624  }
625  Comparator<EMObject> comparator = new EMObjectComparator(ci);
626  if(!ascending)
627  comparator = Collections.reverseOrder(comparator);
628  Collections.sort(emobjects, comparator);
629  for (int i = 0; i < emobjects.size(); i++)
630  emobjects.get(i).setIndex(i);
631 
632  }
633 
634  public void overwrite(String src, String path, boolean[] selection) throws SQLException {
635  try {
636  XmippUtil.copyFile(src, path);
637  // Do not overwrite the parent. This looses the selection. issue #498
638  // if (parent != null) {
639  // parent.overwrite(src, path, null);//this will write parent and siblings
640  // return;
641  // }
642  overwriteBlock(path, selection);
643  if (haschilds) {
644  for (EMObject emo : emobjects) {
645  if (emo.childmd != null) {
646  emo.childmd.overwriteBlock(path, null);
647  }
648  }
649  }
650  } catch (IOException ex) {
651  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
652  }
653 
654  }
655 
656  public void overwriteBlock(String path, boolean[] selection) throws SQLException {//overwrites enabled column in existing sqlite objects table
657  Connection c = null;
658  PreparedStatement stmt = null;
659  try {
660 
661 // Class.forName("org.sqlite.JDBC");
662 // c = DriverManager.getConnection("jdbc:sqlite:" + path);
663  c = getConnection(path);
664 
665  c.setAutoCommit(false);
666  stmt = c.prepareStatement(String.format("UPDATE %sObjects SET %s=?, %s=?, %s=? WHERE id=?;", preffix, enabledci.labelName, labelci.labelName, commentci.labelName));
667  boolean enabled;
668  for (EMObject emo : emobjects)
669  {
670  if(selection != null)
671  {
672  enabled = selection[emo.index];
673  stmt.setInt(1, enabled ? 1 : 0);
674  stmt.setString(2, emo.getLabel());
675  stmt.setString(3, emo.getComment());
676  stmt.setInt(4, emo.getId().intValue());
677  stmt.executeUpdate();
678 
679  }
680  else if (emo.changed) {
681  stmt.setInt(1, emo.isEnabled() ? 1 : 0);
682  stmt.setString(2, emo.getLabel());
683  stmt.setString(3, emo.getComment());
684  stmt.setInt(4, emo.getId().intValue());
685  stmt.executeUpdate();
686 
687  }
688  }
689  c.commit();
690 
691  }
692  catch (Exception e) {
693  e.printStackTrace();
694  if (c != null)
695  try {
696  System.err.print("Transaction is being rolled back");
697  c.rollback();
698  }
699  catch(SQLException excep) {
700  excep.printStackTrace();
701  }
702 
703  }
704  finally {
705  if (stmt != null)
706  stmt.close();
707 
708  c.close();
709  }
710  }
711 
712  @Override
713  public boolean isCTFMd() {
714  return getSetType().equals("SetOfCTF");
715  }
716 
717  @Override
718  public EllipseCTF getEllipseCTF(long id, int D) {
719  if (!isCTFMd()) {
720  return null;
721  }
722  try {
723  EMObject emo = getEMObject(id);
724 
725  double Q0, Cs = 0, Ts = 0, kV = 0, defU = 0, defV = 0, defAngle;
726 
727  Q0 = emo.getValueDouble("_micObj._acquisition._amplitudeContrast");
728  Cs = emo.getValueDouble("_micObj._acquisition._sphericalAberration");
729  Ts = emo.getValueDouble("_micObj._samplingRate");
730  kV = emo.getValueDouble("_micObj._acquisition._voltage");
731 
732  defU = emo.getValueDouble("_defocusU");
733  defV = emo.getValueDouble("_defocusV");
734  defAngle = emo.getValueDouble("_defocusAngle");
735  Double downsampleFactor = emo.getValueDouble("_xmipp_CtfDownsampleFactor");
736  if(downsampleFactor == null)
737  downsampleFactor = 1.;
738  //read params from sqlite
739 
740  return new EllipseCTF(id, Q0, Cs, downsampleFactor, Ts, kV, defU, defV, defAngle, D);
741  } catch (Exception ex) {
742  IJ.error(ex.getMessage());
743  throw new IllegalArgumentException(ex);
744  }
745 
746  }
747 
748  @Override
749  public String getCTFFile(long id) {
750  String psde = getPSDEnhanced(id);
751  if(psde != null)
752  {
753  String ctf = psde.replace("_enhanced_psd.xmp", ".ctfparam");
754  if(new File(ctf).exists())
755  return ctf;
756  }
757  return null;
758  }
759 
760  @Override
761  public String getPSDFile(long id) {
762  return (String) getEMObject(id).getValue("_psdFile");
763  }
764 
765  @Override
766  public String getPSDEnhanced(long id) {
767  return (String) getEMObject(id).getValue("_xmipp_enhanced_psd");
768  }
769 
770  public CTFDescription getCTFDescription(long id)
771  {
772  try {
773  MetaData md = getEllipseCTF(id).getCTFMd();
774  String file = "ctf.xmd";
775  md.write(file);
776  return new CTFDescription(file);
777  } catch (Exception ex) {
778  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
779  throw new IllegalArgumentException(ex);
780  }
781  }
782 
783  public ColumnInfo getGeoMatrixColumn(ColumnInfo ci)
784  {
785  String column = "_transform._matrix";
786  if(ci.labelName.contains("."))
787  column = ci.labelName.substring(0, ci.labelName.lastIndexOf(".") + 1) + column;
788  return getColumnInfo(column);
789  }
790 
791 
792  // Check if the underlying data has geometrical information
793  public boolean containsGeometryInfo(String type) {
794  String column = "_alignment";
795  String value = null;
796  if(properties == null)
797  {
798  if (parent == null)
799  return false;
800  else
801  for(EMObject emo: parent.emobjects)
802  if(preffix.contains(emo.getId().toString()))
803  value = (String)emo.getValue(column);
804  }
805  else
806  value = properties.get(column);
807 
808  if (value == null)
809  return false;
810 
811  return value.equals(type);
812  }
813 
814 
815 
816  public int getEnabledCount()
817  {
818  return enableds;
819  }
820 
821  synchronized void loadNeighborhoodValues(int index, ColumnInfo column) throws SQLException
822  {
823  int neighborhood = 25;
824  loadNeighborhoodValues(index, column, neighborhood);
825  }
826 
827  synchronized void loadNeighborhoodValues(int index, ColumnInfo column, int neighborhood) throws SQLException
828  {
829  Connection c = null;
830  PreparedStatement stmt = null;
831  ResultSet rs = null;
832  try {
833  String name, alias;
834  Object value;
835 // c = getConnection(filename);
836  c = getConnectionReadOnly(filename);
837  String columns = column.comment;
838  ColumnInfo indexci = null;
839  if(column.labelName.endsWith("_filename"))
840  {
841  indexci = getColumnInfo(column.labelName.replace("_filename", "_index"));
842  if(indexci != null)
843  columns += ", " + indexci.comment;
844  }
845  stmt = c.prepareStatement(String.format("SELECT %s FROM %sObjects where Id=?;", columns, preffix));
846  EMObject emo;
847  int fnIndex;
848  for(int i = index; i <= index + neighborhood && i < size(); i ++)
849  {
850 
851  emo = emobjects.get(i);
852  if(!emo.values.containsKey(column))
853  {
854  StopWatch.getInstance().printElapsedTime("reading " + columns + " from " + emo.getId());
855  stmt.setInt(1, emo.getId().intValue());
856  rs = stmt.executeQuery();
857  name = column.labelName;
858  alias = column.comment;
859  switch (column.type) {
860 
861  case MetaData.LABEL_INT:
862  value = rs.getInt(alias);
863  break;
864  case MetaData.LABEL_DOUBLE:
865  value = rs.getFloat(alias);
866  break;
867  case MetaData.LABEL_STRING:
868  value = rs.getString(alias);
869  if (indexci != null) {
870  fnIndex = rs.getInt(indexci.comment);
871  if (fnIndex > 0)
872  value = fnIndex + "@" + value;
873 
874  }
875  break;
876  default:
877 
878  value = rs.getString(alias);
879  }
880  emo.values.put(column, value);
881  }
882  }
883  } catch (Exception ex) {
884  ex.printStackTrace();
885  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
886  }
887  finally {
888  if(rs != null)
889  rs.close();
890  if (stmt != null)
891  stmt.close();
892  c.close();
893  }
894  }
895 
896  public boolean isChanged()
897  {
898 
899  for(EMObject emo: emobjects)
900  if(emo.changed)
901  return true;
902  return false;
903  }
904 
905  boolean isClassificationMd() {
906  String setType = getSetType();
907  if(setType == null)
908  return false;
909  return setType.startsWith("SetOfClasses");
910  }
911 
912 
913  public class EMObject {
914 
915  int index;
916  Map<ColumnInfo, Object> values;
917  boolean changed;
918  ScipionMetaData childmd;
919  ScipionMetaData md;
920 
921 
922  public EMObject(int index, ScipionMetaData md) {
923  this.index = index;
924  values = new HashMap<ColumnInfo, Object>();
925  this.md = md;
926  changed = false;
927  }
928 
929  Object getValue(String column) {
930  ColumnInfo ci = getColumnInfo(column);
931  return getValue(ci);
932  }
933 
934  Object getValue(ColumnInfo c) {
935  if(c == null)
936  return null;
937  if(!values.containsKey(c))
938  try {
939  loadNeighborhoodValues(index, c);
940  } catch (SQLException ex) {
941  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
942  }
943  Object result = values.get(c);
944 
945  return result;
946  }
947 
948 
949 
950 
951  Double getValueDouble(String column) {
952  ColumnInfo ci = getColumnInfo(column);
953  return getValueDouble(ci);
954  }
955 
956  Double getValueDouble(ColumnInfo c) {
957  Object value = getValue(c);
958  if (value != null) {
959  return ((Float) value).doubleValue();//in sqlite double is float
960  }
961  return null;
962  }
963 
964  public void setValue(ColumnInfo ci, Object value) {
965 
966  changed = true;
967  values.put(ci, value);
968 
969  }
970 
971  public Boolean getValueBoolean(String column) {
972  ColumnInfo ci = getColumnInfo(column);
973  if(column == null)
974  return null;
975  Object value = getValue(ci);
976  if(value == null)
977  return null;
978  return (Integer)value == 1;
979  }
980 
981  public boolean isEnabled() {
982  if(!values.containsKey(enabledci))
983  return true;
984  Integer value = (Integer) values.get(enabledci);
985  return value == 1;
986  }
987 
988  public void setEnabled(boolean isenabled) {
989  int value = isenabled ? 1 : 0;
990  if(isEnabled() && !isenabled)
991  enableds --;
992  else if( !isEnabled() && isenabled)
993  enableds ++;
994  setValue(enabledci, value);
995  }
996 
997  public Long getId() {
998  return ((Integer)values.get(idci)).longValue();
999  }
1000 
1001  public String getLabel() {
1002  Object value = getValue(labelci);
1003  if (value != null) {
1004  return ((String) getValue(labelci));
1005  }
1006  return null;
1007  }
1008 
1009  public String getComment() {
1010  Object value = getValue(commentci);
1011  if (value != null) {
1012  return ((String) getValue(commentci));
1013  }
1014  return null;
1015  }
1016 
1017  public void setComment(String comment) {
1018  setValue(commentci, comment);
1019  }
1020 
1021  String getValueString(ColumnInfo ci) {
1022  Object value = getValue(ci);
1023  if (value != null) {
1024  return value.toString();//in sqlite double is float
1025  }
1026  return "";
1027  }
1028 
1029  void setIndex(int index) {
1030  this.index = index;
1031  }
1032 
1033  void setLabel(String label) {
1034  setValue(labelci, label);
1035  }
1036 
1037  public EllipseCTF getEllipseCTF()
1038  {
1039  String comment = getComment();
1040  if(comment == null || comment.isEmpty())
1041  return null;
1042  String[] params = comment.trim().split("\\s+");
1043  double defU = Double.parseDouble(params[0]);
1044  double defV = Double.parseDouble(params[1]);
1045  double angle = Double.parseDouble(params[2]);
1046  double lowFreq = Double.parseDouble(params[3]);
1047  double highFreq = Double.parseDouble(params[4]);
1048  EllipseCTF ctf = md.getEllipseCTF(getId());
1049  ctf.setDefocus(defU, defV, angle);
1050  ctf.setFreqRange(lowFreq, highFreq);
1051  return ctf;
1052  }
1053  }
1054 
1055 
1056 
1057 
1058  public static Connection getConnection(String filename) throws ClassNotFoundException, SQLException
1059  {
1060  return getConnection(filename, null);
1061  }
1062  public static Connection getConnectionReadOnly(String filename) throws ClassNotFoundException, SQLException
1063  {
1064 
1065  SQLiteConfig config = new SQLiteConfig();
1066  config.setReadOnly(true);
1067  Connection c = getConnection(filename, config.toProperties());
1068  c.setReadOnly(true);
1069  return c;
1070  }
1071 
1072  private static Connection getConnection(String filename, Properties properties) throws ClassNotFoundException, SQLException {
1073 
1074  Class.forName("org.sqlite.JDBC");
1075 
1076  Connection c = null ;
1077 
1078  if (properties == null) {
1079  c = DriverManager.getConnection("jdbc:sqlite:" + filename);
1080  } else {
1081  c = DriverManager.getConnection("jdbc:sqlite:" + filename, properties);
1082  }
1083  return c;
1084 
1085  }
1086 
1087 
1088  void loadSelection(String selectedPath) {
1089  try {
1090 
1091  Connection c = getConnectionReadOnly(selectedPath);
1092  if(parent != null)
1093  parent.loadSelection(selectedPath, c);
1094  else
1095  loadSelection(selectedPath, c);
1096  c.close();
1097  } catch (Exception ex) {
1098  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
1099  }
1100  }
1101 
1102 
1103  void loadSelection(String selectedPath, Connection c) {
1104 
1105  try {
1106 
1107  Statement stmt = c.createStatement();
1108  ResultSet rs;
1109  EMObject emo;
1110  String alias;
1111 
1112  String query = String.format("SELECT id, enabled, label, comment FROM %sObjects;", preffix);
1113  rs = stmt.executeQuery(query);
1114  Object enabled, label, comment;
1115  long id;
1116  enableds = 0;
1117  boolean isctfmd = isCTFMd();
1118  EllipseCTF ctf;
1119  while (rs.next()) {
1120  id = rs.getInt("id");
1121  emo = getEMObject(id);
1122  alias = enabledci.comment;
1123  enabled = rs.getInt(alias);
1124  emo.setValue(enabledci, enabled);
1125  alias = labelci.comment;
1126  label = rs.getString(alias);
1127  emo.setValue(labelci, label);
1128  alias = commentci.comment;
1129  comment = rs.getString(alias);
1130  emo.setValue(commentci, comment);
1131  if(emo.isEnabled())
1132  enableds ++;
1133  if(isctfmd)
1134  {
1135  ctf = emo.getEllipseCTF();
1136  if(ctf != null)
1137  ctfs.put(id, ctf);
1138  }
1139 
1140  }
1141 
1142  rs.close();
1143  stmt.close();
1144 
1145  if (haschilds) {
1146  for (EMObject emobject : emobjects) {
1147  if(emobject.childmd != null)
1148  emobject.childmd.loadSelection(selectedPath, c);
1149  }
1150  }
1151  } catch (Exception ex) {
1152  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
1153  }
1154  }
1155 
1156 
1157 
1158  class EMObjectComparator implements Comparator<EMObject> {
1159  private final ColumnInfo ci;
1160 
1161  public EMObjectComparator(ColumnInfo ci)
1162  {
1163  this.ci = ci;
1164  }
1165 
1166  @Override
1167  public int compare(EMObject o1, EMObject o2) {
1168  Comparable value1 = (Comparable)o1.getValue(ci);
1169  Comparable value2 = (Comparable)o2.getValue(ci);
1170  return value1.compareTo(value2);
1171  }
1172 
1173  }
1174 
1175  public String getSetType() {
1176  if(properties == null)
1177  return self + "s";//child md from classes set
1178  if(properties.isEmpty())
1179  return "";
1180  return properties.get("self");
1181  }
1182 
1183  public double[] getStatistics(boolean applyGeo, int label)
1184  {
1185  double[] minMax = new double [2];
1186  ColumnInfo ci = getColumnInfo(label);
1187  if(!ci.render)
1188  throw new IllegalArgumentException("No images to process");
1189  String imageFn, mddir = this.getBaseDir();
1190  ImagePlus imp;
1191  minMax[0] = Double.MAX_VALUE;
1192  minMax[1] = -Double.MAX_VALUE;
1193  double aux;
1194  for (EMObject emo: emobjects)
1195  {
1196  imageFn = emo.getValueString(ci);
1197  if(imageFn != null)
1198  {
1199  imageFn = Filename.findImagePath(imageFn, mddir, true);
1200  if (imageFn != null && Filename.exists(imageFn))
1201  {
1202  imp = new ImagePlusFromFile(imageFn).getImagePlus();
1203  aux = imp.getProcessor().getMin();
1204  if(aux < minMax[0])
1205  minMax[0] = aux;
1206  aux = imp.getProcessor().getMax();
1207  if(aux > minMax[1])
1208  minMax[1] = aux;
1209  }
1210  }
1211  }
1212 
1213  return minMax;
1214  }
1215 
1216  public boolean containsMicrographsInfo()
1217  {
1218  return self.equals("Micrograph") || self.equals("Movie");
1219  }
1220 
1221  public String getSelf()
1222  {
1223  // TODO Auto-generated method stub
1224  return self;
1225  }
1226 
1227  public static boolean isScipionMetaData(String filename)
1228  {
1229  if (!filename.endsWith(".sqlite") && !filename.endsWith(".db"))
1230  return false;
1231  //Now it will check if contains the required tables to be read as scipion metadata, otherwise will be read as xmipp metadata
1232  Connection c;
1233  Statement stmt;
1234  ResultSet rs;
1235  boolean result = true;
1236  try
1237  {
1238 // c = getConnection(filename);
1239  c = getConnectionReadOnly(filename);
1240  stmt = c.createStatement();
1241  String query = "SELECT name FROM sqlite_master WHERE type='table' AND name='Classes';";
1242  rs = stmt.executeQuery(query);
1243  boolean exists = rs.next();
1244  if (!exists)
1245  result = false;
1246  else
1247  {
1248  query = "SELECT name FROM sqlite_master WHERE type='table' AND name='Objects';";
1249  rs = stmt.executeQuery(query);
1250  exists = rs.next();
1251  if (!exists)
1252  result = false;
1253  }
1254  rs.close();
1255  stmt.close();
1256  c.close();
1257  }
1258  catch (Exception e)
1259  {
1260  // TODO Auto-generated catch block
1261  e.printStackTrace();
1262  return false;
1263  }
1264 
1265  return result;
1266  }
1267 
1268 }
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xmipp.viewer.scipion.ScipionMetaData.hasIndex
static boolean hasIndex(String self)
Definition: ScipionMetaData.java:377
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xmipp.viewer.scipion.ScipionMetaData.ScipionMetaData
ScipionMetaData(String dbfile, String preffix)
Definition: ScipionMetaData.java:85
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xmipp.viewer.scipion.ScipionMetaData.EMObject.setValue
void setValue(ColumnInfo ci, Object value)
Definition: ScipionMetaData.java:964
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xmipp.jni.MetaData.LABEL_DOUBLE
static final int LABEL_DOUBLE
Definition: MetaData.java:47
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xmipp.viewer.scipion.ScipionMetaData.getValueObject
synchronized Object getValueObject(int label, long id)
Definition: ScipionMetaData.java:388
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xmipp.jni.MetaData.LABEL_STRING
static final int LABEL_STRING
Definition: MetaData.java:48
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xmipp.viewer.scipion.ScipionMetaData.getValueString
String getValueString(int label, long id)
Definition: ScipionMetaData.java:413
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xmipp.jni.MetaData.write
native void write(String filename)
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xmipp.viewer.scipion.ScipionMetaData.getValueDouble
double getValueDouble(int label, long id)
Definition: ScipionMetaData.java:405
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xmipp.viewer.scipion.ScipionMetaData.getValueFromLabel
synchronized String getValueFromLabel(int index, int label)
Definition: ScipionMetaData.java:263
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xmipp.utils.StopWatch.printElapsedTime
void printElapsedTime(String comment)
Definition: StopWatch.java:43
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xmipp.viewer.scipion.ScipionMetaData.overwrite
void overwrite(String src, String path, boolean[] selection)
Definition: ScipionMetaData.java:634
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xmipp.viewer.scipion.ScipionMetaData.getTypeMapping
static int getTypeMapping(String type)
Definition: ScipionMetaData.java:591
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xmipp.viewer.scipion.ScipionMetaData.getChild
ScipionMetaData getChild(String block)
Definition: ScipionMetaData.java:471
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xmipp.viewer.scipion.ScipionMetaData.setValueInt
boolean setValueInt(int label, int value, long id)
Definition: ScipionMetaData.java:439
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xmipp.viewer.scipion.ScipionMetaData.getCTFDescription
CTFDescription getCTFDescription(long id)
Definition: ScipionMetaData.java:770
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xmipp.viewer.scipion.ScipionMetaData.properties
HashMap< String, String > properties
Definition: ScipionMetaData.java:49
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xmipp.viewer.scipion.ScipionMetaData.getTypeMapping
static String getTypeMapping(int type)
Definition: ScipionMetaData.java:581
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xmipp.jni.Filename.findImagePath
static String findImagePath(String filename, String mdFilename, boolean shouldExist)
Definition: Filename.java:225
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xmipp.viewer.scipion.ScipionMetaData.getConnection
static Connection getConnection(String filename)
Definition: ScipionMetaData.java:1058
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xmipp.jni.EllipseCTF.setFreqRange
void setFreqRange(double lowFreq, double highFreq)
Definition: EllipseCTF.java:72
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xmipp.jni.MetaData.LABEL_INT
static final int LABEL_INT
Definition: MetaData.java:45
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xmipp.jni.EllipseCTF.setDefocus
void setDefocus(double defU, double defV, double angle)
Definition: EllipseCTF.java:166
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xmipp.viewer.scipion.ScipionMetaData.importObjects
void importObjects(MetaData md, long[] ids)
Definition: ScipionMetaData.java:451
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xmipp.viewer.scipion.ScipionMetaData.getGeoMatrixColumn
ColumnInfo getGeoMatrixColumn(ColumnInfo ci)
Definition: ScipionMetaData.java:783
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xmipp.viewer.scipion.ScipionMetaData.idsmap
HashMap< Long, EMObject > idsmap
Definition: ScipionMetaData.java:50
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xmipp.jni.Filename.exists
static boolean exists(String path)
Definition: Filename.java:266
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xmipp.viewer.scipion.ScipionMetaData.getConnectionReadOnly
static Connection getConnectionReadOnly(String filename)
Definition: ScipionMetaData.java:1062
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xmipp.jni.MetaData.ctfs
HashMap< Long, EllipseCTF > ctfs
Definition: MetaData.java:94
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xmipp.viewer.scipion.ScipionMetaData.getStatistics
double [] getStatistics(boolean applyGeo, int label)
Definition: ScipionMetaData.java:1183
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xmipp.viewer.scipion.ScipionMetaData.isScipionMetaData
static boolean isScipionMetaData(String filename)
Definition: ScipionMetaData.java:1227
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xmipp.ij.commons.XmippUtil.copyFile
static void copyFile(String source, String dest)
Definition: XmippUtil.java:84
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xmipp.viewer.scipion.ScipionMetaData.setValueDouble
boolean setValueDouble(int label, double value, long id)
Definition: ScipionMetaData.java:434
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xmipp.viewer.scipion.ScipionMetaData.setValueObject
boolean setValueObject(int label, Object value, long id)
Definition: ScipionMetaData.java:443
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xmipp.viewer.scipion.ScipionMetaData.getStatistics
double [] getStatistics(boolean applyGeo)
Definition: ScipionMetaData.java:614
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xmipp.viewer.scipion.ScipionMetaData.sort
void sort(int sortLabel, boolean ascending)
Definition: ScipionMetaData.java:618
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xmipp.utils.StopWatch.getInstance
static StopWatch getInstance()
Definition: StopWatch.java:26
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xmipp.viewer.scipion.ScipionMetaData.setValueString
boolean setValueString(int label, String value, long id)
Definition: ScipionMetaData.java:429
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xmipp.viewer.scipion.ScipionMetaData.setEnabled
boolean setEnabled(boolean isenabled, long id)
Definition: ScipionMetaData.java:333
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xmipp.jni.MetaData.getBaseDir
String getBaseDir()
Definition: MetaData.java:430
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xmipp.viewer.scipion.ScipionMetaData.getEllipseCTF
EllipseCTF getEllipseCTF(long id, int D)
Definition: ScipionMetaData.java:718
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xmipp.viewer.scipion.ScipionMetaData.getColumnInfo
ColumnInfo getColumnInfo(String labelName)
Definition: ScipionMetaData.java:285
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xmipp.viewer.scipion.ScipionMetaData.overwriteBlock
void overwriteBlock(String path, boolean[] selection)
Definition: ScipionMetaData.java:656
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 package xmipp.utils;
7 
8 import java.io.File;
9 import org.apache.commons.cli.Option;
10 
11 
16 public class ScipionParams extends Params {
17 
18 
19 
20  public String inputid;
21  public String other;
22 
23  public final static String SCIPION = "scipion";
24 
25 
26  public ScipionParams(String args[]) {
27  super(args);
28  }
29 
30  public ScipionParams() {
31  super();
32  }
33 
34  public ScipionParams(Integer port, String inputid, String other) {
35  this.port = port;
36  this.inputid = inputid;
37  this.other = other;
38  }
39 
40  public boolean isScipion()
41  {
42  return cmdLine.hasOption(SCIPION);
43  }
44 
45  public void defineArgs() {
46  super.defineArgs();
47  Option opt = new Option(SCIPION, "");
48  opt.setArgs(3);
49  options.addOption(opt);
50  opt = new Option(OBJECT_CMDS, "");
51  opt.setArgs(Integer.MAX_VALUE);
52  options.addOption(opt);
53  }
54 
55  @Override
56  public void processArgs(String args[]) {
57  super.processArgs(args);
58 
59  if (cmdLine.hasOption(SCIPION)) {
60 
61  String[] cmdargs = cmdLine.getOptionValues(SCIPION);
62  port = Integer.parseInt(cmdargs[0]);
63  inputid = cmdargs[1];
64  other = (cmdargs.length == 3)? cmdargs[2]: "";
65  }
66 
67  }
68 
69  public ScipionParams getScipionParams()
70  {
71  return new ScipionParams(port, inputid, other);
72  }
73 
74 
75 
76 
77 
78 }
xmipp.utils.Params.options
Options options
Definition: Params.java:82
-
xmipp.utils.Params.cmdLine
CommandLine cmdLine
Definition: Params.java:83
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void processArgs(String args[])
Definition: ScipionParams.java:56
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xmipp.utils.ScipionParams.ScipionParams
ScipionParams(String args[])
Definition: ScipionParams.java:26
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xmipp.utils.ScipionParams.getScipionParams
ScipionParams getScipionParams()
Definition: ScipionParams.java:69
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xmipp.utils.ScipionParams.ScipionParams
ScipionParams(Integer port, String inputid, String other)
Definition: ScipionParams.java:34
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xmipp.utils.Params.OBJECT_CMDS
static final String OBJECT_CMDS
Definition: Params.java:50
-
xmipp.utils.ScipionParams.SCIPION
static final String SCIPION
Definition: ScipionParams.java:23
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package  xmipp.viewer.scipion
 
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 package xmipp.viewer.scipion;
7 
8 import xmipp.utils.ScipionParams;
9 import xmipp.ij.commons.XmippApplication;
10 import xmipp.jni.Filename;
11 import xmipp.jni.ImageGeneric;
12 import xmipp.jni.MetaData;
13 import xmipp.utils.DEBUG;
14 import xmipp.utils.Params;
15 import xmipp.utils.StopWatch;
16 import xmipp.utils.XmippDialog;
17 import xmipp.viewer.Viewer;
18 import xmipp.viewer.windows.GalleryJFrame;
19 import xmipp.viewer.windows.ImagesWindowFactory;
20 import static xmipp.viewer.windows.ImagesWindowFactory.openFileAsImage;
21 
26 public class ScipionViewer extends Viewer {
27 
28 
29 
30 
31 
32  public static void main(String args[]) {
33  StopWatch stopWatch = StopWatch.getInstance();
34  stopWatch.printElapsedTime("starting app");
35  // Schedule a job for the event dispatch thread:
36  // creating and showing this application's GUI.
37  final String[] myargs = args;
38 
39  ScipionParams parameters = new ScipionParams(myargs);
40  if(parameters.isScipion())
41  XmippApplication.setIsScipion(true);
42  try {
43  if (parameters.debug) {
44  DEBUG.enableDebug(true);
45  }
46 
47  if (parameters.files != null) {
48  // DEBUG.enableDebug(true);
49  final String[] files = parameters.files;
50 
51  for (int i = 0; i < files.length; i++)
52  openFile(files[i], parameters);
53 
54  }
55 
56  } catch (Exception e) {
57  e.printStackTrace();
58  }
59 
60  }
61 
62 
63 
64  public static void openFile(String filename, ScipionParams parameters) {
65 
66  try {
67 
68  MetaData md;
69  boolean isscipion = ScipionMetaData.isScipionMetaData(filename);
70  if(isscipion)
71  ImagesWindowFactory.openScipionMetadata(filename, parameters);
72  else if (Filename.isMetadata(filename)) {
73  if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_IMAGE)) {
74  openFileAsImage(null, filename, parameters);
75  } else {
76  //parameters.mode = Params.OPENING_MODE_GALLERY;
77  md = new MetaData(filename);
78  new GalleryJFrame(md, parameters);
79  }
80  } else {
81  ImageGeneric img = new ImageGeneric(filename);
82 
83  if (img.isSingleImage()) {
84  openFileAsImage(null, filename, parameters);
85  } else if (img.isStackOrVolume()) {
86  if (parameters.mode
87  .equalsIgnoreCase(Params.OPENING_MODE_IMAGE)) {
88  openFileAsImage(null, filename, parameters);
89  } else {
90  parameters.mode = Params.OPENING_MODE_GALLERY;
91  new GalleryJFrame(filename, parameters);
92  }
93  }
94  }
95 
96  } catch (Exception e) {
97  XmippDialog.showError(null, String.format(
98  "Couldn't open file: '%s'\nError: %s", filename,
99  e.getMessage()));
100  e.printStackTrace();
101  }
102  }
103 
104 
105 
106 }
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xmipp.viewer.scipion.ScipionViewer.main
static void main(String args[])
Definition: ScipionViewer.java:32
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xmipp.utils.StopWatch.printElapsedTime
void printElapsedTime(String comment)
Definition: StopWatch.java:43
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xmipp.ij.commons.XmippApplication.setIsScipion
static void setIsScipion(boolean isscipion)
Definition: XmippApplication.java:48
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xmipp.jni.Filename.isMetadata
static boolean isMetadata(String filename)
Definition: Filename.java:165
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xmipp.viewer.scipion.ScipionViewer.openFile
static void openFile(String filename, ScipionParams parameters)
Definition: ScipionViewer.java:64
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xmipp.viewer.windows.ImagesWindowFactory.openScipionMetadata
static void openScipionMetadata(String filename, Params parameters)
Definition: ImagesWindowFactory.java:197
-
xmipp.utils.Params.OPENING_MODE_GALLERY
static final String OPENING_MODE_GALLERY
Definition: Params.java:29
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xmipp.utils.Params.OPENING_MODE_IMAGE
static final String OPENING_MODE_IMAGE
Definition: Params.java:28
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xmipp.viewer.scipion.ScipionMetaData.isScipionMetaData
static boolean isScipionMetaData(String filename)
Definition: ScipionMetaData.java:1227
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.utils.StopWatch.getInstance
static StopWatch getInstance()
Definition: StopWatch.java:26
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xmipp.utils.Params.files
String files[]
Definition: Params.java:58
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xmipp.utils.DEBUG.enableDebug
static void enableDebug(boolean enable)
Definition: DEBUG.java:14
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1 package xmipp.viewer.particlepicker;
2 
3 public enum Shape
4 {
5  Circle, Rectangle, Center
6 }
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.viewer.ctf;
6 
11 public class SortPSDSTask extends CommandTask {
12 
13  public SortPSDSTask(String filename) {
14  super(getCommand(filename));
15  }
16 
17  public SortPSDSTask(String filename, iTaskCompletionListener commandsListener) {
18  super(getCommand(filename), commandsListener);
19  }
20 
21  public static String getCommand(String filename){
22  return String.format("xmipp_ctf_sort_psds -i %s -o %s", filename, filename);
23  }
24 }
xmipp.viewer.ctf.CommandTask.commandsListener
iTaskCompletionListener commandsListener
Definition: CommandTask.java:23
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xmipp.viewer.ctf.SortPSDSTask.getCommand
static String getCommand(String filename)
Definition: SortPSDSTask.java:21
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SortPSDSTask(String filename, iTaskCompletionListener commandsListener)
Definition: SortPSDSTask.java:17
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1 package xmipp.utils;
2 
3 import java.awt.Component;
4 import java.awt.Container;
5 import javax.swing.Spring;
6 import javax.swing.SpringLayout;
7 
14 public class SpringUtilities {
15 
20  public static void printSizes(Component c) {
21  System.out.println("minimumSize = " + c.getMinimumSize());
22  System.out.println("preferredSize = " + c.getPreferredSize());
23  System.out.println("maximumSize = " + c.getMaximumSize());
24  }
25 
40  public static void makeGrid(Container parent,
41  int rows, int cols,
42  int initialX, int initialY,
43  int xPad, int yPad) {
44  SpringLayout layout;
45  try {
46  layout = (SpringLayout) parent.getLayout();
47  } catch (ClassCastException exc) {
48  System.err.println("The first argument to makeGrid must use SpringLayout.");
49  return;
50  }
51 
52  Spring xPadSpring = Spring.constant(xPad);
53  Spring yPadSpring = Spring.constant(yPad);
54  Spring initialXSpring = Spring.constant(initialX);
55  Spring initialYSpring = Spring.constant(initialY);
56  int max = rows * cols;
57 
58  //Calculate Springs that are the max of the width/height so that all
59  //cells have the same size.
60  Spring maxWidthSpring = layout.getConstraints(parent.getComponent(0)).
61  getWidth();
62  Spring maxHeightSpring = layout.getConstraints(parent.getComponent(0)).
63  getWidth();
64  for (int i = 1; i < max; i++) {
65  SpringLayout.Constraints cons = layout.getConstraints(
66  parent.getComponent(i));
67 
68  maxWidthSpring = Spring.max(maxWidthSpring, cons.getWidth());
69  maxHeightSpring = Spring.max(maxHeightSpring, cons.getHeight());
70  }
71 
72  //Apply the new width/height Spring. This forces all the
73  //components to have the same size.
74  for (int i = 0; i < max; i++) {
75  SpringLayout.Constraints cons = layout.getConstraints(
76  parent.getComponent(i));
77 
78  cons.setWidth(maxWidthSpring);
79  cons.setHeight(maxHeightSpring);
80  }
81 
82  //Then adjust the x/y constraints of all the cells so that they
83  //are aligned in a grid.
84  SpringLayout.Constraints lastCons = null;
85  SpringLayout.Constraints lastRowCons = null;
86  for (int i = 0; i < max; i++) {
87  SpringLayout.Constraints cons = layout.getConstraints(
88  parent.getComponent(i));
89  if (i % cols == 0) { //start of new row
90  lastRowCons = lastCons;
91  cons.setX(initialXSpring);
92  } else { //x position depends on previous component
93  cons.setX(Spring.sum(lastCons.getConstraint(SpringLayout.EAST),
94  xPadSpring));
95  }
96 
97  if (i / cols == 0) { //first row
98  cons.setY(initialYSpring);
99  } else { //y position depends on previous row
100  cons.setY(Spring.sum(lastRowCons.getConstraint(SpringLayout.SOUTH),
101  yPadSpring));
102  }
103  lastCons = cons;
104  }
105 
106  //Set the parent's size.
107  SpringLayout.Constraints pCons = layout.getConstraints(parent);
108  pCons.setConstraint(SpringLayout.SOUTH,
109  Spring.sum(
110  Spring.constant(yPad),
111  lastCons.getConstraint(SpringLayout.SOUTH)));
112  pCons.setConstraint(SpringLayout.EAST,
113  Spring.sum(
114  Spring.constant(xPad),
115  lastCons.getConstraint(SpringLayout.EAST)));
116  }
117 
118  /* Used by makeCompactGrid. */
119  private static SpringLayout.Constraints getConstraintsForCell(
120  int row, int col,
121  Container parent,
122  int cols) {
123  SpringLayout layout = (SpringLayout) parent.getLayout();
124  Component c = parent.getComponent(row * cols + col);
125  return layout.getConstraints(c);
126  }
127 
143  public static void makeCompactGrid(Container parent,
144  int rows, int cols,
145  int initialX, int initialY,
146  int xPad, int yPad) {
147  SpringLayout layout;
148  try {
149  layout = (SpringLayout) parent.getLayout();
150  } catch (ClassCastException exc) {
151  System.err.println("The first argument to makeCompactGrid must use SpringLayout.");
152  return;
153  }
154 
155  //Align all cells in each column and make them the same width.
156  Spring x = Spring.constant(initialX);
157  for (int c = 0; c < cols; c++) {
158  Spring width = Spring.constant(0);
159  for (int r = 0; r < rows; r++) {
160  width = Spring.max(width,
161  getConstraintsForCell(r, c, parent, cols).
162  getWidth());
163  }
164  for (int r = 0; r < rows; r++) {
165  SpringLayout.Constraints constraints =
166  getConstraintsForCell(r, c, parent, cols);
167  constraints.setX(x);
168  constraints.setWidth(width);
169  }
170  x = Spring.sum(x, Spring.sum(width, Spring.constant(xPad)));
171  }
172 
173  //Align all cells in each row and make them the same height.
174  Spring y = Spring.constant(initialY);
175  for (int r = 0; r < rows; r++) {
176  Spring height = Spring.constant(0);
177  for (int c = 0; c < cols; c++) {
178  height = Spring.max(height,
179  getConstraintsForCell(r, c, parent, cols).
180  getHeight());
181  }
182  for (int c = 0; c < cols; c++) {
183  SpringLayout.Constraints constraints =
184  getConstraintsForCell(r, c, parent, cols);
185  constraints.setY(y);
186  constraints.setHeight(height);
187  }
188  y = Spring.sum(y, Spring.sum(height, Spring.constant(yPad)));
189  }
190 
191  //Set the parent's size.
192  SpringLayout.Constraints pCons = layout.getConstraints(parent);
193  pCons.setConstraint(SpringLayout.SOUTH, y);
194  pCons.setConstraint(SpringLayout.EAST, x);
195  }
196 }
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xmipp.utils.SpringUtilities.printSizes
static void printSizes(Component c)
Definition: SpringUtilities.java:20
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xmipp.utils.SpringUtilities.makeGrid
static void makeGrid(Container parent, int rows, int cols, int initialX, int initialY, int xPad, int yPad)
Definition: SpringUtilities.java:40
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xmipp.utils.SpringUtilities.makeCompactGrid
static void makeCompactGrid(Container parent, int rows, int cols, int initialX, int initialY, int xPad, int yPad)
Definition: SpringUtilities.java:143
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.utils;
8 
13 public class StopWatch {
14 
15  /* Private Instance Variables */
17  private long startTime;
18  private static StopWatch stopwatch;
22  private StopWatch() {
23  startTime = System.currentTimeMillis();
24  }
25 
26  public static StopWatch getInstance()
27  {
28  if(stopwatch == null)
29  stopwatch = new StopWatch();
30  return stopwatch;
31  }
32 
38  public double getElapsedTime() {
39  long endTime = System.currentTimeMillis();
40  return (double) (endTime - startTime) / (1000);
41  }
42 
43  public void printElapsedTime(String comment) {
44 // double time = getElapsedTime();
45 // if(comment != null)
46 // System.out.printf("%.2f %s\n", time, comment);
47 // else
48 // System.out.println(time);
49  }
50 
51  public void restart()
52  {
53  startTime = System.currentTimeMillis();
54  }
55 }
-
xmipp.utils.StopWatch.printElapsedTime
void printElapsedTime(String comment)
Definition: StopWatch.java:43
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Definition: StopWatch.java:26
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1 package xmipp.viewer;
2 
3 import java.awt.BasicStroke;
4 import java.awt.Color;
5 import java.awt.Component;
6 import java.awt.Graphics;
7 import java.awt.Graphics2D;
8 import java.awt.Insets;
9 import java.awt.RenderingHints;
10 import javax.swing.border.AbstractBorder;
11 
12 public class StrokeBorder extends AbstractBorder {
13 
14  protected int thickness;
15  protected Color lineColor;
16 
17  public StrokeBorder(Color color, int thickness) {
18  this.lineColor = color;
19  this.thickness = thickness;
20  }
21 
32  @Override
33  public void paintBorder(Component c, Graphics g, int x, int y, int width, int height) {
34  Graphics2D g2d = (Graphics2D) g;
35  g2d.setColor(lineColor);
36  g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
37  float dash[] = {thickness * 2};
38  g2d.setStroke(new BasicStroke(thickness, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER, 1f, dash, 0));
39  g2d.drawRect(x, y, width, height);
40  }
41 
46  @Override
47  public Insets getBorderInsets(Component c) {
48  return new Insets(thickness, thickness, thickness, thickness);
49  }
50 
56  @Override
57  public Insets getBorderInsets(Component c, Insets insets) {
58  insets.left = insets.top = insets.right = insets.bottom = thickness;
59  return insets;
60  }
61 
65  public Color getLineColor() {
66  return lineColor;
67  }
68 
72  public int getThickness() {
73  return thickness;
74  }
75 
79  @Override
80  public boolean isBorderOpaque() {
81  return true;
82  }
83 //
84 // public static void main(String[] args) {
85 // JFrame f = new JFrame();
86 // f.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
87 // JLabel label = new JLabel();
88 // label.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(20, 20, 20, 20), new StrokeBorder(Color.RED, 4)));
89 //
90 // f.getContentPane().add(label);
91 // f.setSize(300, 300);
92 // f.setVisible(true);
93 // }
94 }
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xmipp.viewer.StrokeBorder.getBorderInsets
Insets getBorderInsets(Component c)
Definition: StrokeBorder.java:47
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xmipp.viewer.StrokeBorder.StrokeBorder
StrokeBorder(Color color, int thickness)
Definition: StrokeBorder.java:17
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xmipp.viewer.StrokeBorder.paintBorder
void paintBorder(Component c, Graphics g, int x, int y, int width, int height)
Definition: StrokeBorder.java:33
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Definition: StrokeBorder.java:57
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class  xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker
 
class  xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.UpdateTemplatesTask
 
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package  xmipp.viewer.particlepicker.training.model
 
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SupervisedParticlePicker.java
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 import java.awt.*;
4 import java.io.File;
5 import java.util.ArrayList;
6 import java.util.Arrays;
7 import java.util.List;
8 import java.util.logging.Level;
9 
10 import javax.swing.JFrame;
11 import javax.swing.SwingWorker;
12 
13 import xmipp.jni.Classifier;
14 import xmipp.jni.Filename;
15 import xmipp.jni.ImageGeneric;
16 import xmipp.jni.MDLabel;
17 import xmipp.jni.MDRow;
18 import xmipp.jni.MetaData;
19 import xmipp.jni.Particle;
20 import xmipp.jni.PickingClassifier;
21 import xmipp.utils.XmippDialog;
22 import xmipp.utils.XmippMessage;
23 import xmipp.utils.XmippWindowUtil;
24 import xmipp.viewer.JMetaDataIO;
25 import xmipp.viewer.models.ColumnInfo;
26 import xmipp.viewer.particlepicker.*;
27 import xmipp.viewer.particlepicker.training.AutopickRunnable;
28 import xmipp.viewer.particlepicker.training.CorrectAndAutopickRunnable;
29 import xmipp.viewer.particlepicker.training.TrainRunnable;
30 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame;
31 import xmipp.viewer.particlepicker.training.gui.TemplatesJDialog;
32 import xmipp.viewer.scipion.ScipionMetaData;
33 
40 public class SupervisedParticlePicker extends ParticlePicker
41 {
42 
43  protected List<SupervisedPickerMicrograph> micrographs;
44  private SupervisedPickerMicrograph micrograph;
45  protected int autopickpercent;
46 
47  //used in previous versions
48  private Integer threads = 1;
49  private boolean fastmode = true;
50  private boolean incore = false;
52 
53  public static int dtemplatesnum = 1;
54  private ImageGeneric templates;
55  private ImageGeneric radialtemplates;
56  private String templatesfile;
57  private int templateindex;
58  private Classifier classifier;
59  private UpdateTemplatesTask uttask;
60  private TemplatesJDialog dialog;
61  private boolean isautopick;
62  private boolean existspsd;
63  private boolean hasDefocusU;
64 
65  // private String reviewfile;
66 
67  public SupervisedParticlePicker(String selfile, String outputdir, ParticlePickerParams params)
68  {
69  this(null, selfile, outputdir, params);
70 
71  }
72 
73  public SupervisedParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params)
74  {
75 
76  super(block, selfile, outputdir, params);
77  try
78  {
79  templatesfile = getOutputPath("templates.stk");
80  if (!new File(templatesfile).exists())
81  initTemplates(dtemplatesnum);
82  else
83  {
84  this.templates = new ImageGeneric(templatesfile);
85  templates.read(templatesfile, false);
86  radialtemplates = new ImageGeneric(ImageGeneric.Float);
87  radialtemplates.resize(getSize(), getSize(), 1, getTemplatesNumber());
88  templateindex = (templates.getStatistics()[2] == 0)? 0: getTemplatesNumber();
89  }
90  templates.getRadialAvg(radialtemplates);
91  MDRow[] micsmd = new MDRow[micrographs.size()];
92  MDRow row; int index = 0;
93 
94  if(params.classifierProperties != null)
95  {
96  classifier = new GenericClassifier(params.classifierProperties);
97  for (SupervisedPickerMicrograph m : micrographs)
98  loadMicrographData(m);
99  }
100  else
101  {
102  for (SupervisedPickerMicrograph m : micrographs) {
103  loadMicrographData(m);
104  row = new MDRow();
105  row.setValueString(MDLabel.MDL_MICROGRAPH, m.getFile());
106  micsmd[index] = row;
107  index ++;
108  }
109  classifier = new PickingClassifier(getSize(), getOutputPath("model"), micsmd);
110  }
111  }
112  catch (Exception e)
113  {
114  e.printStackTrace();
115  throw new IllegalArgumentException(e.getMessage());
116  }
117  }
118 
119 
120  public SupervisedParticlePicker(String selfile, String outputdir, Integer threads, boolean fastmode, boolean incore, ParticlePickerParams params)
121  {
122  this(selfile, outputdir, params);
123 
124  this.threads = threads;
125  this.fastmode = fastmode;
126  this.incore = incore;
127 
128  }
129 
130  /* Save changes to the current micrograph(To be removed). */
131  public void saveData()
132  {
133  super.saveData();
134  saveData(micrograph);
135  setChanged(false);
136  setSaved(true);
137  }
138 
139  /* Save changes to ALL micrographs, mainly used when importing. */
140  public void saveAllData()
141  {
142  super.saveData();
143  for (Micrograph m : micrographs)
144  saveData(m);
145  setChanged(false);
146  }
147 
148  public boolean isFastMode()
149  {
150  return fastmode;
151  }
152 
153  public boolean isIncore()
154  {
155  return incore;
156  }
157 
158  public int getThreads()
159  {
160  return threads;
161  }
162 
163  public int getTemplatesNumber()
164  {
165  if (templates == null)
166  return dtemplatesnum;
167  try
168  {
169  return (int) templates.getNDim();
170  }
171  catch (Exception e)
172  {
173  // TODO Auto-generated catch block
174  e.printStackTrace();
175  }
176  return dtemplatesnum;
177  }
178 
179  public void setSize(int size)
180  {
181 
182  super.setSize(size);
183  classifier.setSize(size);
184  }
185 
186  public synchronized void initTemplates()
187  {
188  initTemplates(getTemplatesNumber());
189  }
190 
191  public synchronized void initTemplates(int num)
192  {
193  if (num == 0)
194  return;
195  try
196  {
197  this.templates = new ImageGeneric(ImageGeneric.Float);
198  templates.resize(getSize(), getSize(), 1, num);
199  templates.write(templatesfile);
200  templateindex = 0;
201  radialtemplates = new ImageGeneric(ImageGeneric.Float);
202  radialtemplates.resize(getSize(), getSize(), 1, num);
203  }
204  catch (Exception e)
205  {
206  throw new IllegalArgumentException(e.getMessage());
207  }
208  }
209 
210  public synchronized void setTemplatesNumber(int num)
211  {
212  if (num <= 0)
213  throw new IllegalArgumentException(
214  XmippMessage.getIllegalValueMsgWithInfo("Templates Number", Integer.valueOf(num), "Must have at least one template"));
215  updateTemplatesStack(num, false);
216  saveConfig();
217  }
218 
219  public synchronized ImageGeneric getTemplates()
220  {
221  return templates;
222  }
223 
224  public synchronized void setTemplate(ImageGeneric ig)
225  {
226  float[] matrix;
227  try
228  {
229  // TODO getArrayFloat and setArrayFloat must be call from C both in
230  // one function
231  matrix = ig.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE);
232  templates.setArrayFloat(matrix, ImageGeneric.FIRST_IMAGE + templateindex, ImageGeneric.FIRST_SLICE);
233  templateindex++;
234 
235  }
236  catch (Exception e)
237  {
238  e.printStackTrace();
239  throw new IllegalArgumentException(e.getMessage());
240  }
241  }
242 
243  // to update templates with the right particles
244  public synchronized void resetParticleImages()
245  {
246  for (SupervisedPickerMicrograph m : micrographs)
247  {
248  for (ManualParticle p : m.getManualParticles())
249  p.resetImage();
250 
251  }
252  }
253 
254  public synchronized void updateTemplates(ImageGeneric templates, int templateindex)
255  {
256 
257  try
258  {
259  this.templates = templates;
260  radialtemplates = new ImageGeneric(ImageGeneric.Float);
261  radialtemplates.resize(getSize(), getSize(), 1, getTemplatesNumber());
262  templates.getRadialAvg(radialtemplates);
263  this.templateindex = templateindex;
264  saveTemplates();
265  }
266  catch (Exception e)
267  {
268  throw new IllegalArgumentException(e.getMessage());
269  }
270  }
271 
272  public synchronized void addParticleToTemplates(ManualParticle particle)
273  {
274  try
275  {
276  ImageGeneric igp = particle.getImageGeneric();
277  // will happen only in manual mode
278  if (getTemplateIndex() < getTemplatesNumber())
279  setTemplate(igp);
280  else
281  {
282  double[] align = getTemplates().alignImage(igp);
283  applyAlignment(particle, igp, align);
284  }
285  templates.getRadialAvg(radialtemplates);
286  }
287  catch (Exception e)
288  {
289  throw new IllegalArgumentException(e.getMessage());
290  }
291 
292  }
293 
294  public synchronized void centerParticle(ManualParticle p)
295  {
296 
297  if (getManualParticlesNumber() <= getTemplatesNumber())
298  return;// templates not ready
299  Particle shift = null;
300  try
301  {
302  ImageGeneric igp = p.getImageGeneric();
303 
304  shift = radialtemplates.bestShift(igp);
305  double distance = Math.sqrt(Math.pow(shift.getX(), 2) + Math.pow(shift.getY(), 2)) / getSize();
306  // System.out.printf("normalized distance:%.2f\n", distance);
307  if (distance < 0.25)
308  {
309  p.setX(p.getX() + shift.getX());
310  p.setY(p.getY() + shift.getY());
311 
312  }
313 
314  }
315  catch (Exception e)
316  {
317  // TODO Auto-generated catch block
318  e.printStackTrace();
319  }
320 
321  }
322 
323  public synchronized void applyAlignment(ManualParticle particle, ImageGeneric igp, double[] align)
324  {
325  try
326  {
327  particle.setLastalign(align);
328  templates.applyAlignment(igp, particle.getTemplateIndex(), particle.getTemplateRotation(), particle.getTemplateTilt(), particle
329  .getTemplatePsi());
330  }
331  catch (Exception e)
332  {
333  // TODO Auto-generated catch block
334  e.printStackTrace();
335  }
336 
337  }
338 
339  public String getTemplatesFile()
340  {
341  return templatesfile;
342  }
343 
344  public void saveTemplates()
345  {
346  try
347  {
348  if(templateindex == getTemplatesNumber())
349  templates.write(getTemplatesFile());
350  }
351  catch (Exception e)
352  {
353  throw new IllegalArgumentException(e.getMessage());
354  }
355  }
356 
357  public boolean containsPSD()
358  {
359  return existspsd;
360  }
361 
362  public boolean hasDefocusU() {
363  return hasDefocusU;
364  }
365 
366  @Override
367  public void loadEmptyMicrographs()
368  {
369  String selfile = getMicrographsSelFile();
370  if(selfile.endsWith(".sqlite"))
371  loadEmptyMicrographsFromSqlite();
372  else
373  loadEmptyMicrographsFromMd();
374  }
375 
376  public void loadEmptyMicrographsFromMd()
377  {
378  if (micrographs == null)
379  micrographs = new ArrayList<SupervisedPickerMicrograph>();
380  else
381  micrographs.clear();
382  SupervisedPickerMicrograph micrograph;
383  String psd = null, ctf = null, filename;
384  try
385  {
386  String selfile = getMicrographsSelFile();
387  MetaData md = new MetaData(selfile);
388 
389  //md.removeDisabled();
390 
391  int fileLabel;
392  if (md.containsLabel(MDLabel.MDL_MICROGRAPH))
393  fileLabel = MDLabel.MDL_MICROGRAPH;
394  else if (md.containsLabel(MDLabel.MDL_IMAGE))
395  fileLabel = MDLabel.MDL_IMAGE;
396  else
397  throw new IllegalArgumentException(String.format("Labels MDL_MICROGRAPH or MDL_IMAGE not found in metadata %s", selfile));
398  existspsd = md.containsLabel(MDLabel.MDL_PSD_ENHANCED);
399  boolean existsctf = md.containsLabel(MDLabel.MDL_CTF_MODEL);
400  hasDefocusU = md.containsLabel(MDLabel.MDL_CTF_DEFOCUSV);
401 
402  boolean hasctfinfo = existsctf || existspsd || hasDefocusU;
403 
404  long[] ids = md.findObjects();
405  CtfInfo ctfInfo;
406 
407  for (long id : ids)
408  {
409  ctfInfo = hasctfinfo ? new CtfInfo() : null;
410 
411  filename = md.getValueString(fileLabel, id);
412  if (existspsd)
413  ctfInfo.psd = md.getValueString(MDLabel.MDL_PSD_ENHANCED, id);
414  if (existsctf)
415  ctfInfo.ctf = md.getValueString(MDLabel.MDL_CTF_MODEL, id);
416  if (hasDefocusU)
417  ctfInfo.defocusU = new Float(md.getValueDouble(MDLabel.MDL_CTF_DEFOCUSV, id));
418 
419  micrograph = new SupervisedPickerMicrograph(filename, ctfInfo);
420 
421  micrographs.add(micrograph);
422  }
423  if (micrographs.isEmpty())
424  throw new IllegalArgumentException(String.format("No micrographs specified on %s", getMicrographsSelFile()));
425  md.destroy();
426  }
427  catch (Exception e)
428  {
429  getLogger().log(Level.SEVERE, e.getMessage(), e);
430  throw new IllegalArgumentException(e.getMessage());
431  }
432 
433  }
434 
435  public void loadEmptyMicrographsFromSqlite()
436  {
437  if (micrographs == null)
438  micrographs = new ArrayList<SupervisedPickerMicrograph>();
439  else
440  micrographs.clear();
441  SupervisedPickerMicrograph micrograph;
442  String filename;
443  try
444  {
445  String selfile = getMicrographsSelFile();
446  ScipionMetaData md = new ScipionMetaData(selfile);
447 
448  ColumnInfo ci;
449  if(md.getSelf().equals("Micrograph"))
450  {
451  ci = md.getColumnInfo("_filename");
452  long[] ids = md.findObjects();
453  for (long id : ids)
454  {
455 
456  filename = md.getValueString(ci.label, id);
457  micrograph = new SupervisedPickerMicrograph(filename, null);
458  micrographs.add(micrograph);
459  }
460  }
461  else
462  throw new IllegalArgumentException(String.format("Labels MDL_MICROGRAPH or MDL_IMAGE not found in metadata %s", selfile));
463 
464  if (micrographs.isEmpty())
465  throw new IllegalArgumentException(String.format("No micrographs specified on %s", getMicrographsSelFile()));
466  md.destroy();
467  }
468  catch (Exception e)
469  {
470  getLogger().log(Level.SEVERE, e.getMessage(), e);
471  throw new IllegalArgumentException(e.getMessage());
472  }
473  }
474 
475 
476  @Override
477  public List<SupervisedPickerMicrograph> getMicrographs()
478  {
479  return micrographs;
480  }
481 
482  public synchronized void saveData(Micrograph m)
483  {
484 
485  JMetaDataIO.saveData((SupervisedPickerMicrograph) m, getOutputPath(m.getPosFile()));
486  saveTemplates();
487 
488  }
489 
490  public SupervisedPickerMicrograph getMicrograph()
491  {
492  return micrograph;
493  }
494 
495  @Override
496  public void setMicrograph(Micrograph m)
497  {
498  if (m == null)
499  return;
500  if (m.equals(micrograph))
501  return;
502  this.micrograph = (SupervisedPickerMicrograph) m;
503  }
504 
505  @Override
506  public boolean isValidSize(JFrame parent, int size)
507  {
508 
509 
510  if (size > ParticlePicker.sizemax) {
511  XmippDialog.showInfo(parent, String.format("Max size is %s, %s not allowed", ParticlePicker.sizemax, size));
512  return false;
513  }
514  String outmsg = "";
515  int count;
516  boolean valid = true;
517  List<ManualParticle> outlist = new ArrayList<ManualParticle>();
518  for (SupervisedPickerMicrograph m : micrographs)
519  {
520  count = 0;
521  for (ManualParticle p : m.getParticles())
522  if (!m.fits(p.getX(), p.getY(), size))
523  {
524  outlist.add(p);
525  count ++;
526  valid = false;
527  }
528  if(count > 0)
529  outmsg += String.format("%s %s from micrograph %s will be dismissed if size %s is set.", count, (count == 1)? "particle": "particles", m.getName(), size);
530  }
531  if(valid)
532  return true;
533  else
534  {
535  String msg = outmsg + " Are you sure you want to continue?";
536  valid = XmippDialog.showQuestion(parent, msg);
537  if(valid)
538  for(ManualParticle p: outlist)
539  ((SupervisedPickerMicrograph)p.getMicrograph()).removeParticle(p, this);
540  return valid;
541 
542  }
543  }
544 
545  @Override
546  public void loadConfig()
547  {
548  super.loadConfig();
549  String file = configfile;
550  if (!new File(file).exists())
551  return;
552 
553  try
554  {
555  MetaData md = new MetaData(file);
556  Mode configmode;
557  boolean hasautopercent = md.containsLabel(MDLabel.MDL_PICKING_AUTOPICKPERCENT);
558  long id = md.firstObject();
559 
560  if(hasautopercent)
561  autopickpercent = md.getValueInt(MDLabel.MDL_PICKING_AUTOPICKPERCENT, id);
562 
563  dtemplatesnum = md.getValueInt(MDLabel.MDL_PICKING_TEMPLATES, id);
564  if (dtemplatesnum == 0)
565  dtemplatesnum = 1;// for compatibility with previous projects
566  configmode = Mode.valueOf(md.getValueString(MDLabel.MDL_PICKING_STATE, id));
567  isautopick = configmode == Mode.Supervised || configmode == Mode.Review;
568 
569  if (mode == Mode.Review && configmode == Mode.Manual)//Review mode makes no sense if manual mode
570  throw new IllegalArgumentException("Cannot review picking in manual mode, use manual mode instead");
571 
572  if (mode != Mode.ReadOnly && mode != Mode.Review)
573  mode = configmode;
574 
575  md.destroy();
576  }
577  catch (Exception e)
578  {
579  getLogger().log(Level.SEVERE, e.getMessage(), e);
580  throw new IllegalArgumentException(e.getMessage());
581  }
582  }
583 
584  public boolean isAutopick()
585  {
586  return isautopick;
587  }
588 
589  @Override
590  public synchronized void saveConfig()
591  {
592  JMetaDataIO.saveConfig(this, configfile);
593  }
594 
595  @Override
596  protected synchronized void saveConfig(MetaData md, long id)
597  {
598  try
599  {
600  super.saveConfig(md, id);
601  md.setValueInt(MDLabel.MDL_PICKING_AUTOPICKPERCENT, getAutopickpercent(), id);
602  md.setValueInt(MDLabel.MDL_PICKING_TEMPLATES, getTemplatesNumber(), id);
603  md.setValueString(MDLabel.MDL_PICKING_STATE, mode.toString(), id);
604  md.setValueInt(MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE, getManualParticlesNumber(), id);
605  md.setValueInt(MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE, getAutomaticParticlesNumber(), id);
606 
607  }
608  catch (Exception e)
609  {
610  getLogger().log(Level.SEVERE, e.getMessage(), e);
611  throw new IllegalArgumentException(e.getMessage());
612  }
613  }
614 
615  public void setAutopickpercent(int autopickpercent)
616  {
617  this.autopickpercent = autopickpercent;
618  }
619 
620  public int getAutopickpercent()
621  {
622  if(autopickpercent == 0)
623  autopickpercent = 50;
624  return autopickpercent;
625  }
626 
627  public void setMode(Mode mode)
628  {
629  if (mode == Mode.Supervised && getManualParticlesNumber() < classifier.getTrainingParticlesMinimum())
630  throw new IllegalArgumentException(String.format("You should have at least %s particles to go to %s mode", classifier.getTrainingParticlesMinimum(), Mode.Supervised));
631  this.mode = mode;
632 
633  // If supervised
634  if(mode == Mode.Supervised)
635  isautopick = true;
636  if (mode == Mode.Manual)
637  convertAutomaticToManual();
638 
639  }
640 
641  protected void convertAutomaticToManual()
642  {
643  ManualParticle p;
644  for (SupervisedPickerMicrograph m : micrographs)
645  {
646  m.deleteBelowThreshold();
647  for (AutomaticParticle ap : m.getAutomaticParticles())
648  {
649  if (!ap.isDeleted())
650  {
651  p = new ManualParticle(ap.getX(), ap.getY(), this, m);
652  m.addManualParticle(p, this);
653  }
654  }
655 
656  m.getAutomaticParticles().clear();
657  if (m.hasManualParticles())
658  m.setState(MicrographState.Manual);
659  else
660  m.setState(MicrographState.Available);
661  }
662 
663  saveAllData();
664  updateTemplatesStack(false);
665 
666  }
667 
668  public int getManualParticlesNumber()
669  {
670  int count = 0;
671  for (SupervisedPickerMicrograph m : micrographs)
672  count += m.getManualParticles().size();
673  return count;
674  }
675 
676  public void exportParticles(String file)
677  {
678 
679  try
680  {
681  MetaData md = new MetaData();
682  boolean append = false;
683  long id;
684  for (SupervisedPickerMicrograph m : micrographs)
685  {
686  if (m.isEmpty())
687  continue;
688  for (ManualParticle p : m.getParticles())
689  {
690  id = md.addObject();
691  md.setValueInt(MDLabel.MDL_XCOOR, p.getX(), id);
692  md.setValueInt(MDLabel.MDL_YCOOR, p.getY(), id);
693  md.setValueDouble(MDLabel.MDL_COST, p.getCost(), id);
694  }
695  if (!append)
696  md.write("mic_" + m.getName() + "@" + file);
697  else
698  md.writeBlock("mic_" + m.getName() + "@" + file);
699  append = true;
700  md.clear();
701  }
702  md.destroy();
703 
704  this.setSaved(false);
705  }
706  catch (Exception e)
707  {
708  getLogger().log(Level.SEVERE, e.getMessage(), e);
709  throw new IllegalArgumentException(e.getMessage());
710  }
711  }
712 
713  public int getAutomaticParticlesNumber(double threshold)
714  {
715  int count = 0;
716  for (SupervisedPickerMicrograph m : micrographs)
717  count += m.getAutomaticParticlesNumber(threshold);
718  return count;
719  }
720 
721  public int getAutomaticParticlesNumber()
722  {
723  int count = 0;
724  for (SupervisedPickerMicrograph m : micrographs)
725  count += m.getAutomaticParticlesNumber(m.getThreshold());
726  return count;
727  }
728 
729  public void loadAutomaticParticles(SupervisedPickerMicrograph m, MetaData md)
730  {
731 
732  int x, y;
733  AutomaticParticle particle;
734  Double cost;
735  boolean deleted;
736  try
737  {
738  boolean added = false;
739 
740  for (long id : md.findObjects())
741  {
742 
743  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
744  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
745  cost = md.getValueDouble(MDLabel.MDL_COST, id);
746  if (cost == null)
747  throw new IllegalArgumentException("Invalid format for " + md.getFilename());
748  deleted = (md.getValueInt(MDLabel.MDL_ENABLED, id) == 1) ? false : true;
749  particle = new AutomaticParticle(x, y, this, m, cost, deleted);
750  m.addAutomaticParticle(particle);
751  added = true;
752  }
753  // Change the state of the micrograph if some automatic particles
754  // were added
755  if (added && m.getState() == MicrographState.Available)
756  m.setState(MicrographState.Auto);
757 
758  }
759  catch (Exception e)
760  {
761  getLogger().log(Level.SEVERE, e.getMessage(), e);
762  throw new IllegalArgumentException(e.getMessage());
763  }
764  }
765 
766  public void loadAutomaticParticles(SupervisedPickerMicrograph m, String file)
767  {
768  if (new File(file).exists() && MetaData.containsBlock(file, particlesAutoBlock))// todo: // exists
769  {
770  MetaData md = new MetaData(getParticlesAutoBlock(file));
771  loadAutomaticParticles(m, md);
772  md.destroy();
773  }
774  }
775 
777  public String importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
778  {
779 
780  if (f == Format.Auto)
781  {
782  StringBuffer suffixPtr = new StringBuffer(suffix);
783  f = detectFormat(path, preffix, suffixPtr);
784  suffix = suffixPtr.toString();
785  }
786  if (f == Format.None)
787  throw new IllegalArgumentException("Unable to detect format. You may try specifying format or renaming files");
788 
789  String result = "";
790 
791  String particlesfile = getExportFile(path);
792  if (particlesfile != null && f == Format.Xmipp30)
793  {
794  importAllParticles(particlesfile);
795  return "";
796  }
797 
798  importSize(path, f, scale);
799  String file;
800 
801  for (SupervisedPickerMicrograph m : micrographs)
802  {
803  resetMicrograph(m);
804  file = Filename.join(path, preffix + m.getName() + suffix);
805  if(new File(file).exists())
806  result += importParticlesFromFile(file, f, m, scale, invertx, inverty);
807  }
808 
809 
810 
811  return result;
812  }// function importParticlesFromFolder
813 
814 
815 
817  public String importParticlesFromFile(String path, Format f, SupervisedPickerMicrograph m, float scale, boolean invertx, boolean inverty)
818  {
819  String result = "";
820  try
821  {
822  MetaData md = new MetaData();
823  fillParticlesMdFromFile(path, f, m, md, scale, invertx, inverty);
824  if (md.size() > 0)
825  {
826  //Be sure that width and height are loaded
827  result = importParticlesFromMd(m, md);
828  }
829  md.destroy();
830  }
831  catch (Exception ex)
832  {
833  XmippDialog.showInfo(null, ex.getMessage());
834  }
835  return result;
836  }// function importParticlesFromFile
837 
838  public String importParticlesFromMd(SupervisedPickerMicrograph m, MetaData md)
839  {
840  long[] ids = md.findObjects();
841  int x, y;
842  String result = "";
843  int size = getSize();
844 
845  for (long id : ids)
846  {
847  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
848  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
849  if ( !m.fits(x, y, size))// ignore out of bounds particles
850  {
851  result += XmippMessage.getOutOfBoundsMsg(String.format("Particle on x:%s y:%s\n", x, y)) + " dismissed\n";
852  continue;
853  }
854  m.addManualParticle(new ManualParticle(x, y, this, m, 2), this);
855 
856  }
857  saveData(m);
858 
859  return result;
860  }// function importParticlesFromMd
861 
862  public boolean isReviewFile(String file)
863  {
864  if (!file.endsWith("xmd"))
865  return false;
866  boolean result = false;
867  boolean nullMicrograph = false;
868  try
869  {
870  MetaData md = new MetaData(file);
871 
872  if (md.containsLabel(MDLabel.MDL_XCOOR) && md.containsLabel(MDLabel.MDL_YCOOR) && md.containsLabel(MDLabel.MDL_COST))
873  {
874  String[] blocksArray = MetaData.getBlocksInMetaDataFile(file);
875  List<String> blocks = Arrays.asList(blocksArray);
876 
877  String name;
878  for (String block : blocks)
879  {
880  name = block.replace("mic_", "");
881  if (getMicrograph(name) == null)
882  {
883  nullMicrograph = true;
884  break;
885  }
886  }
887  }
888  md.destroy();
889 
890  if (!nullMicrograph)
891  result = true;
892  }
893  catch (Exception e)
894  {
895  e.printStackTrace();
896  }
897  return result;
898  }
899 
900  public void importAllParticles(String file)
901  {// Expected a file for all
902  // micrographs
903  try
904  {
905  String[] blocksArray = MetaData.getBlocksInMetaDataFile(file);
906  List<String> blocks = Arrays.asList(blocksArray);
907  String block;
908  MetaData md = new MetaData();
909 
910  for (SupervisedPickerMicrograph m : micrographs)
911  {
912  resetMicrograph(m);
913  block = "mic_" + m.getName();
914  if (blocks.contains(block))
915  {
916  String blockName = block + "@" + file;
917  md.read(blockName);
918  importParticlesFromMd(m, md);
919  }
920  }
921  md.destroy();
922  }
923  catch (Exception e)
924  {
925  getLogger().log(Level.SEVERE, e.getMessage(), e);
926  throw new IllegalArgumentException(e.getMessage());
927  }
928 
929  }// function importAllParticles
930 
931  public String importAllParticles(String file, float scale, boolean invertx, boolean inverty)
932  {// Expected a file for all
933  // micrographs
934  try
935  {
936 
937  String[] blocksArray = MetaData.getBlocksInMetaDataFile(file);
938  List<String> blocks = Arrays.asList(blocksArray);
939  String block;
940  MetaData md = new MetaData();
941  int width, height;
942 
943  for (SupervisedPickerMicrograph m : micrographs)
944  {
945  resetMicrograph(m);
946  block = "mic_" + m.getName();
947  if (blocks.contains(block))
948  {
949  String blockName = block + "@" + file;
950  md.read(blockName);
951  width = (int) (m.getWidth() / scale);// original width
952  height = (int) (m.getHeigth() / scale);// original height
953  if (invertx)
954  md.operate(String.format("xcoor=%d-xcoor", width));
955  if (inverty)
956  md.operate(String.format("ycoor=%d-ycoor", height));
957  if (scale != 1.f)
958  md.operate(String.format("xcoor=xcoor*%f,ycoor=ycoor*%f", scale, scale));
959  importParticlesFromMd(m, md);
960  }
961  }
962  md.destroy();
963  }
964  catch (Exception e)
965  {
966  getLogger().log(Level.SEVERE, e.getMessage(), e);
967  throw new IllegalArgumentException(e.getMessage());
968  }
969  return null;
970 
971  }// function importAllParticles
972 
973 
974 
975  public boolean hasManualParticles()
976  {
977  for (SupervisedPickerMicrograph m : micrographs)
978  {
979  if (m.hasManualParticles())
980  return true;
981  }
982  return false;
983  }
984 
985  public synchronized int getTemplateIndex()
986  {
987  return templateindex;
988  }
989 
990 
991  public void loadMicrographData(SupervisedPickerMicrograph m)
992  {
993  try
994  {
995  String file = getOutputPath(m.getPosFile());
996  MicrographState state;
997  int micautopickpercent;
998  if (!new File(file).exists())
999  return;
1000  if (MetaData.containsBlock(file, "header"))
1001  {
1002  MetaData md = new MetaData("header@" + file);
1003  boolean hasautopercent = md.containsLabel(MDLabel.MDL_PICKING_AUTOPICKPERCENT);
1004  long id = md.firstObject();
1005  state = MicrographState.valueOf(md.getValueString(MDLabel.MDL_PICKING_MICROGRAPH_STATE, id));
1006  micautopickpercent = hasautopercent ? md.getValueInt(MDLabel.MDL_PICKING_AUTOPICKPERCENT, id) : getAutopickpercent();
1007  double threshold = md.getValueDouble(MDLabel.MDL_COST, id);
1008  m.setThreshold(threshold);
1009  m.setState(state);
1010  m.setAutopickpercent(micautopickpercent);
1011  md.destroy();
1012  }
1013  loadManualParticles(m, file);
1014  loadAutomaticParticles(m, file);
1015  }
1016  catch (Exception e)
1017  {
1018  getLogger().log(Level.SEVERE, e.getMessage(), e);
1019  throw new IllegalArgumentException(e.getMessage());
1020  }
1021 
1022  }
1023 
1024  public void loadManualParticles(SupervisedPickerMicrograph m, String file)
1025  {
1026  if (new File(file).exists() && MetaData.containsBlock(file, getParticlesBlockName(Format.Xmipp301)))
1027  {
1028 
1029  int x, y;
1030  ManualParticle particle;
1031 
1032  try
1033  {
1034  MetaData md = new MetaData(getParticlesBlock(file));
1035 
1036  for (long id : md.findObjects())
1037  {
1038  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
1039  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
1040  particle = new ManualParticle(x, y, this, m);
1041  m.addManualParticle(particle, this);
1042  }
1043  md.destroy();
1044  }
1045  catch (Exception e)
1046  {
1047  getLogger().log(Level.SEVERE, e.getMessage(), e);
1048  throw new IllegalArgumentException(e.getMessage());
1049  }
1050  }
1051  }
1052 
1062  public void trainAndAutopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph trainmic)
1063  {
1064  frame.getCanvas().setEnabled(false);
1065  XmippWindowUtil.blockGUI(frame, "Training and Autopicking...");
1066  // Change the state of the micrograph and save changes
1067  micrograph.setState(MicrographState.Supervised);
1068  saveData(micrograph);
1069  setChanged(false);
1070  // Create the metadata with each micrograph and its .pos file
1071  // Add all micrographs with manual particles except the train
1072  // micrograph
1073  ArrayList<MDRow> trainRows = new ArrayList<MDRow>();
1074  for (SupervisedPickerMicrograph m : micrographs)
1075  {
1076  if (m.hasManualParticles() && !m.equals(trainmic))
1077  addMicrographPos(trainRows, m);
1078  }
1079  // Add the train micrograph as the last one
1080 
1081  addMicrographPos(trainRows, trainmic);
1082 
1083  new Thread(new TrainRunnable(frame, trainRows.toArray(new MDRow[]{}), trainmic), "TrainAndAutopick").start();
1084  }
1085 
1087  private void addMicrographPos(List<MDRow> trainRows, SupervisedPickerMicrograph micrograph)
1088  {
1089  String posfile = getOutputPath(micrograph.getPosFile());
1090  MDRow row = new MDRow();
1091  row.setValueString(MDLabel.MDL_MICROGRAPH, micrograph.getFile());
1092  row.setValueString(MDLabel.MDL_MICROGRAPH_PARTICLES, posfile);
1093  trainRows.add(row);
1094 
1095  }
1096 
1097  @Override
1098  public int getParticlesCount() {
1099  return getManualParticlesNumber() + getAutomaticParticlesNumber();
1100  }
1101 
1102  public void loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
1103  {
1104  Rectangle rectangle = micrograph.getRectangle();
1105  int x, y;
1106  double cost;
1107  AutomaticParticle ap;
1108  for (Particle row: autopickRows)
1109  {
1110  x = row.getX();
1111  y = row.getY();
1112  cost = row.getCost();
1113  ap = new AutomaticParticle(x, y, SupervisedParticlePicker.this, micrograph, cost, false);
1114  if (rectangle != null && rectangle.contains(new Point(x, y)))
1115  {
1116  ap.setDeleted(true);
1117  ap.setCost(-1);
1118  }
1119  micrograph.addAutomaticParticle(ap);
1120  }
1121  }
1122 
1123 
1124  public void autopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph next)
1125  {
1126  frame.getCanvas().setEnabled(false);
1127  XmippWindowUtil.blockGUI(frame, "Autopicking...");
1128 
1129  try {
1130  new Thread(new AutopickRunnable(frame, next), "Autopick").start();
1131  }catch (Exception e){
1132  this.logger.log(Level.SEVERE,"Autopick thread failed.");
1133  }
1134 
1135 
1136  }
1137 
1138  public Classifier getClassifier() {
1139  return classifier;
1140  }
1141 
1142 
1143 
1144  public void correctAndAutopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph current, SupervisedPickerMicrograph next)
1145  {
1146  current.setState(MicrographState.Corrected);
1147  if (getMode() == Mode.Supervised && next.getState() == MicrographState.Available)
1148  next.setState(MicrographState.Supervised);
1149  saveData(current);
1150 
1151 
1152  MDRow[] autoRows = getAutomaticRows(current);
1153  MDRow[] addedRows = getAddedRows(current);
1154  frame.getCanvas().setEnabled(false);
1155 
1156  boolean isautopick = getMode() == Mode.Supervised && next.getState() == MicrographState.Available;
1157  // Show progress wheel
1158  if(isautopick)
1159  XmippWindowUtil.blockGUI(frame, "Correcting and Autopicking...");
1160  else
1161  XmippWindowUtil.blockGUI(frame, "Correcting ...");
1162 
1163  try {
1164  new Thread(new CorrectAndAutopickRunnable(frame, addedRows, autoRows, next), "CorrectAndAutopick").start();
1165  }catch (Exception e){
1166  this.logger.log(Level.SEVERE,"Correct and Autopick thread failed.");
1167  }
1168 
1169  }
1170 
1171  private MDRow[] getAddedRows(SupervisedPickerMicrograph m)
1172  {
1173  Rectangle correctout = m.getRectangle();
1174  ArrayList<MDRow> rows = new ArrayList<MDRow>();
1175  MDRow row;
1176  for (ManualParticle p : m.getManualParticles())
1177  if (correctout == null || !correctout.contains(new Point(p.getX(), p.getY())))
1178  {
1179  row = new MDRow();
1180  row.setValueInt(MDLabel.MDL_XCOOR, p.getX());
1181  row.setValueInt(MDLabel.MDL_YCOOR, p.getY());
1182  rows.add(row);
1183  }
1184  return rows.toArray(new MDRow[]{});
1185  }
1186  // Returns all automatic rows that matches the conditions, threshold is taken into account.
1187  private MDRow[] getAutomaticRows(SupervisedPickerMicrograph m)
1188  {
1189  ArrayList<MDRow> rows = new ArrayList<MDRow>();
1190  MDRow row;
1191  try
1192  {
1193 
1194  for (AutomaticParticle p : m.getAutomaticParticles())
1195  {
1196  row = new MDRow();
1197  row.setValueInt(MDLabel.MDL_XCOOR, p.getX());
1198  row.setValueInt(MDLabel.MDL_YCOOR, p.getY());
1199  row.setValueDouble(MDLabel.MDL_COST, p.getCost());
1200  // row.setValueInt(MDLabel.MDL_ENABLED, p.isDeleted()? -1: 1);
1201  row.setValueInt(MDLabel.MDL_ENABLED, p.isUnavailable()? -1: 1);
1202  rows.add(row);
1203  }
1204  }
1205  catch (Exception e)
1206  {
1207  getLogger().log(Level.SEVERE, e.getMessage(), e);
1208  throw new IllegalArgumentException(e.getMessage());
1209  }
1210  return rows.toArray(new MDRow[]{});
1211  }
1212 
1213 
1214  public void resetMicrograph(SupervisedPickerMicrograph micrograph)
1215  {
1216  micrograph.getManualParticles().clear();
1217  micrograph.getAutomaticParticles().clear();
1218  micrograph.setState(MicrographState.Available);
1219  micrograph.setThreshold(0);
1220  micrograph.resetParticlesRectangle();
1221  new File(getOutputPath(micrograph.getPosFile())).delete();
1222 
1223  }
1224 
1225  //This method will only be called from the interface if xmipp picker is used
1226  public void correct()
1227  {
1228  micrograph.setState(MicrographState.Corrected);
1229  saveData(micrograph);
1230  MDRow[] manualRows = getAddedRows(micrograph);
1231  MDRow[] autoRows = getAutomaticRows(micrograph);
1232  ((PickingClassifier)classifier).correct(manualRows, autoRows);
1233  }
1234 
1235  public int getParticlesThreshold() {
1236  return classifier.getTrainingParticlesMinimum();
1237  }
1238 
1239 
1240  public void updateTemplatesStack(boolean resize)
1241  {
1242  updateTemplatesStack(getTemplatesNumber(), resize);
1243  }
1244 
1245  public void updateTemplatesStack(int num, boolean resize)
1246  {
1247  if(mode != Mode.Manual)
1248  return;
1249  initTemplates(num);//to avoid any error with templates while updating
1250  new UpdateTemplatesTask(resize).execute();
1251  }
1252 
1253  public void setTemplatesDialog(TemplatesJDialog d)
1254  {
1255  dialog = d;
1256  }
1257 
1258  public class UpdateTemplatesTask extends SwingWorker<String, Object>
1259  {
1260  private final boolean resize;
1261  public UpdateTemplatesTask(boolean resize)
1262  {
1263  this.resize = resize;
1264  }
1265 
1266  @Override
1267  protected String doInBackground() throws Exception
1268  {
1269  try
1270  {
1271  if(uttask != null)
1272  uttask.cancel(true);
1273  uttask = this;
1274 
1275 
1276  ImageGeneric templates = new ImageGeneric(ImageGeneric.Float);
1277  templates.resize(getSize(), getSize(), 1, getTemplatesNumber());
1278 
1279  ImageGeneric igp;
1280  List<ManualParticle> particles;
1281 
1282  ManualParticle particle;
1283  double[] align;
1284 
1285  //FIXME: the template update needs to be done in a
1286  // more efficient way, now we are using this maxcount
1287  // to limit the number of particles used in the update
1288  int count = 0;
1289  int maxcount = 50;
1290  //FIXME: This is a tweak to avoid losing time with big particles
1291  if (getSize() > 256)
1292  maxcount = 10;
1293  float[] matrix;
1294  int templateindex = 0;
1295  for (SupervisedPickerMicrograph m : getMicrographs())
1296  {
1297  particles = m.getManualParticles();
1298  for (int i = 0; i < particles.size(); i++)
1299  {
1300  if(isCancelled())
1301  return null;
1302  if(count < maxcount)
1303  {
1304  particle = particles.get(i);
1305  if(resize)
1306  particle.resetImage();
1307  igp = particle.getImageGeneric();
1308  if (templateindex < getTemplatesNumber())
1309  {
1310  matrix = igp.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE);
1311  templates.setArrayFloat(matrix, ImageGeneric.FIRST_IMAGE + templateindex, ImageGeneric.FIRST_SLICE);
1312  templateindex ++;
1313  }
1314  else
1315  {
1316  align = templates.alignImage(igp);
1317  particle.setLastalign(align);
1318  templates.applyAlignment(igp, particle.getTemplateIndex(), particle.getTemplateRotation(), particle.getTemplateTilt(), particle.getTemplatePsi());
1319  }
1320  count++;
1321  }
1322 
1323  }
1324  }
1325 
1326  updateTemplates(templates, templateindex);
1327  }
1328  catch (Exception e)
1329  {
1330  e.printStackTrace();
1331  throw new IllegalArgumentException(e);
1332  }
1333  return "";
1334  }
1335 
1336  @Override
1337  protected void done() {
1338  if(dialog != null && dialog.isVisible())
1339  dialog.loadTemplates(true);
1340  }
1341 
1342  }
1343 
1344  public boolean isCorrectPending()//TO BE COMPLETED
1345  {
1346  return getMode() == Mode.Supervised && getMicrograph().getState() == MicrographState.Supervised && isChanged();
1347  }
1348 
1349  public Color getAutomaticColor() {
1350  return getMode() == Mode.Automatic ? getColor() : moveColorHue(getColor(), 0.66f);
1351  }
1352 
1353  public Color getDeletedColor() {
1354 
1355  return moveColorHue(getColor(), 0.33f);
1356  }
1357 
1358  private Color moveColorHue(Color color, float hueValue){
1359  // Get saturation and brightness.
1360  float[] hsbVals = new float[3];
1361  Color.RGBtoHSB(color.getRed(), color.getGreen(), color.getBlue(), hsbVals);
1362 
1363  // Pass .5 (= 180 degrees) as HUE
1364  float newHue = hsbVals[0] - hueValue;
1365 
1366  if (newHue < 0) newHue = newHue + 1f;
1367 
1368  Color newColor = new Color(Color.HSBtoRGB(newHue, hsbVals[1], hsbVals[2]));
1369  return newColor;
1370  }
1371 
1372 }
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xmipp.jni.Particle.setCost
void setCost(double cost)
Definition: Particle.java:47
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xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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xmipp.jni.ImageGeneric.FIRST_SLICE
static final int FIRST_SLICE
Definition: ImageGeneric.java:9
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xmipp.jni.Classifier.setSize
abstract void setSize(int psize)
- -
xmipp.utils.XmippWindowUtil.blockGUI
static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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xmipp.jni.MDRow.setValueString
native boolean setValueString(int label, String value)
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xmipp.jni.ImageGeneric.getNDim
native long getNDim()
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xmipp.jni.MetaData.addObject
native long addObject()
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xmipp.jni.MetaData.setValueString
native boolean setValueString(int label, String value, long objId)
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.SupervisedParticlePicker
SupervisedParticlePicker(String selfile, String outputdir, ParticlePickerParams params)
Definition: SupervisedParticlePicker.java:67
- -
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.applyAlignment
synchronized void applyAlignment(ManualParticle particle, ImageGeneric igp, double[] align)
Definition: SupervisedParticlePicker.java:323
-
xmipp.jni.Particle.setX
void setX(int x)
Definition: Particle.java:30
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xmipp.viewer.particlepicker.ParticlePicker.detectFormat
Format detectFormat(String path, String preffix, StringBuffer suffix)
Definition: ParticlePicker.java:295
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xmipp.viewer.scipion.ScipionMetaData.getValueString
String getValueString(int label, long id)
Definition: ScipionMetaData.java:413
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xmipp.jni.Filename.join
static String join(String... paths)
Definition: Filename.java:473
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xmipp.jni.MetaData.write
native void write(String filename)
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xmipp.jni.MetaData.clear
native void clear()
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xmipp.jni.MDLabel.MDL_PICKING_AUTOPICKPERCENT
static final int MDL_PICKING_AUTOPICKPERCENT
< Micrograph state for particle picking
Definition: MDLabel.java:286
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xmipp.jni.MDLabel.MDL_PICKING_MICROGRAPH_STATE
static final int MDL_PICKING_MICROGRAPH_STATE
< State for particle picking
Definition: MDLabel.java:285
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importAllParticles
String importAllParticles(String file, float scale, boolean invertx, boolean inverty)
Definition: SupervisedParticlePicker.java:931
- -
xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MetaData.writeBlock
native void writeBlock(String filename)
-
xmipp.jni.MetaData.read
final void read(String filename)
Definition: MetaData.java:125
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xmipp.jni.MDLabel.MDL_COST
static final int MDL_COST
< Store a score for the coords. consensus (it will change the behavoir of the viewer) ...
Definition: MDLabel.java:46
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xmipp.jni.MetaData.getBlocksInMetaDataFile
static native String [] getBlocksInMetaDataFile(String filename)
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xmipp.jni.ImageGeneric.write
native void write(String filename)
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xmipp.jni.MDLabel.MDL_CTF_MODEL
static final int MDL_CTF_MODEL
< Parameters file for the CTF Model (std::string)
Definition: MDLabel.java:80
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xmipp.jni.MDLabel.MDL_PICKING_TEMPLATES
static final int MDL_PICKING_TEMPLATES
< Color for particle picking
Definition: MDLabel.java:283
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.SupervisedParticlePicker
SupervisedParticlePicker(String selfile, String outputdir, Integer threads, boolean fastmode, boolean incore, ParticlePickerParams params)
Definition: SupervisedParticlePicker.java:120
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFolder
String importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: SupervisedParticlePicker.java:777
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xmipp.jni.ImageGeneric.getStatistics
native double [] getStatistics()
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xmipp.viewer.JMetaDataIO.saveData
static void saveData(SupervisedPickerMicrograph m, String path)
Definition: JMetaDataIO.java:30
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xmipp.jni.ImageGeneric.setArrayFloat
native void setArrayFloat(float data[], long select_image, int slice)
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MetaData.containsBlock
static boolean containsBlock(String file, String block)
Definition: MetaData.java:230
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xmipp.utils.XmippDialog.showQuestion
static boolean showQuestion(JFrame parent, String message)
Definition: XmippDialog.java:258
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.jni.MetaData.size
native int size()
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.SupervisedParticlePicker
SupervisedParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params)
Definition: SupervisedParticlePicker.java:73
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromMd
String importParticlesFromMd(SupervisedPickerMicrograph m, MetaData md)
Definition: SupervisedParticlePicker.java:838
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFile
String importParticlesFromFile(String path, Format f, SupervisedPickerMicrograph m, float scale, boolean invertx, boolean inverty)
Definition: SupervisedParticlePicker.java:817
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xmipp.jni.MDLabel.MDL_PSD_ENHANCED
static final int MDL_PSD_ENHANCED
< A Power Spectrum Density file name (std::string)
Definition: MDLabel.java:309
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xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
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xmipp.jni.MDLabel.MDL_CTF_DEFOCUSV
static final int MDL_CTF_DEFOCUSV
< Defocus U (Angstroms)
Definition: MDLabel.java:87
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.addManualParticle
void addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:122
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xmipp.jni.MDLabel.MDL_MICROGRAPH_PARTICLES
static final int MDL_MICROGRAPH_PARTICLES
< Unique identifier of a movie.
Definition: MDLabel.java:231
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadAutomaticParticles
void loadAutomaticParticles(SupervisedPickerMicrograph m, String file)
Definition: SupervisedParticlePicker.java:766
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadParticles
void loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
Definition: SupervisedParticlePicker.java:1102
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xmipp.viewer.JMetaDataIO.saveConfig
static void saveConfig(SupervisedParticlePicker picker, String path)
Definition: JMetaDataIO.java:92
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.MetaData.setValueDouble
native boolean setValueDouble(int label, double value, long objId)
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.jni.ImageGeneric.resize
void resize(int w, int h)
Definition: ImageGeneric.java:90
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xmipp.utils.XmippMessage.getIllegalValueMsgWithInfo
static String getIllegalValueMsgWithInfo(String field, Object value, String message)
Definition: XmippMessage.java:79
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xmipp.jni.MetaData.firstObject
native long firstObject()
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xmipp.jni.ImageGeneric.applyAlignment
native void applyAlignment(ImageGeneric img, int index, double rot, double tilt, double psi)
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.trainAndAutopick
void trainAndAutopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph trainmic)
Definition: SupervisedParticlePicker.java:1062
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xmipp.jni.ImageGeneric.getRadialAvg
synchronized native void getRadialAvg(ImageGeneric radialimg)
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xmipp.jni.MetaData.getFilename
String getFilename()
Definition: MetaData.java:418
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xmipp.jni.MDLabel.MDL_IMAGE
static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
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xmipp.jni.MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE
static final int MDL_PICKING_AUTOPARTICLES_SIZE
< Particle size for particle picking
Definition: MDLabel.java:288
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xmipp.utils.XmippMessage.getOutOfBoundsMsg
static String getOutOfBoundsMsg(Object o)
Definition: XmippMessage.java:56
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadAutomaticParticles
void loadAutomaticParticles(SupervisedPickerMicrograph m, MetaData md)
Definition: SupervisedParticlePicker.java:729
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xmipp.jni.Classifier.getTrainingParticlesMinimum
abstract int getTrainingParticlesMinimum()
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.autopick
void autopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph next)
Definition: SupervisedParticlePicker.java:1124
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xmipp.jni.ImageGeneric.bestShift
native Particle bestShift(ImageGeneric img)
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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xmipp.jni.MDLabel.MDL_PICKING_STATE
static final int MDL_PICKING_STATE
< Number of templates
Definition: MDLabel.java:284
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.updateTemplates
synchronized void updateTemplates(ImageGeneric templates, int templateindex)
Definition: SupervisedParticlePicker.java:254
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xmipp.jni.MetaData.operate
native void operate(String operateStr)
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xmipp.jni.MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE
static final int MDL_PICKING_MANUALPARTICLES_SIZE
< Number of automatic particles picked
Definition: MDLabel.java:289
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xmipp.viewer.particlepicker.ParticlePicker.importSize
void importSize(String path, Format f, double scale)
Definition: ParticlePicker.java:643
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xmipp.jni.Particle.setY
void setY(int y)
Definition: Particle.java:38
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xmipp.jni.ImageGeneric.getArrayFloat
native float [] getArrayFloat(long select_image, int slice)
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.correctAndAutopick
void correctAndAutopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph current, SupervisedPickerMicrograph next)
Definition: SupervisedParticlePicker.java:1144
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xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromFile
void fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
Definition: ParticlePicker.java:497
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xmipp.jni.ImageGeneric.alignImage
synchronized native double [] alignImage(ImageGeneric img)
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xmipp.jni.ImageGeneric.Float
static final int Float
Definition: ImageGeneric.java:24
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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SupervisedPickerCanvas.java File Reference
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class  xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas
 
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package  xmipp.viewer.particlepicker.training.gui
 
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SupervisedPickerCanvas.java
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1 package xmipp.viewer.particlepicker.training.gui;
2 
3 import java.awt.*;
4 import java.awt.event.KeyEvent;
5 import java.awt.event.MouseEvent;
6 import java.util.List;
7 import javax.swing.SwingUtilities;
8 
9 
10 import xmipp.viewer.particlepicker.ParticlePickerCanvas;
11 import xmipp.viewer.particlepicker.PickerParticle;
12 import xmipp.viewer.particlepicker.training.model.AutomaticParticle;
13 import xmipp.viewer.particlepicker.training.model.CenterParticleTask;
14 import xmipp.viewer.particlepicker.training.model.ManualParticle;
15 import xmipp.viewer.particlepicker.training.model.Mode;
16 import xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask;
17 import xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker;
18 import xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph;
19 
20 public class SupervisedPickerCanvas extends ParticlePickerCanvas
21 {
22 
23  public static final int POLIGONAL_MODE_KEY = KeyEvent.VK_C;
24  private Point linearPickingStartPoint;
25 
26 
27  public SupervisedPickerCanvas(SupervisedPickerJFrame frame)
28  {
29  super(frame);
30 
31  active = getLastManualParticle();
32 
33  }
34 
35  protected ManualParticle getLastManualParticle(){
36 
37  if (getMicrograph().getParticles().isEmpty())
38  return null;
39  return getMicrograph().getLastAvailableParticle(getFrame().getThreshold());
40  }
41  @Override
42  public ManualParticle getActive(){
43  return (ManualParticle) active;
44  }
45 
46  protected ManualParticle getLastParticle(){
47  return getLastManualParticle();
48  }
49 
50 
51  public void mousePressed(MouseEvent e)
52  {
53  super.mousePressed(e);
54 
55  int x = offScreenX(e.getX());
56  int y = offScreenY(e.getY());
57 
58  if (frame.isPickingAvailable(e))
59  {
60  if (frame.isEraserMode(e)){
61  erase(e);
62  return;
63  }
64 
65  // Filament/linear picking
66  if (frame.isLinearMode()) {
67  linearPickingMousePressed(x,y, isKeyPressed(POLIGONAL_MODE_KEY));
68  return;
69  }
70 
71  ManualParticle p = getMicrograph().getParticle(x, y);
72  if (p == null)
73  p = getMicrograph().getAutomaticParticle(x, y, getFrame().getThreshold());
74 
75  if (p != null && SwingUtilities.isLeftMouseButton(e)){
76  active = p;
77  repaint();
78 
79  }else if (SwingUtilities.isLeftMouseButton(e)){
80  addParticle(x, y, true);
81  }
82  }
83  }
84 
85  protected void addParticle( int x, int y, boolean refresh) {
86 
87  ManualParticle p;
88  if (micrograph.fits(x, y, frame.getParticlePicker().getSize()))
89  {
90 
91  p = new ManualParticle(x, y, frame.getParticlePicker(), micrograph);
92  getMicrograph().addManualParticle(p, getParticlePicker());
93 
94  if(getFrame().centerParticle())
95  new CenterParticleTask(this, getParticlePicker(), p).execute();
96 
97  active = p;
98  if(picker.getMode() == Mode.Manual)
99  new ParticleToTemplatesTask(getActive()).execute();
100 
101  if (refresh) refresh();
102  }
103  }
104 
105  private void linearPickingMousePressed(int x, int y, boolean continuous){
106 
107  Point point = new Point(x,y);
108 
109  if (haveFirstPoint()) {
110  finishLinearPicking(point, continuous);
111  } else {
112  startLinearPicking(point);
113  }
114  }
115 
116  private boolean haveFirstPoint() {
117  return linearPickingStartPoint != null;
118  }
119 
120  private void startLinearPicking(Point point) {
121 
122  this.linearPickingStartPoint = point;
123  }
124 
125  private void finishLinearPicking(Point point, boolean continuous) {
126 
127  addParticlesInLine(point);
128 
129  // Start from here.
130  if (continuous) {
131  this.linearPickingStartPoint = point;
132  } else {
133  resetLinearPicking();
134  }
135 
136  }
137 
138  public void resetLinearPicking(){
139  this.linearPickingStartPoint = null;
140  }
141 
142  private void addParticlesInLine(Point endPoint) {
143 
144  // To be moved to the interface!!
145  int gap = this.getFrame().getStep();
146 
147  // Get the distance diff (x,y) between ent and start
148  double lengthX = endPoint.getX() - this.linearPickingStartPoint.getX();
149  double lengthY = endPoint.getY() - this.linearPickingStartPoint.getY();
150 
151  // Get the angle (tan-1: inverse)
152  double angle = Math.atan2(lengthY, lengthX);
153 
154  // Calculate the number length of the line
155  double lineLength = Math.sqrt(Math.pow(lengthY,2) + Math.pow(lengthX,2));
156 
157  // Calculate number of segments for the iteration
158  int segmentsNum = (int) Math.round(lineLength/gap);
159 
160  double actualGap = lineLength/segmentsNum;
161 
162  // Now create as one particle each segment of size "gap"
163  for (int step = 0; step <= segmentsNum; step++){
164 
165  // Calculate the X
166  int x = (int)Math.round(this.linearPickingStartPoint.getX() + (Math.cos(angle)*step*actualGap));
167  int y = (int)Math.round(this.linearPickingStartPoint.getY() + (Math.sin(angle)*step*actualGap));
168 
169  addParticle(x,y,step==segmentsNum);
170 
171  }
172 
173  }
174 
178  @Override
179  public void mouseDragged(MouseEvent e)
180  {
181 
182  super.mouseDragged(e);
183  if (SwingUtilities.isLeftMouseButton(e))
184  {
185  int x = offScreenX(e.getX());
186  int y = offScreenY(e.getY());
187  if (frame.isPickingAvailable(e))
188  {
189  if (frame.isEraserMode(e))
190  {
191  erase(e);
192  return;
193  }
194  if (active == null)
195  return;
196 
197  ManualParticle activeParticle = getActive();
198 
199  if (!micrograph.fits(x, y, activeParticle.getParticlePicker().getSize()))
200  return;
201  if (active instanceof AutomaticParticle)
202  {
203  getMicrograph().removeParticle(activeParticle, getParticlePicker());
204  active = new ManualParticle(activeParticle.getX(), activeParticle.getY(), picker, micrograph);
205  getMicrograph().addManualParticle((ManualParticle) active, getParticlePicker());
206  refresh();
207 
208  }else{
209  setActiveMoved(true);
210  moveActiveParticle(x, y);
211  }
212 
213  manageActive(x, y);
214 
215  }
216  }
217  }
218 
219  @Override
220  public void mouseReleased(MouseEvent e)
221  {
222 
223  super.mouseReleased(e);
224  int x = offScreenX(e.getX());
225  int y = offScreenY(e.getY());
226  if (frame.isPickingAvailable(e))
227  {
228  if (frame.isEraserMode(e))
229  {
230  erase(e);
231  return;
232  }
233  //deleting when mouse released, takes less updates to templates and frame
234  if (active != null && SwingUtilities.isLeftMouseButton(e) && e.isShiftDown())
235  {
236  getMicrograph().removeParticle(getActive(), getParticlePicker());
237  active = getLastManualParticle();
238  refresh();
239 
240  }
241  else
242  manageActive(x, y);
243  if (activemoved)
244  {
245  setActiveMoved(false);
246  if(picker.getMode() == Mode.Manual)
247 // TasksManager.getInstance().addTask(new ParticleToTemplatesTask(active));
248  new ParticleToTemplatesTask(getActive()).execute();
249  }
250  }
251  }
252 
253  public void manageActive(int x, int y)
254  {
255 
256  ManualParticle activeParticle = getActive();
257 
258  if (!activemoved)
259  return;
260 
261  if (!micrograph.fits(x, y, activeParticle.getSize()))
262  return;
263 
264  if (active instanceof AutomaticParticle && !((AutomaticParticle) active).isDeleted())
265  {
266 
267  getMicrograph().removeParticle(activeParticle, getParticlePicker());
268  active = new ManualParticle(activeParticle.getX(), activeParticle.getY(), activeParticle.getParticlePicker(), micrograph);
269  getMicrograph().addManualParticle(activeParticle, getParticlePicker());
270  repaint();
271  }
272  else
273  {
274  //changing particle position requires to remove it from template and add it again
275  moveActiveParticle(x, y);
276  repaint();
277 
278  }
279  frame.setChanged(true);
280  }
281 
282  protected void doCustomPaint(Graphics2D g2)
283  {
284 
285  List<ManualParticle> particles;
286  int index;
287  SupervisedParticlePicker picker = getParticlePicker();
288  Color color = picker.getColor();
289  Color autoColor = picker.getAutomaticColor();
290  Color delColor = picker.getDeletedColor();
291  if (!getMicrograph().isEmpty()) {
292  particles = getMicrograph().getManualParticles();
293  g2.setColor(color);
294 
295  for (index = 0; index < particles.size(); index++)
296  drawShape(g2, particles.get(index), false, thinContinuousSt);
297 
298  List<AutomaticParticle> autoparticles = getMicrograph().getAutomaticParticles();
299  for (AutomaticParticle autoparticle : autoparticles)
300  if (!autoparticle.isDeleted() && autoparticle.getCost() >= getFrame().getThreshold()){
301  g2.setColor(autoColor);
302  drawShape(g2, autoparticle, false, thinContinuousSt);
303  }else if (autoparticle.isUnavailable() && picker.isShowDeleted()) {
304  g2.setColor(delColor);
305  drawShape(g2, autoparticle, false, thinContinuousSt);
306  }
307  }
308  if (active != null)
309  {
310  boolean isauto = active instanceof AutomaticParticle;
311 
312  color = isauto? Color.red.darker(): Color.red;
313  g2.setColor(color);
314  drawShape(g2, getActive(), true, activest);
315  }
316  Rectangle autopickout = getMicrograph().getRectangle();
317  if (autopickout != null && getMicrograph().hasManualParticles())
318  {
319  g2.setColor(Color.yellow);
320  g2.setStroke(continuousst);
321  int x = getXOnImage((int) autopickout.getX());
322  int y = getYOnImage((int) autopickout.getY());
323  g2.drawRect(x, y, (int) (autopickout.getWidth() * magnification), (int) (autopickout.getHeight() * magnification));
324  }
325  }
326 
327 
328 
329  @Override
330  public void refreshActive(PickerParticle p)
331  {
332  if (p == null)
333  // active = null;
334  active = getLastParticle();
335  else
336  active = p;
337  repaint();
338 
339  }
340 
341  @Override
342  public SupervisedPickerJFrame getFrame()
343  {
344  return (SupervisedPickerJFrame)frame;
345  }
346 
347  @Override
348  protected void removeParticle(PickerParticle particleToRemove) {
349  getMicrograph().removeParticle(particleToRemove,getParticlePicker());
350  }
351 
352  @Override
353  public SupervisedPickerMicrograph getMicrograph()
354  {
355  return (SupervisedPickerMicrograph)micrograph;
356  }
357 
358 
359  @Override
360  public SupervisedParticlePicker getParticlePicker()
361  {
362  // TODO Auto-generated method stub
363  return (SupervisedParticlePicker)picker;
364  }
365 
366 
367  public void keyPressed(KeyEvent e){
368 
369  super.keyPressed(e);
370 
371  if (e.getKeyCode() == KeyEvent.VK_ESCAPE){
372 
373  if (haveFirstPoint()){
374  resetLinearPicking();
375  }
376  }
377  }
378 
379  public void mouseMoved(MouseEvent e) {
380  super.mouseMoved(e);
381 
382  if (getFrame().isLinearMode())
383  paintLine(e);
384  }
385 
386  private void paintLine(MouseEvent e){
387 
388  if (haveFirstPoint()){
389 
390  Graphics g = this.getGraphics();
391 
392  // Repaint
393  this.paint(g);
394  // Draw a line from the first point to the current mouse cursor point.
395 
396  g.setColor(Color.YELLOW);
397  g.drawLine(getXOnImage(this.linearPickingStartPoint.x), getYOnImage(this.linearPickingStartPoint.y), e.getX(),e.getY());
398  }
399 
400  }
401 
402 }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.setChanged
abstract void setChanged(boolean changed)
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.addManualParticle
void addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:122
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.removeParticle
void removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:140
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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package  xmipp.viewer.particlepicker.training.gui
 
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SupervisedPickerJFrame.java
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1 package xmipp.viewer.particlepicker.training.gui;
2 
3 import xmipp.jni.Classifier;
4 import xmipp.jni.Classifier.Parameter;
5 import xmipp.utils.*;
6 import xmipp.viewer.ctf.CTFAnalyzerJFrame;
7 import xmipp.viewer.particlepicker.*;
8 import xmipp.viewer.particlepicker.training.model.*;
9 
10 import javax.swing.*;
11 import javax.swing.event.ChangeEvent;
12 import javax.swing.event.ChangeListener;
13 import javax.swing.table.TableColumnModel;
14 import java.awt.*;
15 import java.awt.event.*;
16 import java.io.File;
17 import java.text.NumberFormat;
18 import java.util.HashMap;
19 import java.util.List;
20 import java.util.logging.Level;
21 import java.util.logging.Logger;
22 
23 public class SupervisedPickerJFrame extends ParticlePickerJFrame {
24 
25  public static final Color THRESHOLD_LABEL_CHANGE_COLOR = Color.DARK_GRAY;
26  protected SupervisedPickerCanvas canvas;
27  protected JMenuBar mb;
28  protected SupervisedParticlePicker ppicker;
29  protected JPanel micrographpn;
30  protected MicrographsTableModel micrographsmd;
31 
32  protected float positionx;
33  protected JButton iconbt;
34  protected JLabel manuallb;
35  protected JLabel autolb;
36  protected JLabel savedlb;
37 
38  protected JSlider thresholdsl;
39  protected JPanel thresholdpn;
40  protected JFormattedTextField thresholdtf;
41 
42  protected JToggleButton centerparticlebt;
43  protected JMenuItem exportmi;
44  protected JToggleButton autopickchb;
45  protected JPanel sppickerpn;
46 
47  protected JMenuItem templatesmi;
48  TemplatesJDialog templatesdialog;
49  protected JLabel checkpercentlb;
50  protected JFormattedTextField autopickpercenttf;
51  protected JLabel thresholdlb;
52  protected JPanel gpickerpn;
53  private JButton autopickbt;
54  private HashMap<JTextField, Parameter> paramtfs;
55 
56  @Override
57  public SupervisedParticlePicker getParticlePicker() {
58  return ppicker;
59  }
60 
61  public SupervisedPickerJFrame(SupervisedParticlePicker picker) {
62 
63  super(picker);
64  try {
65  this.ppicker = picker;
66  initComponents();
67  setChanged(false);
68  Classifier c = ppicker.getClassifier();
69  if(c instanceof GenericClassifier) {
70  GenericClassifier gc = (GenericClassifier)c;
71  if (!gc.hasInitialCoordinates())
72  ppicker.autopick(this, getMicrograph());
73  }
74  } catch (IllegalArgumentException ex) {
75  //close();
76  throw ex;
77  }
78  }
79 
80  public boolean isCenterParticle() {
81  return centerparticlebt.isSelected();
82  }
83 
84  public boolean centerParticle() {
85  return centerparticlebt.isSelected() && isNormalMode();
86  }
87 
88  @Override
89  public ParticlesDialog initParticlesJDialog() {
90  return new ParticlesDialog(this);
91  }
92 
93  public SupervisedPickerMicrograph getMicrograph() {
94  return ppicker.getMicrograph();
95  }
96 
97  public double getThreshold() {
98  if (thresholdsl == null) {
99  return 0;
100  }
101  return thresholdsl.getValue() / 100.0;
102  }
103 
104  @Override
105  public List<? extends ManualParticle> getAvailableParticles() {
106  return getMicrograph().getAvailableParticles(getThreshold());
107  }
108 
109  public String importParticlesFromFile(Format format, String file, float scale, boolean invertx, boolean inverty) {
110  if (!new File(file).exists()) {
111  throw new IllegalArgumentException(XmippMessage.getNoSuchFieldValueMsg("file", file));
112  }
113  String result = "";
114  if (ppicker.isReviewFile(file)) {
115  result = ppicker.importAllParticles(file, scale, invertx, inverty);
116  ppicker.saveAllData();
117  } else {
118  result = importMicrographParticles(format, file, scale, invertx, inverty);
119  }
120  setChanged(false);
121  getCanvas().repaint();
122  updateMicrographsModel();
123  updateSize(ppicker.getSize());//will also update templates
124  canvas.refreshActive(null);
125 
126  return result;
127  }
128 
129  public String importMicrographParticles(Format format, String file, float scale, boolean invertx, boolean inverty) {
130 
131  String filename = Micrograph.getName(file, 1);
132  // validating you want use this file for this micrograph with different
133  // name
134  if (!filename.equals(getMicrograph().getName())) {
135  String msg = String.format("Are you sure you want to import data from file\n%s to micrograph %s ?", file, getMicrograph().getName());
136  boolean importdata = XmippDialog.showQuestion(this, msg);
137  if (!importdata) {
138  return null;
139  }
140  }
141  ppicker.resetMicrograph(getMicrograph());
142  String result = ppicker.importParticlesFromFile(file, format, getMicrograph(), scale, invertx, inverty);
143  ppicker.saveData(getMicrograph());
144  return result;
145  }
146 
147  public void updateSize(int size) {
148  try {
149 
150  super.updateSize(size);
151  ppicker.updateTemplatesStack(true);
152 
153 
154  } catch (Exception e) {
155  e.printStackTrace();
156  XmippDialog.showError(this, e.getMessage());
157  }
158  }
159 
160  @Override
161  public String importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty) {
162  String result = "";
163 
164  if (new File(dir).isDirectory()) {
165  result = ppicker.importParticlesFromFolder(dir, format, preffix, suffix, scale, invertx, inverty);
166  boolean resize = ((Integer)sizetf.getValue()).intValue() != ppicker.getSize();
167  sizetf.setValue(ppicker.getSize());
168  getCanvas().repaint();
169  updateMicrographsModel(true);
170  getCanvas().refreshActive(null);
171  ppicker.updateTemplatesStack(resize);
172 
173 
174  } else // only can choose file if TrainingPickerJFrame instance
175  {
176  result = importParticlesFromFile(format, dir, scale, invertx, inverty);
177  }
178  return result;
179 
180  }
181 
182 
183  protected void initializeCanvas() {
184 
185  if (canvas == null) {
186  canvas = new SupervisedPickerCanvas(this);
187  } else {
188  canvas.updateMicrograph();
189  }
190 
191  }
192 
193  protected void formatMicrographsTable() {
194  int totalWidth = 630;
195  int micWidth = 440;
196 
197  if (ppicker.containsPSD()) // shrink columns to make space for PSD
198  {
199  totalWidth -= 115;
200  micWidth -= 115;
201  }
202 
203  micrographstb.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
204 
205  TableColumnModel tcm = micrographstb.getColumnModel();
206  tcm.getColumn(0).setPreferredWidth(40);
207 
208  if (ppicker.hasDefocusU())
209  {
210  micWidth -= 70;
211  tcm.getColumn(4).setPreferredWidth(70);
212  }
213 
214  tcm.getColumn(1).setPreferredWidth(micWidth);
215  tcm.getColumn(2).setPreferredWidth(70);
216  tcm.getColumn(3).setPreferredWidth(80);
217  micrographstb.setPreferredScrollableViewportSize(new Dimension(totalWidth, 304));
218  micrographstb.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
219  int index = ppicker.getMicrographIndex();
220  if (index != -1) {
221  micrographstb.setRowSelectionInterval(index, index);
222  }
223  }
224 
225  void updateColor() {
226  color = ppicker.getColor();
227  colorbt.setIcon(new ColorIcon(color));
228  canvas.repaint();
229  ppicker.saveConfig();
230  }
231  public void setChanged(boolean changed) {
232  ppicker.setChanged(changed);
233  savemi.setEnabled(changed);
234  savebt.setEnabled(changed);
235  }
236 
237  public void setThresholdChanged(boolean changed){
238 
239  if (changed){
240  this.thresholdlb.setForeground(THRESHOLD_LABEL_CHANGE_COLOR);
241  this.setChanged(true);
242  } else {
243  this.thresholdlb.setForeground(Color.BLACK);
244  }
245  }
246  public boolean hasThresholdChanged(){
247  return this.thresholdlb.getForeground() == THRESHOLD_LABEL_CHANGE_COLOR;
248  }
249 
250  public void setSaved(boolean saved) {
251  ppicker.setSaved(saved);
252  // Do not print anything: for debugging --> savedlb.setText(saved?"Saved":"");
253  }
254 
255  public void updateMicrographsModel(boolean all) {
256 
257  if (particlesdialog != null)
258  loadParticles(false);
259  int index = ppicker.getMicrographIndex();
260 
261  if (all)
262  micrographsmd.fireTableRowsUpdated(0, micrographsmd.getRowCount() - 1);
263  else
264  micrographsmd.fireTableRowsUpdated(index, index);
265 
266  micrographstb.setRowSelectionInterval(index, index);
267  manuallb.setText(Integer.toString(ppicker.getManualParticlesNumber()));
268  autolb.setText(Integer.toString(ppicker.getAutomaticParticlesNumber()));
269  }
270 
271  public ParticlePickerCanvas getCanvas() {
272  return canvas;
273  }
274 
275  private void initComponents() {
276  try {
277 
278  setResizable(false);
279  setTitle();
280  initMenuBar();
281  setJMenuBar(mb);
282 
283  GridBagConstraints constraints = new GridBagConstraints();
284  constraints.insets = new Insets(0, 5, 0, 5);
285  constraints.anchor = GridBagConstraints.WEST;
286  setLayout(new GridBagLayout());
287 
288  centerparticlebt = new JToggleButton(bundle.getString("center"), XmippResource.getIcon("center.png"));
289  initToolBar();
290  centerparticlebt.setSelected(true);
291  tb.add(centerparticlebt);
292  add(tb, XmippWindowUtil.getConstraints(constraints, 0, 0, 2, 1, GridBagConstraints.WEST));
293 
294  //add(shapepn, XmippWindowUtil.getConstraints(constraints, 1, 1));
295 
296 
297  initSupervisedPickerPane();
298  if(!ppicker.getClassifier().needsTraining())
299  {
300  sppickerpn.setVisible(false);
301  initGenericPickerPane();
302  add(gpickerpn, XmippWindowUtil.getConstraints(constraints, 0, 3, 2, 1, GridBagConstraints.HORIZONTAL));
303  }
304  else
305  add(sppickerpn, XmippWindowUtil.getConstraints(constraints, 0, 3, 1, 1, GridBagConstraints.HORIZONTAL));
306  add(sppickerpn, XmippWindowUtil.getConstraints(constraints, 1, 3, 1, 1, GridBagConstraints.HORIZONTAL));
307  enableSupervised(ppicker.getMode() == Mode.Supervised);
308  initMicrographsPane();
309  add(micrographpn, XmippWindowUtil.getConstraints(constraints, 0, 4, 2, 1, GridBagConstraints.HORIZONTAL));
310  JPanel actionspn = new JPanel(new FlowLayout(FlowLayout.RIGHT));
311  actionspn.add(closebt);
312  actionspn.add(savebt);
313  actionspn.add(saveandexitbt);
314  add(actionspn, XmippWindowUtil.getConstraints(constraints, 0, 5, 2, 1, GridBagConstraints.HORIZONTAL));
315  if (ppicker.getMode() == Mode.ReadOnly) {
316  enableEdition(false);
317  }
318  pack();
319  positionx = 0.9f;
320  XmippWindowUtil.setLocation(positionx, 0.2f, this);
321  setVisible(true);
322  } catch (Exception e) {
323  e.printStackTrace();
324  throw new IllegalArgumentException(e.getMessage());
325  }
326  }
327 
328  void loadTemplates() {
329 
330  try {
331  if (templatesdialog == null) {
332  templatesdialog = new TemplatesJDialog(this);
333  ppicker.setTemplatesDialog(templatesdialog);
334  ParticleToTemplatesTask.setTemplatesDialog(templatesdialog);
335  } else {
336  templatesdialog.setVisible(true);
337  }
338  } catch (Exception e) {
339  XmippDialog.showError(this, e.getMessage());
340  }
341 
342  }
343 
344  private void initSupervisedPickerPane() {
345 
346  sppickerpn = new JPanel(new FlowLayout(FlowLayout.LEFT));
347  sppickerpn.setBorder(BorderFactory.createTitledBorder(bundle.getString("autopick")));
348  autopickchb = new JToggleButton("Activate Training", XmippResource.getIcon("pick.png"));
349  autopickchb.setSelected(ppicker.isAutopick());
350  autopickchb.setText(ppicker.isAutopick()? "Deactivate Training": "Activate Training");
351  autopickchb.addActionListener(new ActionListener() {
352 
353  @Override
354  public void actionPerformed(ActionEvent e) {
355  try {
356  boolean isautopick = autopickchb.isSelected();
357 
358  SupervisedPickerMicrograph trainmic = null;
359  if (isautopick) {
360  trainmic = getTrainMic();
361  isautopick = trainmic != null;
362  }
363  if (isautopick) {
364  ppicker.setMode(Mode.Supervised);
365  ppicker.trainAndAutopick(SupervisedPickerJFrame.this, trainmic);
366  setTitle();
367 
368  } else if (autopickchb.isSelected()) {
369  autopickchb.setSelected(false);
370  } else {
371  boolean ismanual = XmippDialog
372  .showQuestion(SupervisedPickerJFrame.this, "After this operation automatic particles will be converted to manual and classifier training lost. Are you sure you want to continue? ");
373  if (ismanual) {
374  ppicker.setMode(Mode.Manual);
375  resetbt.setEnabled(true);
376  ppicker.saveAllData();
377  updateMicrographsModel(true);
378  if (autopickchb.isSelected()) {
379  autopickchb.setSelected(false);
380  }
381  getMicrograph().resetParticlesRectangle();
382  canvas.refreshActive(null);
383  setTitle();
384  } else {
385  autopickchb.setSelected(true);
386  }
387  }
388 
389  ppicker.saveConfig();
390  enableSupervised(autopickchb.isSelected());
391  autopickchb.setText(autopickchb.isSelected()? "Deactivate Training": "Activate Training");
392 
393  } catch (Exception ex) {
394  ex.printStackTrace();
395  XmippDialog.showError(SupervisedPickerJFrame.this, ex.getMessage());
396  autopickchb.setSelected(false);
397  return;
398  }
399  }
400  });
401  sppickerpn.add(autopickchb);
402  initThresholdPane();
403  sppickerpn.add(thresholdpn);
404  checkpercentlb = new JLabel("Explore (%):");
405  sppickerpn.add(checkpercentlb);
406  autopickpercenttf = new JFormattedTextField(NumberFormat.getIntegerInstance());
407  autopickpercenttf.setColumns(3);
408  autopickpercenttf.setValue(ppicker.getAutopickpercent());
409  autopickpercenttf.setEnabled(ppicker.getMode() == Mode.Supervised || ppicker.getMode() == Mode.Manual);
410  autopickpercenttf.addActionListener(new ActionListener()
411  {
412 
413  @Override
414  public void actionPerformed(ActionEvent arg0)
415  {
416 
417  setAutopickPercent();
418 
419  }
420  });
421 
422  sppickerpn.add(autopickpercenttf);
423 
424  }
425 
426  protected void setAutopickPercent()
427  {
428  if (autopickpercenttf.getValue() == null || ((Number)autopickpercenttf.getValue()).intValue() <= 0)
429  {
430  XmippDialog.showInfo(this, XmippMessage.getEmptyFieldMsg("Check (%)"));
431  autopickpercenttf.setValue(getMicrograph().getAutopickpercent());
432  return;
433  }
434 
435  int autopickpercent = ((Number) autopickpercenttf.getValue()).intValue();
436  getMicrograph().setAutopickpercent(autopickpercent);
437  ppicker.setAutopickpercent(autopickpercent);
438  ppicker.saveConfig();
439  }
440 
441  protected void enableSupervised(boolean selected) {
442 
443  thresholdsl.setEnabled(selected);
444  thresholdlb.setEnabled(selected);
445  thresholdtf.setEnabled(selected);
446  sizelb.setEnabled(!selected);
447  // in sup mode size cannot be changed
448  sizetf.setEnabled(!selected);
449  sizelb.setEnabled(!selected);
450  importmi.setEnabled(!selected);
451  //autopickpercenttf.setEnabled(selected);
452 
453  pack();
454 
455  }
456 
457  public boolean isSupervised() {
458  return autopickchb.isSelected();
459  }
460 
461  protected void enableEdition(boolean isenable) {
462  super.enableEdition(isenable);
463  centerparticlebt.setEnabled(isenable);
464  if (ppicker.getMode() != Mode.Review) {
465  autopickchb.setEnabled(isenable);
466  thresholdpn.setEnabled(isenable);
467  }
468  saveandexitbt.setEnabled(isenable);
469  if(ppicker.isScipionSave())
470  {
471  Color color = isenable? XmippWindowUtil.firebrick: XmippWindowUtil.LIGHT_BLUE;
472  Color forecolor = isenable? Color.WHITE: Color.GRAY;
473  saveandexitbt.setBackground(color);
474  saveandexitbt.setForeground(forecolor);
475  }
476 
477  }
478 
479  public void initMenuBar() {
480  mb = new JMenuBar();
481 
482  // Setting menus
483  exportmi = new JMenuItem("Export coordinates...", XmippResource.getIcon("export_wiz.gif"));
484 
485  exportmi.addActionListener(new ActionListener() {
486 
487  @Override
488  public void actionPerformed(ActionEvent e) {
489  XmippFileChooser fc = new XmippFileChooser();
490  int returnVal = fc.showOpenDialog(SupervisedPickerJFrame.this);
491 
492  try {
493  if (returnVal == XmippFileChooser.APPROVE_OPTION) {
494  File file = fc.getSelectedFile();
495  ppicker.exportParticles(file.getAbsolutePath());
496  showMessage("Export successful");
497  }
498  } catch (Exception ex) {
499  showException(ex);
500  }
501  }
502  });
503  filemn.add(importmi);
504  if (ppicker.getMode() != Mode.Manual) {
505  importmi.setEnabled(false);
506  }
507  filemn.add(exportmi);
508  filemn.add(exitmi);
509 
510  JMenu windowmn = new JMenu(bundle.getString("window"));
511 
512  mb.add(filemn);
513  mb.add(filtersmn);
514  mb.add(windowmn);
515  mb.add(helpmn);
516  // importffilemi.setText("Import from File...");
517 
518  windowmn.add(pmi);
519  windowmn.add(ijmi);
520 
521 
522  templatesmi = new JMenuItem("Templates");
523  templatesmi.addActionListener(new ActionListener() {
524 
525  @Override
526  public void actionPerformed(ActionEvent arg0) {
527  loadTemplates();
528  }
529  });
530  windowmn.add(templatesmi);
531 
532  }
533 
534 
535 
536  private void initThresholdPane() {
537 
538  // Create the panel for the threshold
539  thresholdpn = new JPanel();
540 
541  // Add the threshold label
542  thresholdlb = new JLabel("Threshold:");
543  thresholdpn.add(thresholdlb);
544 
545  final ParticlePicker picker = this.getParticlePicker();
546  thresholdlb.addMouseListener(new MouseAdapter()
547  {
548  public void mouseClicked(MouseEvent e)
549  {
550  // Show deleted particles
551  if (e.getClickCount() == 3) {
552  picker.toggleShowDeleted();
553  }
554 
555  }
556  });
557 
558 
559  // Add and configure the threshold slider
560  thresholdsl = new JSlider(0, 100, 0);
561  thresholdsl.setPaintTicks(false);
562  thresholdsl.setMajorTickSpacing(5);
563  int height = (int) thresholdsl.getPreferredSize().getHeight();
564  thresholdsl.setPreferredSize(new Dimension(50, height));
565  thresholdpn.add(thresholdsl);
566 
567  // Add the threshold text field
568  thresholdtf = new JFormattedTextField(NumberFormat.getNumberInstance());
569  thresholdtf.setColumns(3);
570  thresholdtf.setValue(0);
571  thresholdpn.add(thresholdtf);
572  thresholdtf.addActionListener(new ActionListener() {
573 
574  @Override
575  public void actionPerformed(ActionEvent e) {
576 
577  double threshold = Double.parseDouble(thresholdtf.getText()) * 100;
578  setThresholdValue(threshold);
579 
580  }
581  });
582 
583  // Link the slider to the text field
584  thresholdsl.addChangeListener(new ChangeListener() {
585 
586  @Override
587  public void stateChanged(ChangeEvent e) {
588  if (thresholdsl.getValueIsAdjusting()) {
589  return;
590  }
591  double threshold = (double) thresholdsl.getValue() / 100;
592  if (getMicrograph().getThreshold() != threshold) {
593  thresholdtf.setText(String.format("%.2f", threshold));
594  setThresholdChanges();
595  }
596  }
597  });
598  }
599 
600  private void setThresholdValue(double threshold) {
601  if (Math.abs(threshold) <= 100) {
602  thresholdsl.setValue((int) threshold);
603  setThresholdChanges();
604  }
605  }
606 
607  private void setThresholdChanges() {
608 
609  getMicrograph().setThreshold(getThreshold());
610  updateMicrographsModel();
611  canvas.repaint();
612  if (particlesdialog != null) {
613  loadParticles(false);
614  }
615 
616  this.setThresholdChanged(true);
617  }
618 
619  private void initMicrographsPane() {
620  GridBagConstraints constraints = new GridBagConstraints();
621  constraints.insets = new Insets(0, 5, 0, 5);
622  constraints.anchor = GridBagConstraints.NORTHWEST;
623  micrographpn = new JPanel(new GridBagLayout());
624  micrographpn.setBorder(BorderFactory.createTitledBorder("Micrographs"));
625 
626 
627  if(ppicker.containsPSD())
628  {
629  iconbt = new JButton(Micrograph.getNoImageIcon());
630  iconbt.setToolTipText("Load CTF Profile");
631  iconbt.setBorderPainted(false);
632  iconbt.setContentAreaFilled(false);
633  iconbt.setFocusPainted(false);
634  iconbt.setOpaque(false);
635  iconbt.setMargin(new Insets(0, 0, 0, 0));
636  iconbt.addActionListener(new ActionListener() {
637 
638  @Override
639  public void actionPerformed(ActionEvent arg0) {
640  String psd = getMicrograph().getPSD();
641  String ctf = getMicrograph().getCTF();
642  if (psd != null && ctf != null) {
643  try {
644  new CTFAnalyzerJFrame(psd, ctf, psd);
645  } catch (Exception ex) {
646  Logger.getLogger(SupervisedPickerJFrame.class.getName()).log(Level.SEVERE, null, ex);
647  }
648  }
649 
650  }
651  });
652  micrographpn.add(iconbt, XmippWindowUtil.getConstraints(constraints, 1, 0, 1));
653  }
654 
655  JScrollPane sp = new JScrollPane();
656  micrographsmd = new MicrographsTableModel(this);
657  micrographstb.setModel(micrographsmd);
658  formatMicrographsTable();
659  sp.setViewportView(micrographstb);
660  micrographpn.add(sp, XmippWindowUtil.getConstraints(constraints, 0, 0, 1));
661 
662  // Info panel
663  JPanel infopn = new JPanel();
664  manuallb = new JLabel(Integer.toString(ppicker.getManualParticlesNumber()));
665  autolb = new JLabel(Integer.toString(ppicker.getAutomaticParticlesNumber()));
666  infopn.add(new JLabel("Manual:"));
667  infopn.add(manuallb);
668  infopn.add(new JLabel("Automatic:"));
669  infopn.add(autolb);
670 
671  // Saved
672  savedlb = new JLabel("");
673  infopn.add(savedlb);
674 
675  micrographpn.add(infopn, XmippWindowUtil.getConstraints(constraints, 0, 1, 1));
676  JPanel buttonspn = new JPanel(new FlowLayout(FlowLayout.LEFT));
677 
678  buttonspn.add(resetbt);
679  buttonspn.add(usezoombt);
680  micrographpn.add(buttonspn, XmippWindowUtil.getConstraints(constraints, 0, 2, 2));
681 
682  }
683 
684  protected synchronized void loadMicrograph() {
685 
686  if (micrographstb.getSelectedRow() == -1) {
687  return;// Probably from fireTableDataChanged raised
688  } // is same micrograph??
689  int micindex = ppicker.getMicrographIndex();
690 
691  int index = micrographstb.getSelectedRow();
692  if (micindex == index && canvas != null && canvas.getIw().isVisible()) {
693  return;
694  }
695 
696  // Save particles first before moving and loading the clicked micrograph.
697  if (ppicker.isChanged() && ppicker.getMode() != Mode.Supervised)
698  {
699  if (!saveData(false)) {
700  micrographstb.getSelectionModel().setSelectionInterval(micindex,micindex);
701  return;
702  }
703  }
704 
705  SupervisedPickerMicrograph next = ppicker.getMicrographs().get(index);
706  SupervisedPickerMicrograph current = getMicrograph();
707  current.resetParticlesRectangle();
708  if (!current.equals(next))// app just started
709  {
710  int result = tryCorrectAndAutopick(current, next);
711 
712  if (result == XmippQuestionDialog.CANCEL_OPTION) {
713  micrographstb.setRowSelectionInterval(micindex, micindex);
714  return;
715  }
716 
717  }
718  ppicker.setMicrograph(next);
719  ppicker.saveConfig();
720  Mode mode = ppicker.getMode();
721 
722  if (mode == Mode.Supervised) {
723  resetbt.setEnabled(next.getState() != MicrographState.Manual);
724  double threshold = next.getThreshold();
725  if(threshold == 0 && next.getAutomaticParticlesNumber() == 0)
726  {
727  threshold = current.getThreshold();
728  next.setThreshold(threshold);
729  this.setThresholdChanged(true);
730  }else{
731  this.setThresholdChanged(false);
732  }
733  thresholdsl.setValue((int) (threshold * 100));
734  thresholdtf.setValue(threshold);
735  }
736  else if (mode == Mode.Automatic) {
737  resetbt.setEnabled(false);
738  }
739 
740  initializeCanvas();
741  if(ppicker.containsPSD())
742  iconbt.setIcon(next.getCTFIcon());
743 
744  pack();
745 
746  if (particlesdialog != null) {
747  loadParticles(false);
748  }
749 
750  }
751 
752  private int tryCorrectAndAutopick(SupervisedPickerMicrograph current, SupervisedPickerMicrograph next) {
753  int result = 3;
754 
755  boolean isautopick = (ppicker.getMode() == Mode.Supervised || ppicker.getMode() == Mode.Automatic) && next.getState() == MicrographState.Available;
756  if (ppicker.isCorrectPending()) {
757  // Do not ask...always correct ans autopick.
758  // String msg = String.format("Would you like to correct training with added and deleted particles from micrograph %s?", current.getName());
759  // result = XmippDialog.showQuestionYesNoCancel(this, msg);
760  result = XmippQuestionDialog.YES_OPTION;
761  //if (result == XmippQuestionDialog.YES_OPTION) {
762  ppicker.correctAndAutopick(this, current, next);
763  isautopick = false;
764  //}
765  //if (result == XmippQuestionDialog.CANCEL_OPTION)
766  // isautopick = false;
767  }
768  if (isautopick)// if not done before
769  {
770  ppicker.autopick(this, next);
771  }
772 
773  return result;
774  }
775 
776  protected void resetMicrograph() {
777  ppicker.resetMicrograph(getMicrograph());
778  canvas.refreshActive(null);
779  updateMicrographsModel();
780  ppicker.updateTemplatesStack(false);
781 
782  if (ppicker.getMode() == Mode.Supervised) {
783  ppicker.autopick(this, getMicrograph());
784  }
785  }
786 
787  public boolean isPickingAvailable(MouseEvent e) {
788  if (!super.isPickingAvailable(e)) {
789  return false;
790  }
791  return getMicrograph().getState() != MicrographState.Corrected;
792  }
793 
794  public SupervisedPickerMicrograph getTrainMic() {
795  String trainmsg = "Classifier training for autopick requires that the previous micrographs and the particle's region detected to be fully picked. "
796  + "Are you sure you want to continue?";
797  if (ppicker.getManualParticlesNumber() < ppicker.getParticlesThreshold()) {
798  XmippDialog.showInfo(this, String
799  .format("You should have at least %s particles to go to %s mode", ppicker.getParticlesThreshold(), Mode.Supervised));
800  return null;
801  }
802  boolean isvalidrect = false;
803  int index = micrographstb.getSelectedRow();
804  SupervisedPickerMicrograph rectmic = null;
805  while (index >= 0)
806  {
807  rectmic = ppicker.getMicrographs().get(index);
808  if (rectmic.hasManualParticles())
809  {
810  rectmic.initParticlesRectangle(ppicker);
811  isvalidrect = rectmic.isValid(ppicker);
812  if(isvalidrect)
813  break;
814  else
815  rectmic.resetParticlesRectangle();
816  }
817  index --;
818  }
819  if(index < 0)
820  {
821  index = micrographstb.getSelectedRow() + 1;
822  while (index < ppicker.getMicrographs().size())
823  {
824  rectmic = ppicker.getMicrographs().get(index);
825  if (rectmic.hasManualParticles())
826  {
827  rectmic.initParticlesRectangle(ppicker);
828  isvalidrect = rectmic.isValid(ppicker);
829  if(isvalidrect)
830  break;
831  }
832  index ++;
833  }
834  }
835 
836  if(index < 0 || index == ppicker.getMicrographs().size())
837  {
838  canvas.repaint();
839  XmippDialog.showError(this, "No valid training rectangle could be found in micrographs picked. Particles might be too few.");
840  rectmic.resetParticlesRectangle();
841  canvas.repaint();
842  return null;
843  }
844  trainmsg = "";
845  if(rectmic.equals(getMicrograph()))
846  {
847  canvas.repaint();
848  trainmsg += "Classifier requires that the region detected and the micrographs previously picked to be fully picked. "
849  + "Are you sure you want to continue?";
850  }
851  else
852  trainmsg += "Classifier requires that the micrographs previously picked to be fully picked. "
853  + "Are you sure you want to continue?";
854  int result = XmippDialog
855  .showQuestionYesNoCancel(this, trainmsg);
856  if (result == XmippQuestionDialog.CANCEL_OPTION) {
857  canvas.repaint();
858  rectmic.resetParticlesRectangle();
859  }
860  if(result != XmippQuestionDialog.YES_OPTION)
861  rectmic = null;
862  return rectmic;
863  }
864 
865 
866 
867  public void close() {
868  if (ppicker.isCorrectPending()) {
869  boolean iscorrect = XmippDialog.showQuestion(this, "Would you like to correct training with added and deleted particles?");
870  if (iscorrect) {
871  ppicker.correct();
872  }
873  }
874  super.close();
875  }
876 
877  public String getResetMsg() {
878  String msg = super.getResetMsg();
879  if (ppicker.getMode() == Mode.Supervised) {
880  msg += "\nParticles will be automatically picked again";
881  }
882  return msg;
883  }
884 
885 
886 
887  protected void initGenericPickerPane()
888  {
889  gpickerpn = new JPanel(new FlowLayout(FlowLayout.LEFT));
890  gpickerpn.setBorder(BorderFactory.createTitledBorder("Autopick"));
891  List<Classifier.Parameter> parameters = ppicker.getClassifier().getParams();
892  paramtfs = new HashMap<JTextField, Classifier.Parameter>();
893  JTextField tf;
894  JLabel lb;
895  for(Classifier.Parameter param: parameters)
896  {
897  lb = new JLabel(param.label);
898  lb.setToolTipText(param.help);
899  gpickerpn.add(lb);
900  tf = new JTextField(3);
901  tf.setToolTipText(param.help);
902  tf.setText(param.value);
903  tf.setActionCommand(param.name);
904  tf.addFocusListener(new FocusListener()
905  {
906 
907  @Override
908  public void focusLost(FocusEvent e)
909  {
910  if(e.isTemporary())
911  return;
912  JTextField tf = (JTextField)e.getComponent();
913  updateParam(tf);
914  }
915 
916  @Override
917  public void focusGained(FocusEvent e)
918  {
919  // TODO Auto-generated method stub
920 
921  }
922  });
923  tf.addActionListener(new ActionListener()
924  {
925  @Override
926  public void actionPerformed(ActionEvent e)
927  {
928  JTextField tf = (JTextField)e.getSource();
929  updateParam(tf);
930  for(SupervisedPickerMicrograph m: ppicker.getMicrographs())
931  ppicker.resetMicrograph(m);
932  ppicker.autopick(SupervisedPickerJFrame.this, getMicrograph());
933 
934  }
935  });
936  gpickerpn.add(tf);
937  paramtfs.put(tf, param);
938  if(param.name.equals("diameter") || param.name.equals("boxSize"))//classifier diameter and particle size are the same
939  updateSize(Integer.parseInt(tf.getText()));
940  }
941  autopickbt = XmippWindowUtil.getTextButton("Run", new ActionListener(){
942 
943  @Override
944  public void actionPerformed(ActionEvent arg0)
945  {
946  for(SupervisedPickerMicrograph m: ppicker.getMicrographs())
947  ppicker.resetMicrograph(m);
948  ppicker.autopick(SupervisedPickerJFrame.this, getMicrograph());
949 
950  }});
951  autopickbt.setBackground(XmippWindowUtil.firebrick);
952  autopickbt.setForeground(Color.WHITE);
953  gpickerpn.add(autopickbt);
954  }
955 
956  protected void updateParam(JTextField tf)
957  {
958  Classifier.Parameter param = paramtfs.get(tf);
959  if(param.value.equals(tf.getText()))
960  return;
961  if(param.name.equals("diameter") || param.name.equals("boxSize"))//classifier diameter and particle size are the same
962  updateSize(Integer.parseInt(tf.getText()));
963  param.value = tf.getText();
964  }
965  @Override
966  protected void showHideModeParameters(){
967  super.showHideModeParameters();
968  centerparticlebt.setVisible(isNormalMode());
969  }
970 
971 }
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xmipp.jni.Classifier.getParams
List< Classifier.Parameter > getParams()
Definition: Classifier.java:42
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xmipp.utils.XmippWindowUtil.firebrick
static final Color firebrick
Definition: XmippWindowUtil.java:57
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xmipp.viewer.particlepicker.Micrograph.getName
static String getName(String file, int level)
Definition: Micrograph.java:140
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFolder
String importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: SupervisedParticlePicker.java:777
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xmipp.utils.XmippWindowUtil.LIGHT_BLUE
static final Color LIGHT_BLUE
Definition: XmippWindowUtil.java:61
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.importParticlesFromFile
String importParticlesFromFile(Format format, String file, float scale, boolean invertx, boolean inverty)
Definition: SupervisedPickerJFrame.java:109
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xmipp.utils.XmippDialog.showQuestion
static boolean showQuestion(JFrame parent, String message)
Definition: XmippDialog.java:258
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFile
String importParticlesFromFile(String path, Format f, SupervisedPickerMicrograph m, float scale, boolean invertx, boolean inverty)
Definition: SupervisedParticlePicker.java:817
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.importMicrographParticles
String importMicrographParticles(Format format, String file, float scale, boolean invertx, boolean inverty)
Definition: SupervisedPickerJFrame.java:129
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boolean showInfo(String message)
Definition: XmippDialog.java:199
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static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.trainAndAutopick
void trainAndAutopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph trainmic)
Definition: SupervisedParticlePicker.java:1062
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xmipp.utils.XmippWindowUtil.getTextButton
static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.autopick
void autopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph next)
Definition: SupervisedParticlePicker.java:1124
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static String getNoSuchFieldValueMsg(String field, Object value)
Definition: XmippMessage.java:52
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xmipp.utils.XmippDialog.showQuestionYesNoCancel
static int showQuestionYesNoCancel(JFrame parent, String message)
Definition: XmippDialog.java:274
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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abstract void refreshActive(PickerParticle p)
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void correctAndAutopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph current, SupervisedPickerMicrograph next)
Definition: SupervisedParticlePicker.java:1144
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xmipp.utils.XmippMessage.getEmptyFieldMsg
static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.importParticles
String importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: SupervisedPickerJFrame.java:161
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SupervisedPickerMicrograph.java File Reference
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class  xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph
 
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package  xmipp.viewer.particlepicker.training.model
 
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SupervisedPickerMicrograph.java
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1 package xmipp.viewer.particlepicker.training.model;
2 
3 import java.io.File;
4 import java.util.ArrayList;
5 import java.util.List;
6 import xmipp.jni.Particle;
7 import xmipp.utils.XmippMessage;
8 import xmipp.viewer.particlepicker.CtfInfo;
9 import xmipp.viewer.particlepicker.Micrograph;
10 import xmipp.viewer.particlepicker.PickerParticle;
11 import java.awt.Rectangle;
12 
13 public class SupervisedPickerMicrograph extends Micrograph
14 {
15 
16  private boolean autopicking = false;
17  private List<ManualParticle> manualparticles;
18  private List<AutomaticParticle> autoparticles;
19  private MicrographState state;
20  private int autopickpercent;
21  private double threshold = 0.0;
22  private Rectangle rectangle;
23 
24  public double getThreshold() {
25  return threshold;
26  }
27 
28 
29 
30  public void setThreshold(double threshold) {
31  this.threshold = threshold;
32  }
33 
34 
35 
36  public SupervisedPickerMicrograph(String file, CtfInfo ctfInfo)
37  {
38  super(file, ctfInfo);
39 
40  this.manualparticles = new ArrayList<ManualParticle>();
41  this.autoparticles = new ArrayList<AutomaticParticle>();
42  state = MicrographState.Available;
43  }
44 
45 
46 
47 
48  public boolean isAutopicking()
49  {
50  return autopicking;
51  }
52 
53  public void setAutopicking(boolean autopicking)
54  {
55  this.autopicking = autopicking;
56  }
57 
58  public static String getName(String file)
59  {
60  String[] tokens = file.split(File.separator);
61  if (tokens.length < 2)
62  throw new IllegalArgumentException("Name for micrograph" + "is taken from parent dir, invalid path " + file);
63  return tokens[tokens.length - 2];
64  }
65 
66 
67 
68  public ManualParticle getParticle(int x, int y)
69  {
70  for (ManualParticle p : getManualParticles())
71  if (p.contains(x, y))
72  return p;
73  return null;
74  }
75 
76  public AutomaticParticle getAutomaticParticle(int x, int y, double threshold)
77  {
78  for (AutomaticParticle p : getAutomaticParticles())
79  if (!p.isDeleted() && p.getCost() >= threshold && p.contains(x, y))
80  return p;
81  return null;
82  }
83 
84 
85  public boolean hasManualParticles()
86  {
87  if (getManualParticles().size() > 0)
88  return true;
89  return false;
90 
91  }
92 
93  public void removeParticles(int x, int y, SupervisedParticlePicker ppicker)
94  {
95  List<ManualParticle> particles = new ArrayList<ManualParticle>();
96 
97  for (ManualParticle p : getManualParticles())
98  if (p.contains(x, y))
99  particles.add(p);
100  for (ManualParticle p : particles)
101  removeParticle(p, ppicker);
102  particles.clear();
103  for (AutomaticParticle p : getAutomaticParticles())
104  if (p.contains(x, y))
105  particles.add(p);
106 
107  for (ManualParticle p : particles)
108  removeParticle(p, ppicker);
109 
110  }
111 
112  public List<ManualParticle> getManualParticles()
113  {
114  return manualparticles;
115  }
116 
117  public List<AutomaticParticle> getAutomaticParticles()
118  {
119  return autoparticles;
120  }
121 
122  public void addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)
123  {
124  manualparticles.add(p);
125 
126  if (state == MicrographState.Available || state == MicrographState.Auto)
127  {
128  if (ppicker.getMode() == Mode.Manual)
129  state = MicrographState.Manual;
130  else if (ppicker.getMode() == Mode.Review)
131  state = MicrographState.Review;
132  else
133  throw new IllegalArgumentException(
134  String.format("Micrograph %s could not update its state to %s and can't keep previous state %s and have particles", getName(), state, MicrographState.Available));
135  }
136 
137 
138  }
139 
140  public void removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)
141  {
142  if (p == null)
143  throw new IllegalArgumentException(XmippMessage.getEmptyFieldMsg("particle"));
144  if (p instanceof AutomaticParticle)
145  {
146  if (ppicker.getMode() != Mode.Review)
147  ((AutomaticParticle) p).setDeleted(true);
148  else
149  autoparticles.remove(p);
150  // deleting could be the first thing to do after autopick, so I have
151  // to mark micrograph on this choice too
152  if (state == MicrographState.Auto && ppicker.getMode() == Mode.Review)
153  state = MicrographState.Review;
154  }
155  else
156  manualparticles.remove(p);
157 
158 
159  }
160 
161  public boolean hasAutomaticParticles()
162  {
163  return autoparticles.size() != 0;
164  }
165 
166  public boolean isEmpty()
167  {
168  return manualparticles.isEmpty() && autoparticles.isEmpty();
169  }
170 
171  public int getAutomaticParticlesNumber(double threshold)
172  {
173  if (autoparticles.isEmpty())
174  return 0;
175  return autoparticles.size() - getAutomaticParticlesDeleted(threshold);
176  }
177 
178  public int getAutomaticParticlesNumber()
179  {
180  if (autoparticles.isEmpty())
181  return 0;
182  return autoparticles.size() - getAutomaticParticlesDeleted();
183  }
184 
185  public synchronized void addAutomaticParticle(AutomaticParticle p)
186  {
187  autoparticles.add(p);
188 
189  }
190 
191 
192 
193  public MicrographState getState()
194  {
195  return state;
196  }
197 
198  public void setState(MicrographState state)
199  {
200  if (state == MicrographState.Available && !(manualparticles.isEmpty() || autoparticles.isEmpty()))
201  throw new IllegalArgumentException("Micrograph has data. Can not be " + MicrographState.Available);
202  this.state = state;
203  }
204 
205  public Mode getStep()
206  {
207  if (state == MicrographState.Manual)
208  return Mode.Manual;
209  if (state == MicrographState.Available)
210  return Mode.Available;
211  return Mode.Supervised;
212  }
213 
214  public int getAutomaticParticlesDeleted()
215  {
216  int count = 0;
217  for (AutomaticParticle p : autoparticles)
218  if (p.isDeleted())
219  count++;
220  return count;
221  }
222 
223 
224 
225  public synchronized int getAutomaticParticlesDeleted(double threshold)
226  {
227  int count = 0;
228  for (AutomaticParticle p : autoparticles)
229  if (p.isDeleted() || p.getCost() < threshold)
230  count++;
231  return count;
232  }
233 
234 
235  public List<ManualParticle> getParticles()
236  {
237  ArrayList<ManualParticle> result = new ArrayList<ManualParticle>();
238  result.addAll(manualparticles);
239  result.addAll(autoparticles);
240  return result;
241  }
242 
243  public List<ManualParticle> getAvailableParticles(double threshold)
244  {
245  ArrayList<ManualParticle> result = new ArrayList<ManualParticle>();
246  result.addAll(manualparticles);
247  for (AutomaticParticle ap : autoparticles)
248  if (!ap.isDeleted() && ap.getCost() >= threshold)
249  result.add(ap);
250  return result;
251  }
252 
253  public ManualParticle getLastAvailableParticle(double threshold)
254  {
255  AutomaticParticle ap;
256  for (int i = autoparticles.size() - 1; i >= 0; i--)
257  {
258  ap = autoparticles.get(i);
259  if (!ap.isDeleted() && ap.getCost() >= threshold)
260  return ap;
261  }
262  if (!manualparticles.isEmpty())
263  return manualparticles.get(manualparticles.size() - 1);
264  return null;
265 
266  }
267 
268 
269 
270  @Override
271  public boolean hasData()
272  {
273  return !isEmpty();
274  }
275 
276  @Override
277  public List<? extends PickerParticle> getParticleList() {
278  return getParticles();
279  }
280 
281  public int getAutopickpercent()
282  {
283  return autopickpercent;
284  }
285 
286  public void setAutopickpercent(int autopickpercent)
287  {
288  this.autopickpercent = autopickpercent;
289  }
290 
291  public void initParticlesRectangle(SupervisedParticlePicker picker)
292  {
293  double x1 = Double.POSITIVE_INFINITY, y1 = Double.POSITIVE_INFINITY, x2 = Double.NEGATIVE_INFINITY, y2 = Double.NEGATIVE_INFINITY;
294  List<ManualParticle> particles = getParticles();
295  if(particles.isEmpty())
296  return;
297  for(Particle p: getParticles())
298  {
299  if(p.getX() < x1)
300  x1 = p.getX();
301  if(p.getY() < y1)
302  y1 = p.getY();
303  if(p.getX() > x2)
304  x2 = p.getX();
305  if(p.getY() > y2)
306  y2 = p.getY();
307  }
308 
309  int radius = picker.getRadius();
310  radius = radius + radius/5;
311  int x = Math.max(0, (int)(x1 - radius));
312  int y = Math.max(0, (int)(y1 - radius));
313  int width = Math.min((int)(x2 - x + radius), this.getWidth() - 1);
314  int height = Math.min((int)(y2 - y + radius), this.getHeigth() - 1);
315  rectangle = new Rectangle(x, y, width, height);
316  return;
317 
318  }
319 
320  public void resetParticlesRectangle()
321  {
322  rectangle = null;
323  }
324 
325  public boolean isValid(SupervisedParticlePicker picker)
326  {
327  int count = getParticles().size();
328  if(count <= 3)
329  return false;
330  return true;
331 
332  }
333 
334  public void deleteBelowThreshold() {
335  // TODO Auto-generated method stub
336  for (AutomaticParticle p : autoparticles)
337  if(!p.isDeleted())
338  p.setDeleted(p.getCost() < getThreshold());
339  }
340 
341  public Rectangle getRectangle() {
342  return rectangle;
343  }
344 
345 
346 
347 }
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.addManualParticle
void addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:122
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.removeParticle
void removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:140
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.removeParticles
void removeParticles(int x, int y, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:93
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xmipp.jni.Particle.getCost
double getCost()
Definition: Particle.java:42
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static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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1 package xmipp.viewer.particlepicker.training;
2 
3 
4 import java.util.logging.Level;
5 import javax.swing.SwingUtilities;
6 import org.apache.commons.cli.ParseException;
7 import xmipp.ij.commons.XmippApplication;
8 import xmipp.utils.XmippDialog;
9 import xmipp.viewer.particlepicker.ParticlePicker;
10 import xmipp.viewer.particlepicker.ParticlePickerParams;
11 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame;
12 import xmipp.viewer.particlepicker.training.model.Mode;
13 import xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker;
14 
15 public class SupervisedPickerRunner implements Runnable {
16  private ParticlePickerParams params;
17 
18  public SupervisedPickerRunner(String[] args) {
19  params = new ParticlePickerParams(args);
20  }
21 
22  @Override
23  public void run() {
24 
25  try {
26  SupervisedParticlePicker ppicker = null;
27 
28  ppicker = new SupervisedParticlePicker(params.inputfile, params.outputdir, params.threads,
29  params.fast, params.incore, params);
30  if(params.isScipion())
31  XmippApplication.setIsScipion(true);
32  new SupervisedPickerJFrame(ppicker);
33  } catch (Exception e) {
34  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
35  if (!e.getMessage().isEmpty())
36  XmippDialog.showException(null, e);
37  }
38  }
39 
40  public static void main(String[] args) {
41  SupervisedPickerRunner spr = new SupervisedPickerRunner(args);
42  SwingUtilities.invokeLater(spr);
43  }
44 }
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static void setIsScipion(boolean isscipion)
Definition: XmippApplication.java:48
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Definition: XmippDialog.java:217
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.utils;
6 
7 import java.awt.event.ActionEvent;
8 import java.awt.event.ActionListener;
9 import javax.swing.Timer;
10 
15 public class TaskTimer implements ActionListener {
16 
17  Runnable runnable;
18  Timer timer;
19 
20  public TaskTimer(Runnable runnable) {
21  this.runnable = runnable;
22  timer = new Timer(500, this);
23  timer.setRepeats(false); // Repeats only once.
24  }
25 
26  public void start() {
27  if (timer.isRunning()) {
28  timer.restart();
29  } else {
30  timer.start();
31  }
32  }
33 
34  public boolean isRunning() {
35  return timer.isRunning();
36  }
37 
38  public void actionPerformed(ActionEvent e) {
39  runnable.run();
40  }
41 }
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Definition: TaskTimer.java:38
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TaskTimer(Runnable runnable)
Definition: TaskTimer.java:20
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1 package xmipp.utils;
2 
3 public interface Task
4 {
5  public void doTask();
6 }
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1 package xmipp.viewer.ctf;
2 
3 import java.util.Arrays;
4 
5 /*
6  * To change this template, choose Tools | Templates
7  * and open the template in the editor.
8  */
13 public class TasksEngine implements iTaskCompletionListener {
14 
15  private int tasks = 0;
16  private iCTFGUI gui;
17 
18  public TasksEngine(iCTFGUI gui) {
19  this.gui = gui;
20  }
21 
22  public synchronized void add(CommandTask task) {
23 
24  //System.out.println("running task " + Arrays.toString(task.commands.toArray()));
25 
26  gui.setRowBusy(task.row);
27  tasks++;
28  task.start();
29  }
30 
31  private boolean allDone() {
32  return tasks == 0;
33  }
34 
35  public synchronized void done(CommandTask task) {
36  if (allDone()) { // In the end, sortPSDs is executed. After that it's done.
37  gui.done();
38  } else {
39  tasks--;
40  gui.setRowIdle(task.row);
41 
42  // It's done, so sortPSDS is executed in background, and after that,
43  // main GUI is updated.
44 // if (allDone()) {
45 // SortPSDSTask sortPSDS = new SortPSDSTask(gui.getFilename(), this);
46 // sortPSDS.start();
47 // }
48  }
49  }
50 }
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synchronized void add(CommandTask task)
Definition: TasksEngine.java:22
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xmipp.viewer.ctf.iCTFGUI.setRowIdle
void setRowIdle(int row)
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xmipp.viewer.ctf.TasksEngine.done
synchronized void done(CommandTask task)
Definition: TasksEngine.java:35
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void setRowBusy(int row)
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package  xmipp.viewer.particlepicker.training.gui
 
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1 package xmipp.viewer.particlepicker.training.gui;
2 
3 import ij.ImagePlus;
4 import java.awt.Dimension;
5 import java.awt.GridBagConstraints;
6 import java.awt.GridBagLayout;
7 import java.awt.Insets;
8 import java.awt.event.ActionEvent;
9 import java.awt.event.ActionListener;
10 import java.text.NumberFormat;
11 import javax.swing.ImageIcon;
12 import javax.swing.JDialog;
13 import javax.swing.JFormattedTextField;
14 import javax.swing.JLabel;
15 import javax.swing.JPanel;
16 import javax.swing.SwingConstants;
17 import xmipp.ij.commons.XmippImageConverter;
18 import xmipp.jni.ImageGeneric;
19 import xmipp.utils.XmippDialog;
20 import xmipp.utils.XmippMessage;
21 import xmipp.utils.XmippWindowUtil;
22 import xmipp.viewer.particlepicker.training.model.Mode;
23 
24 public class TemplatesJDialog extends JDialog
25 {
26 
27  protected SupervisedPickerJFrame frame;
28  protected JPanel templatespn;
29  protected int width, height;
30  private JFormattedTextField templatestf;
31 
32  public TemplatesJDialog(SupervisedPickerJFrame frame)
33  {
34  super(frame);
35  this.frame = frame;
36  initComponents();
37  }
38 
39  public void loadTemplates(boolean resize)
40  {
41  try
42  {
43  ImageGeneric templates = frame.getParticlePicker().getTemplates();
44  int size = frame.getParticlePicker().getSize();
45  templatespn.removeAll();
46  templatespn.setPreferredSize(new Dimension((int) (size * templates.getNDim() + 50), size + 5));
47 
48  if(frame.getParticlePicker().hasManualParticles())
49  {
50  ImagePlus template;
51  for (int i = 0; i < frame.getParticlePicker().getTemplatesNumber(); i ++)
52  {
53  template = XmippImageConverter.convertToImagePlus(templates, ImageGeneric.FIRST_IMAGE + i);
54  templatespn.add(new JLabel(new ImageIcon(template.getImage()), SwingConstants.CENTER));
55  }
56  }
57  }
58  catch (Exception e)
59  {
60  // TODO Auto-generated catch block
61  e.printStackTrace();
62 
63  }
64  templatespn.repaint();
65  pack();
66  }
67 
68  private void initComponents()
69  {
70  setDefaultCloseOperation(HIDE_ON_CLOSE);
71  setTitle("Templates");
72  GridBagConstraints constraints = new GridBagConstraints();
73  constraints.insets = new Insets(0, 5, 0, 5);
74  constraints.anchor = GridBagConstraints.WEST;
75  setLayout(new GridBagLayout());
76  add(new JLabel("Templates:"), XmippWindowUtil.getConstraints(constraints, 0, 0));
77 
78  templatestf = new JFormattedTextField(NumberFormat.getNumberInstance());
79  templatestf.setColumns(3);
80  templatestf.setValue(frame.getParticlePicker().getTemplatesNumber());
81 
82  templatestf.addActionListener(new ActionListener()
83  {
84 
85  @Override
86  public void actionPerformed(ActionEvent arg0)
87  {
88  setTemplates();
89  }
90  });
91  templatestf.setEnabled(frame.getParticlePicker().getMode() == Mode.Manual);
92  add(templatestf, XmippWindowUtil.getConstraints(constraints, 1, 0));
93  templatespn = new JPanel();
94  add(templatespn, XmippWindowUtil.getConstraints(constraints, 0, 1, 2, GridBagConstraints.HORIZONTAL));
95 
96  loadTemplates(true);
97 
98  XmippWindowUtil.setLocation(0.6f, 0, this);
99  setVisible(true);
100 
101  }
102 
103  public void close()
104  {
105  setVisible(false);
106  dispose();
107 
108  }
109 
110  protected void setTemplates()
111  {
112  if (templatestf.getValue() == null || ((Number)templatestf.getValue()).intValue() <= 0)
113  {
114  XmippDialog.showInfo(frame, XmippMessage.getOutOfBoundsMsg("Templates"));
115  templatestf.setValue(frame.getParticlePicker().getTemplatesNumber());
116  return;
117  }
118 
119  int templates = ((Number) templatestf.getValue()).intValue();
120  if (templates != frame.getParticlePicker().getTemplatesNumber())
121  {
122  frame.getParticlePicker().setTemplatesNumber(templates);
123  frame.loadTemplates();
124  }
125 
126  }
127 
128 
129 }
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static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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boolean showInfo(String message)
Definition: XmippDialog.java:199
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static String getOutOfBoundsMsg(Object o)
Definition: XmippMessage.java:56
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static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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package  xmipp.viewer.windows
 
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 
6 /*
7  * JFrameTextFile.java
8  *
9  * Created on 12-dic-2010, 0:46:53
10  */
11 package xmipp.viewer.windows;
12 
13 import ij.IJ;
14 
15 import java.awt.Dimension;
16 import java.io.BufferedReader;
17 import java.io.File;
18 import java.io.FileNotFoundException;
19 import java.io.FileReader;
20 import javax.swing.JDialog;
21 import javax.swing.JFrame;
22 
23 import xmipp.utils.XmippDialog;
24 
29 public class TextfileJFrame extends JFrame {
30 
32  public TextfileJFrame(String filename) {
33  super(filename);
34  setPreferredSize(new Dimension(600, 400));
35  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
36  initComponents();
37  loadFile(filename);
38  pack();
39  }
40 
41  private void loadFile(String filename) {
42  File file = new File(filename);
43 
44  try {
45  BufferedReader inputStream = new BufferedReader(new FileReader(file));
46 
47  String line;
48  StringBuilder text = new StringBuilder();
49  while ((line = inputStream.readLine()) != null) {
50  text.append(line);
51  text.append("\n");
52  }
53 
54  jepEditorPane.setText(text.toString());
55  } catch (FileNotFoundException fnfex) {
56  IJ.error("File not found: " + fnfex.getMessage());
57  } catch (Exception ex) {
58  ex.printStackTrace(System.err);
59  IJ.error(ex.getMessage());
60  }
61  }
62 
68  @SuppressWarnings("unchecked")
69  // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
70  private void initComponents() {
71  jspEditor = new javax.swing.JScrollPane();
72  jepEditorPane = new javax.swing.JEditorPane();
73  jepEditorPane.setEditable(false);
74  //jepEditorPane.setPreferredSize(new java.awt.Dimension(300, 300));
75  jspEditor.setViewportView(jepEditorPane);
76  getContentPane().add(jspEditor, java.awt.BorderLayout.CENTER);
77 
78  }// </editor-fold>//GEN-END:initComponents
79 
80  private void jbOkActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jbOkActionPerformed
81  setVisible(false);
82  }//GEN-LAST:event_jbOkActionPerformed
83 
84  private javax.swing.JEditorPane jepEditorPane;
85  private javax.swing.JPanel jpButtons;
86  private javax.swing.JScrollPane jspEditor;
87  // End of variables declaration//GEN-END:variables
88 }
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class  xmipp.jni.TiltPairAligner
 
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package  xmipp.jni
 
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1 package xmipp.jni;
2 
3 public class TiltPairAligner
4 {
5  //Load the native library
6  static
7  {
8  System.loadLibrary("XmippJNI");
9  storeIds();
10  }
11  // hold pointer to Image class in C++ space
12  private long peer;
13 
14  public native void addParticleToAligner(int x1, int y1, int x2, int y2);
15 
16  public native Particle getTiltedParticle(int x1, int y1);
17 
18  public native Particle getUntiltedParticle(int x1, int y1);
19 
20  public native double[] computeAngles();
21 
22  // caching some ids
23  private static native void storeIds();
24 
25  public native void clear();
26 
27  // functions to create images
28  private native void create();
29 
30  // destructor
31  private synchronized native void destroy();
32 
33  // non-native functions
34  // constructor
35  public TiltPairAligner()
36  {
37  create();
38  }
39 
40  // Should be called by GarbageCollector before destroying
41  @Override
42  protected void finalize() throws Throwable
43  {
44  super.finalize();
45  destroy();
46  }
47 
48 
49 
50 }
- -
xmipp.jni.TiltPairAligner.getUntiltedParticle
native Particle getUntiltedParticle(int x1, int y1)
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native Particle getTiltedParticle(int x1, int y1)
- -
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native void addParticleToAligner(int x1, int y1, int x2, int y2)
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xmipp.jni.TiltPairAligner.computeAngles
native double [] computeAngles()
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- - diff --git a/html/TiltPairParticlesDialog_8java.html b/html/TiltPairParticlesDialog_8java.html deleted file mode 100644 index 6888854c..00000000 --- a/html/TiltPairParticlesDialog_8java.html +++ /dev/null @@ -1,95 +0,0 @@ - - - - - - - -Xmipp: xmippViz/java/src/xmipp/viewer/particlepicker/tiltpair/gui/TiltPairParticlesDialog.java File Reference - - - - - - - - - -
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class  xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialog
 
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package  xmipp.viewer.particlepicker.tiltpair.gui
 
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1 package xmipp.viewer.particlepicker.tiltpair.gui;
2 
3 import java.awt.Dimension;
4 import java.util.List;
5 
6 import xmipp.utils.XmippMessage;
7 import xmipp.utils.XmippWindowUtil;
8 import xmipp.viewer.particlepicker.ParticleCanvas;
9 import xmipp.viewer.particlepicker.ParticlePickerJFrame;
10 import xmipp.viewer.particlepicker.ParticlesDialog;
11 import xmipp.viewer.particlepicker.PickerParticle;
12 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle;
13 
14 public class TiltPairParticlesDialog extends ParticlesDialog
15 {
16 
17 
18  public TiltPairParticlesDialog(ParticlePickerJFrame frame)
19  {
20 
21  super(frame);
22 
23  }
24 
25  public void loadParticles(boolean changesize)
26  {
27 
28  List<? extends PickerParticle> particles = frame.getAvailableParticles();
29  side = frame.getSide();
30 
31  if (side == 0)
32  throw new IllegalArgumentException(XmippMessage.getOutOfBoundsMsg("side"));
33 
34  if (particles.isEmpty())
35  {
36  particlespn.removeAll();
37  width = side * 6 + 10;
38  height = maxHeight;
39  sp.setPreferredSize(new Dimension(width, height));
40  pack();
41  return;
42  }
43 
44  if (changesize)// first time or keep size
45  {
46  columns = 3;//Math.min(200, particles.size() * side * 2) / (side * 2);
47  rows = (int) Math.ceil(particles.size() / (float) columns);
48  width = side * columns * 2;
49  height = Math.min(maxHeight, side * rows);
50  boolean scroll = (height < rows * side);
51  width = width + (scroll ? 40 : 20);
52  height = height + (scroll ? 0 : 20);
53  sp.setPreferredSize(new Dimension(width, height));
54  }
55  else
56  {
57  Dimension d = sp.getSize();
58  width = (int) d.getWidth();
59  height = (int)d.getHeight();
60  columns = (int) d.getWidth() / (side * 2);
61  rows = (int) Math.ceil((particles.size() / (float) columns));
62  }
63  sp.setPreferredSize(new Dimension(width, height));
64 
65  particlespn.removeAll();
66  particles = frame.getAvailableParticles();
67  int index = 0;
68  ParticleCanvas c;
69  PickerParticle p;
70  UntiltedParticle up;
71 
72  for (int i = 0; i < rows; i++)
73  for (int j = 0; j < columns * 2; j+= 2, index ++)
74  {
75  if (index == particles.size())
76  break;
77  p = particles.get(index);
78  c = p.getParticleCanvas(frame);
79  up = (UntiltedParticle) p;
80  particlespn.add(c, XmippWindowUtil.getConstraints(constraints, j, i, 1));
81 
82  if (up.getTiltedParticle() != null)
83  particlespn.add(up.getTiltedParticle().getParticleCanvas(frame), XmippWindowUtil.getConstraints(constraints, j + 1, i, 1));
84  }
85 
86  sp.getVAdjustable().setValue(sp.getVAdjustable().getMaximum());
87  sp.getHAdjustable().setValue(sp.getHAdjustable().getMaximum());
88 
89  pack();
90 
91  }
92 }
-
xmipp.viewer.particlepicker.ParticlePickerJFrame.getAvailableParticles
abstract List<? extends PickerParticle > getAvailableParticles()
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xmipp.utils.XmippMessage.getOutOfBoundsMsg
static String getOutOfBoundsMsg(Object o)
Definition: XmippMessage.java:56
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xmipp.viewer.particlepicker.PickerParticle.getParticleCanvas
ParticleCanvas getParticleCanvas(ParticlePickerJFrame frame)
Definition: PickerParticle.java:38
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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class  xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame
 
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package  xmipp.viewer.particlepicker.tiltpair.gui
 
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TiltPairPickerJFrame.java
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1 package xmipp.viewer.particlepicker.tiltpair.gui;
2 
3 import ij.IJ;
4 
5 import java.awt.Color;
6 import java.awt.Dimension;
7 import java.awt.FlowLayout;
8 import java.awt.GridBagConstraints;
9 import java.awt.GridBagLayout;
10 import java.awt.Insets;
11 import java.awt.event.ActionEvent;
12 import java.awt.event.ActionListener;
13 import java.util.List;
14 
15 import javax.swing.BorderFactory;
16 import javax.swing.JCheckBoxMenuItem;
17 import javax.swing.JLabel;
18 import javax.swing.JMenu;
19 import javax.swing.JMenuBar;
20 import javax.swing.JMenuItem;
21 import javax.swing.JPanel;
22 import javax.swing.JScrollPane;
23 import javax.swing.JTable;
24 import javax.swing.ListSelectionModel;
25 
26 import xmipp.ij.commons.XmippApplication;
27 import xmipp.utils.XmippDialog;
28 import xmipp.utils.XmippWindowUtil;
29 import xmipp.viewer.particlepicker.Format;
30 import xmipp.viewer.particlepicker.ParticlePickerCanvas;
31 import xmipp.viewer.particlepicker.ParticlePickerJFrame;
32 import xmipp.viewer.particlepicker.ParticlesDialog;
33 import xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker;
34 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph;
35 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle;
36 import xmipp.viewer.particlepicker.training.model.Mode;
37 import xmipp.viewer.particlepicker.training.model.ManualParticle;
38 
39 public class TiltPairPickerJFrame extends ParticlePickerJFrame {
40 
41  private TiltPairPicker tppicker;
42  private JMenuBar mb;
43  private JPanel micrographpn;
44  private UntiltedMicrographCanvas canvas;
45  private MicrographPairsTableModel micrographsmd;
46 
47  private float position;
48 
49  private JLabel upslb;
50  private TiltedMicrographCanvas tiltedcanvas;
51  private JCheckBoxMenuItem anglesmi;
52  private JMenuItem importffilesmi;
53  private ImportParticlesFromFilesTiltPairJDialog importffilesjd;
54 
55  public TiltPairPicker getParticlePicker() {
56  return tppicker;
57  }
58 
59  public TiltPairPickerJFrame(TiltPairPicker picker) {
60  super(picker);
61  tppicker = picker;
62  initComponents();
63  setChanged(false);
64  }
65 
66  private void initComponents() {
67  setResizable(false);
68  setTitle("Xmipp Tilt Pair Picker - " + tppicker.getMode());
69  initMenuBar();
70  setJMenuBar(mb);
71 
72  GridBagConstraints constraints = new GridBagConstraints();
73  constraints.insets = new Insets(0, 5, 0, 5);
74  constraints.anchor = GridBagConstraints.WEST;
75  setLayout(new GridBagLayout());
76 
77  initToolBar();
78  add(tb);
79 
80  initMicrographsPane();
81  add(micrographpn, XmippWindowUtil.getConstraints(constraints, 0, 2, 3));
82  JPanel actionspn = new JPanel(new FlowLayout(FlowLayout.RIGHT));
83  actionspn.add(savebt);
84  actionspn.add(closebt);
85  actionspn.add(saveandexitbt);
86  add(actionspn, XmippWindowUtil.getConstraints(constraints, 0, 3, 3,
87  GridBagConstraints.HORIZONTAL));
88 
89  actionspn.add(savebt);
90  actionspn.add(saveandexitbt);
91  add(actionspn, XmippWindowUtil.getConstraints(constraints, 0, 3, 3, 1,
92  GridBagConstraints.HORIZONTAL));
93 
94  enableEdition(tppicker.getMode() != Mode.ReadOnly);
95  pack();
96  position = 0.95f;
97  XmippWindowUtil.setLocation(position, 0.5f, this);
98  setVisible(true);
99  }
100 
101  protected void enableEdition(boolean enable) {
102  super.enableEdition(enable);
103  importffilesmi.setEnabled(enable);
104  }
105 
106  public void initMenuBar() {
107  mb = new JMenuBar();
108 
109  filemn.add(importmi);
110  if (tppicker.getMode() != Mode.Manual)
111  importmi.setEnabled(false);
112  importffilesmi = new JMenuItem("Import coordinates from files...");
113  importffilesmi.addActionListener(new ActionListener() {
114 
115  @Override
116  public void actionPerformed(ActionEvent arg0) {
117  showImportFromFilesDialog();
118 
119  }
120  });
121  filemn.add(importffilesmi, 1);
122  filemn.add(exitmi);
123  // Setting menus
124  JMenu viewmn = new JMenu("View");
125  mb.add(filemn);
126  mb.add(filtersmn);
127  mb.add(viewmn);
128  mb.add(helpmn);
129 
130  anglesmi = new JCheckBoxMenuItem("Angles");
131  // anglesmi.setEnabled(false);
132  anglesmi.addActionListener(new ActionListener() {
133 
134  @Override
135  public void actionPerformed(ActionEvent e) {
136  if (anglesmi.isSelected()
137  && !tppicker.getMicrograph().anglesAvailable())
138  XmippDialog
139  .showInfo(TiltPairPickerJFrame.this,
140  "Angles will not be accurate until more than 10 pairs are registered");
141  canvas.repaint();
142  tiltedcanvas.repaint();
143  }
144  });
145  viewmn.add(anglesmi);
146  viewmn.add(pmi);
147  viewmn.add(ijmi);
148  }
149 
150  @Override
151  protected void setCanvasCursor(){
152  super.setCanvasCursor();
153  tiltedcanvas.setCustomCursor();
154  }
155  protected void showImportFromFilesDialog() {
156  if (importffilesjd == null)
157  importffilesjd = new ImportParticlesFromFilesTiltPairJDialog(this);
158  importffilesjd.showDialog();
159  }
160 
161  private void initMicrographsPane() {
162  GridBagConstraints constraints = new GridBagConstraints();
163  constraints.insets = new Insets(0, 5, 0, 5);
164  constraints.anchor = GridBagConstraints.NORTHWEST;
165  micrographpn = new JPanel(new GridBagLayout());
166  micrographpn.setBorder(BorderFactory.createTitledBorder("Micrographs"));
167  JScrollPane sp = new JScrollPane();
168  micrographsmd = new MicrographPairsTableModel(this);
169  micrographstb.setModel(micrographsmd);
170  formatMicrographsTable();
171 
172  sp.setViewportView(micrographstb);
173  micrographpn.add(sp,
174  XmippWindowUtil.getConstraints(constraints, 0, 0, 1));
175  JPanel infopn = new JPanel();
176  upslb = new JLabel(Integer.toString(tppicker.getUntiltedNumber()));
177  infopn.add(new JLabel("Particles:"));
178  infopn.add(upslb);
179  micrographpn.add(infopn,
180  XmippWindowUtil.getConstraints(constraints, 0, 1, 1));
181  JPanel buttonspn = new JPanel(new FlowLayout(FlowLayout.LEFT));
182 
183  buttonspn.add(resetbt);
184  buttonspn.add(usezoombt);
185  micrographpn.add(buttonspn,
186  XmippWindowUtil.getConstraints(constraints, 0, 2, 2));
187 
188  }
189 
190  private void formatMicrographsTable() {
191  micrographstb.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
192  micrographstb.getColumnModel().getColumn(0).setPreferredWidth(35);
193  micrographstb.getColumnModel().getColumn(1).setPreferredWidth(220);
194  micrographstb.getColumnModel().getColumn(2).setPreferredWidth(220);
195  micrographstb.getColumnModel().getColumn(3).setPreferredWidth(65);
196  micrographstb.getColumnModel().getColumn(4).setPreferredWidth(70);
197  micrographstb
198  .setPreferredScrollableViewportSize(new Dimension(610, 304));
199  micrographstb.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
200  int index = tppicker.getMicrographIndex();
201  if (index != -1)
202  micrographstb.setRowSelectionInterval(index, index);
203  }
204 
205  public void updateSize(int size) {
206  super.updateSize(size);
207  tiltedcanvas.repaint();
208  }
209 
210  public void setChanged(boolean changed) {
211  tppicker.setChanged(changed);
212  savemi.setEnabled(changed);
213  savebt.setEnabled(changed);
214  }
215 
216  public void updateMicrographsModel(boolean all) {
217  if (particlesdialog != null)
218  loadParticles(false);
219  int index = tppicker.getMicrographIndex();
220  if (all)
221  micrographsmd.fireTableRowsUpdated(0,
222  micrographsmd.getRowCount() - 1);
223  else
224  micrographsmd.fireTableRowsUpdated(index, index);
225  micrographstb.setRowSelectionInterval(index, index);
226  upslb.setText(Integer.toString(tppicker.getUntiltedNumber()));
227  // anglesmi.setEnabled(tppicker.getMicrograph().getAddedCount() >= 4);
228  }
229 
230  void initializeCanvas() {
231  if (canvas == null) {
232  canvas = new UntiltedMicrographCanvas(this);
233  tiltedcanvas = new TiltedMicrographCanvas(this);
234  tiltedcanvas.getIw().setLocation(canvas.getIw().getWidth(), canvas.getIw().getLocation().y);
235  List<UntiltedParticle> particles = getMicrograph().getParticles();
236 
237  // needs both canvas to be initialized
238  if (!particles.isEmpty())
239  canvas.refreshActive(particles.get(particles.size() - 1));
240  } else {
241  canvas.updateMicrograph();
242  tiltedcanvas.updateMicrograph();
243 
244  }
245  }
246 
247  public ParticlePickerCanvas getCanvas() {
248  return canvas;
249  }
250 
251  public UntiltedMicrograph getMicrograph() {
252  return tppicker.getMicrograph();
253  }
254 
255  public int getParticleSize() {
256  return (int) sizetf.getValue();
257  }
258 
259  public Color getColor() {
260  return tppicker.getColor();
261  }
262 
263  @Override
264  public List<? extends ManualParticle> getAvailableParticles() {
265  return getMicrograph().getParticles();
266  }
267 
268  public TiltedMicrographCanvas getTiltedCanvas() {
269  return tiltedcanvas;
270  }
271 
272  public boolean drawAngles() {
273  return anglesmi.isSelected();
274  }
275 
276  @Override
277  public void changeShapes() {
278  canvas.repaint();
279  tiltedcanvas.repaint();
280  }
281 
282  public String importParticlesFromFolder(Format format, String dir, String preffix, String suffix,
283  float scale, boolean invertx, boolean inverty) {
284  String result = tppicker.importParticlesFromFolder(dir, format, preffix, suffix, scale,
285  invertx, inverty);
286  sizetf.setValue(tppicker.getSize());
287  getCanvas().repaint();
288  updateMicrographsModel(true);
289  getCanvas().refreshActive(null);
290  tiltedcanvas.repaint();
291  return result;
292  }
293 
294  @Override
295  protected void resetMicrograph() {
296  tppicker.resetMicrograph(getMicrograph());
297  canvas.refreshActive(null);
298  updateMicrographsModel();
299 
300  }
301 
302  @Override
303  protected void reloadImage() {
304  getCanvas().updateMicrograph();
305  getTiltedCanvas().updateMicrograph();
306 
307  }
308 
309  @Override
310  protected void loadMicrograph() {
311  if (this.micrographstb.getSelectedRow() == -1)
312  return;// Probably from fireTableDataChanged raised
313 
314  int index = tppicker.getMicrographIndex();
315 
316  if (index == micrographstb.getSelectedRow() && canvas != null && canvas.getIw().isVisible())
317  // micrograph open, no need to reopen
318  return;
319 
320  if (tppicker.isChanged()){
321  if (!saveData(false)) {
322  micrographstb.getSelectionModel().setSelectionInterval(index, index);
323  return;
324  }
325  }
326 
327  getMicrograph().releaseImage();
328 
329  index = micrographstb.getSelectedRow();
330  tppicker.setMicrograph(tppicker.getMicrographs().get(index));
331 
332  setChanged(false);
333  // anglesmi.setEnabled(getMicrograph().getAddedCount() >= 4);
334  initializeCanvas();
335 
336  pack();
337  if (particlesdialog != null)
338  loadParticles(false);
339  }
340 
341 // @Override
342 // protected void openHelpURl() {
343 // XmippWindowUtil
344 // .openURI("http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Micrograph_tiltpair_picking_v3");
345 // }
346 
347  public String importParticlesFromFiles(Format format, String file1,
348  String file2, float scale, boolean invertx, boolean inverty) {
349 
350  getMicrograph().reset(tppicker);
351  String result = tppicker.importParticlesFromFiles(file1, file2, format,
352  getMicrograph(), scale, invertx, inverty);
353  tppicker.saveData(getMicrograph());
354 
355  getCanvas().repaint();
356  tiltedcanvas.repaint();
357  updateMicrographsModel();
358  updateSize(tppicker.getSize());
359  canvas.refreshActive(null);
360  return result;
361  }
362 
363  @Override
364  public String importParticles(Format format, String dir, String preffix, String suffix,float scale,
365  boolean invertx, boolean inverty) {
366  return importParticlesFromFolder(format, dir,preffix, suffix, scale, invertx, inverty);
367 
368  }
369 
370  @Override
371  public ParticlesDialog initParticlesJDialog() {
372  return new TiltPairParticlesDialog(this);
373  }
374 
375  public void close()
376  {
377  setVisible(false);
378  dispose();
379  if (getCanvas() != null)
380  {
381  getCanvas().getIw().close();
382  if(getTiltedCanvas() != null)
383  getTiltedCanvas().getIw().close();
384  }
385 
386  XmippApplication.removeInstance(false);
387 
388  }
389 
390  public void applyFilter(String filter)
391  {
392  IJ.run(getMicrograph().getImagePlus(), filter, "");
393  IJ.run(getMicrograph().getTiltedMicrograph().getImagePlus(), filter, "");
394  }
395 
396 }// class TiltPairPickerJFrame
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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.importParticlesFromFolder
String importParticlesFromFolder(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPickerJFrame.java:282
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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.importParticlesFromFiles
String importParticlesFromFiles(Format format, String file1, String file2, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPickerJFrame.java:347
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFolder
String importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPicker.java:308
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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.importParticles
String importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPickerJFrame.java:364
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFiles
String importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPicker.java:351
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abstract void refreshActive(PickerParticle p)
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static void removeInstance(boolean isijwindow)
Definition: XmippApplication.java:28
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static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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package  xmipp.viewer.particlepicker.tiltpair
 
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1 package xmipp.viewer.particlepicker.tiltpair;
2 
3 
4 import java.util.logging.Level;
5 
6 import javax.swing.SwingUtilities;
7 
8 import xmipp.ij.commons.XmippApplication;
9 import xmipp.utils.XmippDialog;
10 import xmipp.viewer.particlepicker.ParticlePicker;
11 import xmipp.viewer.particlepicker.ParticlePickerParams;
12 import xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame;
13 import xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker;
14 
15 public class TiltPairPickerRunner implements Runnable {
16 
17 
18 
19  private final ParticlePickerParams params;
20 
21 
22  public TiltPairPickerRunner(String[] args) {
23 
24  params = new ParticlePickerParams(args);
25 
26  }
27  // 0 --> input metadata
28  // 1 --> output dir
29  // 2 --> mode
30 
31 
32 
33 
34  @Override
35  public void run() {
36  try {
37 
38  TiltPairPicker ppicker = null;
39  ppicker = new TiltPairPicker(params.inputfile, params.outputdir, params);
40 
41  if(params.isScipion())
42  XmippApplication.setIsScipion(true);
43 
44  new TiltPairPickerJFrame(ppicker);
45  } catch (Exception e) {
46  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
47  if (!e.getMessage().isEmpty())
48  XmippDialog.showError(null, e.getMessage());
49 
50  }
51 
52  }
53 
54  public static void main(String[] args) {
55  TiltPairPickerRunner spr = new TiltPairPickerRunner(args);
56  SwingUtilities.invokeLater(spr);
57 
58  }
59 
60 }
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static void setIsScipion(boolean isscipion)
Definition: XmippApplication.java:48
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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package  xmipp.viewer.particlepicker.tiltpair.model
 
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TiltPairPicker.java
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1 package xmipp.viewer.particlepicker.tiltpair.model;
2 
3 import java.io.File;
4 import java.util.ArrayList;
5 import java.util.List;
6 import java.util.logging.Level;
7 import javax.swing.JFrame;
8 import xmipp.jni.Filename;
9 import xmipp.jni.MDLabel;
10 import xmipp.jni.MetaData;
11 import xmipp.utils.Params;
12 import xmipp.utils.XmippDialog;
13 import xmipp.viewer.particlepicker.Format;
14 import xmipp.viewer.particlepicker.Micrograph;
15 import xmipp.viewer.particlepicker.ParticlePicker;
16 import xmipp.viewer.particlepicker.ParticlePickerParams;
17 import xmipp.viewer.particlepicker.training.model.Mode;
18 
19 
26 public class TiltPairPicker extends ParticlePicker
27 {
28 
29  protected List<UntiltedMicrograph> micrographs;
30  private UntiltedMicrograph micrograph;
31 
32  public TiltPairPicker(String selfile, String outputdir, ParticlePickerParams params)
33  {
34  super(selfile, outputdir, params);
35 
36  for (UntiltedMicrograph um : micrographs)
37  loadMicrographParticles(um);
38 
39  }
40 
41  public void loadData()
42  {
43  try
44  {
45  loadEmptyMicrographs();
46  for (UntiltedMicrograph um : micrographs)
47  loadMicrographParticles(um);
48 
49  }
50  catch (Exception e)
51  {
52  getLogger().log(Level.SEVERE, e.getMessage(), e);
53  throw new IllegalArgumentException(e);
54  }
55 
56  }
57 
58  public void loadEmptyMicrographs()
59  {
60  try
61  {
62  MetaData md = new MetaData(selfile);
63  // md.readPlain(pairsfile, "image tilted_image");
64  if (micrographs == null)
65  this.micrographs = new ArrayList<UntiltedMicrograph>();
66  else
67  micrographs.clear();
68  UntiltedMicrograph untiltedmicrograph;
69  TiltedMicrograph tiltedmicrograph;
70  String image, tiltedimage;
71 
72  long[] ids = md.findObjects();
73  for (long id : ids)
74  {
75  image = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
76  tiltedimage = md.getValueString(MDLabel.MDL_MICROGRAPH_TILTED, id);
77  tiltedmicrograph = new TiltedMicrograph(tiltedimage);
78  untiltedmicrograph = new UntiltedMicrograph(image, tiltedmicrograph);
79  tiltedmicrograph.setUntiltedMicrograph(untiltedmicrograph);
80  micrographs.add(untiltedmicrograph);
81 
82  }
83  md.destroy();
84  if (micrographs.isEmpty())
85  throw new IllegalArgumentException(String.format("No micrographs specified on %s", selfile));
86 
87 
88  }
89  catch (Exception e)
90  {
91  getLogger().log(Level.SEVERE, e.getMessage(), e);
92  throw new IllegalArgumentException(e);
93  }
94 
95  }
96 
97  public void loadMicrographParticles(UntiltedMicrograph micrograph)
98  {
99  String ufile = getOutputPath(micrograph.getPosFile());
100  String tfile = getOutputPath(micrograph.getTiltedMicrograph().getPosFile());
101  if (Filename.exists(ufile) && Filename.exists(tfile))
102  loadMicrographData(micrograph, ufile, tfile);
103  }
104 
105  /* Return number of particles loaded */
106  public String loadMicrographParticles(UntiltedMicrograph um, MetaData uMd, MetaData tMd)
107  {
108  String result = "";
109  um.reset(this);
110  UntiltedParticle up;
111  TiltedParticle tp;
112  TiltedMicrograph tm = um.getTiltedMicrograph();
113  int x, y;
114  long[] uIds = uMd.findObjects();
115  long[] tIds = tMd.findObjects();
116  long id;
117  for (int i = 0; i < uIds.length; ++i)
118  {
119  // Add untilted particle
120  id = uIds[i];
121  x = uMd.getValueInt(MDLabel.MDL_XCOOR, id);
122  y = uMd.getValueInt(MDLabel.MDL_YCOOR, id);
123 
124  // Set tilted pair particle
125  if (i < tIds.length)
126  {
127  up = new UntiltedParticle(x, y, um, this);
128  um.addParticle(up);
129  id = tIds[i];
130  x = tMd.getValueInt(MDLabel.MDL_XCOOR, id);
131  y = tMd.getValueInt(MDLabel.MDL_YCOOR, id);
132  if (x <= 0 || y <= 0)
133  {
134  result += String.format("Tilted particle at %s centered on %s,%s with negative coordinates dismissed.\n", getMicrograph()
135  .getName(), x, y);
136  continue;
137  }
138  tp = new TiltedParticle(x, y, up);
139  up.setTiltedParticle(tp);
140  tm.addParticle(tp);
141  }
142  else
143  result += String.format("%s centered on (%s,%s), ", getMicrograph().getName(), x, y);
144  }
145  if(!result.isEmpty())
146  result = "Particles at: " + result + "without tilted pairs dismissed";
147 
148  um.initAligner();
149 
150  return result;
151  }// loadMicrographs
152 
153  public void loadMicrographData(UntiltedMicrograph um, String uPosFile, String tPosFile)
154  {
155  try
156  {
157  MetaData uMd = new MetaData(getParticlesBlock(uPosFile));
158  MetaData tMd = new MetaData(getParticlesBlock(tPosFile));
159  loadMicrographParticles(um, uMd, tMd);
160  uMd.destroy();
161  tMd.destroy();
162  }
163  catch (Exception e)
164  {
165  getLogger().log(Level.SEVERE, e.getMessage(), e);
166  throw new IllegalArgumentException(e.getMessage());
167  }
168  }
169 
170  public int getNextFreeMicrograph()
171  {
172  int count = 0;
173  for (UntiltedMicrograph m : micrographs)
174  {
175  if (m.hasData())
176  return count;
177  count++;
178  }
179  return -1;
180  }
181 
182  public List<UntiltedMicrograph> getMicrographs()
183  {
184  return micrographs;
185  }
186 
187  public void resetMicrograph(UntiltedMicrograph m)
188  {
189  m.reset(this);
190  saveData(m);
191  }
192 
193  public int getUntiltedNumber()
194  {
195  int count = 0;
196  for (UntiltedMicrograph um : micrographs)
197  count += um.getParticles().size();
198  return count;
199  }
200 
201  public int getTiltedNumber()
202  {
203  int count = 0;
204  for (UntiltedMicrograph um : micrographs)
205  count += um.getTiltedMicrograph().getParticles().size();
206  return count;
207  }
208 
209 
210  public void saveData()
211  {
212  super.saveData();
213  saveData(micrograph);//every time you switch micrograph data is saved
214  setChanged(false);
215  }
216 
217 
218  public void saveMicrographAngles(UntiltedMicrograph m)
219  {
220  try
221  {
222  MetaData anglesmd;
223  anglesmd = new MetaData(selfile);
224 
225  long micId = -1; //Current micrograph id
226  long [] ids = anglesmd.findObjects();
227  String micFile = m.getFile();
228 
229  for (long mid: ids)
230  {
231  if (micFile.equals(anglesmd.getValueString(MDLabel.MDL_MICROGRAPH, mid)))
232  {
233  micId = mid;
234  break;
235  }
236  }
237 
238  if (micId == -1)
239  throw new Exception("Micrograph " + micrograph.getFile() + " was not found in metadata");
240 
241  anglesmd.setValueDouble(MDLabel.MDL_ANGLE_Y, m.getUntiltedAngle(), micId);
242  anglesmd.setValueDouble(MDLabel.MDL_ANGLE_Y2, m.getTiltedAngle(), micId);
243  anglesmd.setValueDouble(MDLabel.MDL_ANGLE_TILT, m.getTiltAngle(), micId);
244  anglesmd.writeBlock(selfile);
245 
246  }
247  catch (Exception e)
248  {
249  getLogger().log(Level.SEVERE, e.getMessage(), e);
250  throw new IllegalArgumentException(e.getMessage());
251  }
252 
253  }
254 
255  @Override
256  public void saveData(Micrograph m)
257  {
258  UntiltedMicrograph um = (UntiltedMicrograph) m;
259  String file = getOutputPath(um.getPosFile());
260  long id;
261 
262  try
263  {
264 
265  if (!m.hasData()){
266  new File(file).delete();
267  }
268  else
269  {
270  TiltedParticle tp;
271  MetaData mdU = new MetaData(); // untilted micrograph particles
272  MetaData mdT = new MetaData(); // tilted micrograph particles
273 
274  for (UntiltedParticle p : um.getParticles())
275  {
276  tp = p.getTiltedParticle();
277  if (tp != null)
278  {
279  id = mdU.addObject();
280  mdU.setValueInt(MDLabel.MDL_XCOOR, p.getX(), id);
281  mdU.setValueInt(MDLabel.MDL_YCOOR, p.getY(), id);
282 
283  id = mdT.addObject();
284  mdT.setValueInt(MDLabel.MDL_XCOOR, tp.getX(), id);
285  mdT.setValueInt(MDLabel.MDL_YCOOR, tp.getY(), id);
286  }
287  }
288 
289  mdU.writeWithException(getParticlesBlock(file));
290  file = getOutputPath(um.getTiltedMicrograph().getPosFile());
291  mdT.writeWithException(getParticlesBlock(file));
292 
293  mdU.destroy();
294  mdT.destroy();
295  }
296  saveMicrographAngles(um);
297  }
298  catch (Exception e)
299  {
300  getLogger().log(Level.SEVERE, e.getMessage(), e);
301  throw new IllegalArgumentException(e.getMessage());
302  }
303 
304  }
305 
306 
307 
308  public String importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
309  {
310  if (f == Format.Auto)
311  {
312  StringBuffer suffixPtr = new StringBuffer(suffix);
313  f = detectFormat(path, preffix, suffixPtr);
314  suffix = suffixPtr.toString();
315  }
316  if (f == Format.None)
317  throw new IllegalArgumentException("Unable to detect format");
318  System.out.println(suffix);
319  String uFn, tFn, file;
320  String result = "";
321  importSize(path, f, scale);
322 
323  MetaData uMd = new MetaData();
324  MetaData tMd = new MetaData();
325  for(UntiltedMicrograph m: micrographs)
326  {
327  uFn = null; tFn = null;
328  file = Filename.join(path, preffix + m.getName() + suffix);
329  if(new File(file).exists())
330  uFn = file;
331  file = Filename.join(path, preffix + m.getTiltedMicrograph().getName() + suffix);
332  if(new File(file).exists())
333  tFn = file;
334 
335  if(uFn != null && tFn != null)
336  {
337  uMd.clear();
338  tMd.clear();
339  result += importParticlesFromFiles(uFn, tFn, f, m, scale, invertx, inverty, uMd, tMd);
340  saveData(m);
341  }
342  }
343  uMd.destroy();
344  tMd.destroy();
345  super.saveData();
346 
347 
348  return result;
349  }// function importParticlesFromFolder
350 
351  public String importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty)
352  {
353  MetaData uMd = new MetaData();
354  MetaData tMd = new MetaData();
355  String result = importParticlesFromFiles(uPath, tPath, f, um, scale, invertx, inverty, uMd, tMd);
356  uMd.destroy();
357  tMd.destroy();
358  return result;
359 
360  }
361 
362  public String importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty, MetaData uMd, MetaData tMd)
363  {
364  fillParticlesMdFromFile(uPath, f, um, uMd, scale, invertx, inverty);
365  fillParticlesMdFromFile(tPath, f, um.getTiltedMicrograph(), tMd, scale, invertx, inverty);
366  String result = loadMicrographParticles(um, uMd, tMd);
367 
368  return result;
369  }// function importParticlesFromFiles
370 
371 
372 
373  public UntiltedMicrograph getMicrograph()
374  {
375  return micrograph;
376  }
377 
378  @Override
379  public void setMicrograph(Micrograph m)
380  {
381  this.micrograph = (UntiltedMicrograph) m;
382 
383  }
384 
385  @Override
386  public boolean isValidSize(JFrame parent, int size)
387  {
388  boolean valid = true;
389  UntiltedMicrograph um = getMicrograph();
390  for (UntiltedParticle p : um.getParticles())
391  if (!getMicrograph().fits(p.getX(), p.getY(), size))
392  {
393  valid = false;
394  break;
395  }
396  for (TiltedParticle p : um.getTiltedMicrograph().getParticles())
397  if (!um.getTiltedMicrograph().fits(p.getX(), p.getY(), size))
398  {
399  valid = false;
400  break;
401  }
402  if (!valid)
403  XmippDialog.showInfo(parent, String.format("Particles out of bounds, %s not allowed.", size));
404  return valid;
405  }
406 
407  @Override
408  public int getParticlesCount() {
409  return getUntiltedNumber();
410 
411  }
412 
413  @Override
414  protected synchronized void saveConfig(MetaData md, long id)
415  {
416  try
417  {
418  super.saveConfig(md, id);
419  md.setValueInt(MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE, getParticlesCount(), id);
420 
421 
422  }
423  catch (Exception e)
424  {
425  getLogger().log(Level.SEVERE, e.getMessage(), e);
426  throw new IllegalArgumentException(e.getMessage());
427  }
428  }
429 
430 }// class TiltPairPicker
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xmipp.viewer.particlepicker.ParticlePicker.detectFormat
Format detectFormat(String path, String preffix, StringBuffer suffix)
Definition: ParticlePicker.java:295
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static final int MDL_ANGLE_Y
< difference between two angles (double,degrees)
Definition: MDLabel.java:23
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static String join(String... paths)
Definition: Filename.java:473
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native void clear()
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static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MetaData.writeBlock
native void writeBlock(String filename)
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void setUntiltedMicrograph(UntiltedMicrograph untiltedmicrograph)
Definition: TiltedMicrograph.java:73
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xmipp.jni.MDLabel.MDL_MICROGRAPH_TILTED
static final int MDL_MICROGRAPH_TILTED
< Name of the original micrograph, MDL_MICROGRAPH is probably a downsampled version of this one (std:...
Definition: MDLabel.java:233
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFolder
String importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPicker.java:308
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.TiltPairPicker
TiltPairPicker(String selfile, String outputdir, ParticlePickerParams params)
Definition: TiltPairPicker.java:32
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographData
void loadMicrographData(UntiltedMicrograph um, String uPosFile, String tPosFile)
Definition: TiltPairPicker.java:153
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographParticles
void loadMicrographParticles(UntiltedMicrograph micrograph)
Definition: TiltPairPicker.java:97
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native long [] findObjects()
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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void writeWithException(String xmippFilename)
Definition: MetaData.java:706
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boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.jni.MetaData.setValueDouble
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xmipp.jni.Filename.exists
static boolean exists(String path)
Definition: Filename.java:266
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFiles
String importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPicker.java:351
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.saveConfig
synchronized void saveConfig(MetaData md, long id)
Definition: TiltPairPicker.java:414
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographParticles
String loadMicrographParticles(UntiltedMicrograph um, MetaData uMd, MetaData tMd)
Definition: TiltPairPicker.java:106
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xmipp.jni.MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE
static final int MDL_PICKING_MANUALPARTICLES_SIZE
< Number of automatic particles picked
Definition: MDLabel.java:289
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xmipp.jni.MDLabel.MDL_ANGLE_TILT
static final int MDL_ANGLE_TILT
< difference between rot angles (double,degrees)
Definition: MDLabel.java:16
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xmipp.viewer.particlepicker.ParticlePicker.importSize
void importSize(String path, Format f, double scale)
Definition: ParticlePicker.java:643
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xmipp.jni.MDLabel.MDL_ANGLE_Y2
static final int MDL_ANGLE_Y2
< Angle between y-axis and tilt-axis (double, degrees) for untilted micrographs
Definition: MDLabel.java:24
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromFile
void fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
Definition: ParticlePicker.java:497
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFiles
String importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty, MetaData uMd, MetaData tMd)
Definition: TiltPairPicker.java:362
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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package  xmipp.viewer.particlepicker.tiltpair.gui
 
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TiltedMicrographCanvas.java
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1 package xmipp.viewer.particlepicker.tiltpair.gui;
2 
3 import java.awt.*;
4 import java.awt.event.MouseEvent;
5 
6 import java.util.List;
7 
8 import javax.swing.SwingUtilities;
9 
10 import xmipp.jni.Particle;
11 import xmipp.utils.XmippDialog;
12 import xmipp.utils.XmippMessage;
13 import xmipp.viewer.particlepicker.*;
14 import xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker;
15 import xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph;
16 import xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle;
17 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph;
18 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle;
19 
20 public class TiltedMicrographCanvas extends ParticlePickerCanvas
21 {
22 
23  // Fields
24  // Untilted references
25  private UntiltedMicrograph um;
26  private UntiltedMicrographCanvas uc;
27 
28  // Constructors
29  public TiltedMicrographCanvas(TiltPairPickerJFrame frame)
30  {
31  super(frame, frame.getMicrograph().getTiltedMicrograph());
32  this.um = frame.getMicrograph();
33  this.uc = (UntiltedMicrographCanvas) frame.getCanvas();
34 
35  }
36 
37  // Fields getters and setters
38  @Override
39  public TiltPairPickerJFrame getFrame() {return (TiltPairPickerJFrame)frame;}
40 
41  @Override
42  public TiltedParticle getActive() { return uc.getActiveTiltedParticle();}
43 
44  @Override
45  public TiltedMicrograph getMicrograph() {return (TiltedMicrograph)micrograph;}
46 
47  @Override
48  protected TiltedParticle getLastParticle()
49  {
50  return uc.getLastParticle().getTiltedParticle();
51  }
52 
53  @Override
54  public TiltPairPicker getParticlePicker()
55  {
56  return (TiltPairPicker)picker;
57  }
58 
59  // Methods
60  public void updateMicrograph()
61  {
62  um = getFrame().getMicrograph();
63  TiltedMicrograph m = getFrame().getMicrograph().getTiltedMicrograph();
64  updateMicrograph(m);
65  }
66 
67  public void zoomIn(int sx, int sy)
68  {
69  super.zoomIn(sx, sy);
70 
71  if(getParticlePicker().getZoom() != uc.getMagnification())
72  uc.zoomIn(sx, sy);
73  }
74 
75  public void zoomOut(int sx, int sy)
76  {
77  super.zoomOut(sx, sy);
78 
79  if(getParticlePicker().getZoom() != uc.getMagnification())
80  uc.zoomOut(sx, sy);
81  }
82 
83  private void addParticle(int x, int y)
84  {
85  try
86  {
87 
88  Particle p = um.getAlignedUntiltedParticle(x, y);
89  if (!um.fits(p.getX(), p.getY(), getParticlePicker().getSize()))
90  throw new IllegalArgumentException(XmippMessage.getOutOfBoundsMsg("Untilted particle"));
91  UntiltedParticle up = new UntiltedParticle(p.getX(), p.getY(), um, getParticlePicker());
92  TiltedParticle tp = new TiltedParticle(x, y, up);
93  up.setTiltedParticle(tp);
94  um.addParticle(up);
95  getMicrograph().addParticle(tp);
96  refreshActive(tp);
97  frame.updateMicrographsModel();
98  frame.setChanged(true);
99  }
100  catch (Exception e)
101  {
102  e.printStackTrace();
103  XmippDialog.showInfo(frame, e.getMessage());
104  }
105 
106  }
107  @Override
108  protected void removeParticle(PickerParticle particleToRemove) {
109 
110  TiltedParticle toRemove = (TiltedParticle) particleToRemove;
111  uc.removeParticle(toRemove.getUntiltedParticle());
112 
113  }
114 
115  @Override
116  public void refreshActive(PickerParticle p)
117  {
118  if (p != null){
119  active = p;
120  frame.getCanvas().refreshActive(((TiltedParticle) p).getUntiltedParticle());
121  }
122  }
123 
124  protected void manageActive(int x, int y)
125  {
126  if (!activemoved)
127  return;
128  if (uc.getActive().isAdded())
129  um.initAligner();
130  setActiveMoved(false);
131  }
132 
133  @Override
134  protected void doCustomPaint(Graphics2D g2)
135  {
136 
137  g2.setColor(getFrame().getColor());
138  List<TiltedParticle> particles = um.getTiltedMicrograph().getParticles();
139  for (TiltedParticle p : particles)
140  {
141  drawShape(g2, p, false);
142  }
143 
144  if (uc.getActiveTiltedParticle() != null)
145  {
146  g2.setColor(Color.red);
147  drawShape(g2, uc.getActive().getTiltedParticle(), true);
148  }
149  if (getFrame().drawAngles())
150  drawLine(Math.toRadians(um.getTiltedAngle()), g2);
151 
152  }
153 
154  // Event listeners
155 
161  public void mousePressed(MouseEvent e)
162  {
163  super.mousePressed(e);
164 
165  if (frame.isPickingAvailable(e))
166  {
167  if (frame.isEraserMode(e))
168  {
169  eraseAndSync(e);
170  return;
171  }
172 
173  int x = super.offScreenX(e.getX());
174  int y = super.offScreenY(e.getY());
175 
176  TiltedParticle p = um.getTiltedMicrograph().getParticle(x, y, getFrame().getParticleSize());
177  if (p != null)
178  {
179  if (SwingUtilities.isLeftMouseButton(e) && e.isShiftDown())
180  uc.removeParticle(p.getUntiltedParticle());
181  else if (SwingUtilities.isLeftMouseButton(e))
182  refreshActive(p);
183  }
184  else if (SwingUtilities.isLeftMouseButton(e) && um.fits(x, y, getFrame().getParticleSize()))
185  {
186  TiltedParticle tp = getMicrograph().getParticle(x, y, getParticlePicker().getSize());
187  //associate tilted particle for first cases
188  if (um.getAddedCount() < UntiltedMicrograph.getAlignmentMin())
189  {
190  UntiltedParticle uactive = uc.getActive();
191  if (uactive != null && uactive.getTiltedParticle() == null)
192  {
193  p = new TiltedParticle(x, y, uactive);
194  uactive.setTiltedParticle(p);
195  um.getTiltedMicrograph().addParticle(p);
196  um.addParticleToAligner(uactive, true);
197  frame.updateMicrographsModel();
198  }
199  }
200  else if(tp == null)//generate untilted particle
201  addParticle(x, y);
202  }
203  frame.setChanged(true);
204  repaint();
205  }
206  }
207 
208  private void eraseAndSync(MouseEvent e) {
209  erase(e);
210  getFrame().getCanvas().repaint();
211 
212  }
213 
214  public void mousePressed(int x, int y)
215  {
216  setupScroll(x, y);
217  }
218 
222  public void syncWithUntiltedCanvas(int x, int y)
223  {
224 
225  scroll(x,y);
226 
227  }
228 
229  @Override
230  public void mouseDragged(MouseEvent e)
231  {
232  super.mouseDragged(e);
233 
234  if (frame.isPickingAvailable(e)){
235 
236  if (frame.isEraserMode(e))
237  {
238  eraseAndSync(e);
239  return;
240  }
241 
242  int x = super.offScreenX(e.getX());
243  int y = super.offScreenY(e.getY());
244 
245  if (uc.getActive().getTiltedParticle() != null && um.fits(x, y, getFrame().getParticleSize())){
246  setActiveMoved(true);
247  moveActiveParticle(x, y);
248  }
249 
250  frame.setChanged(true);
251  repaint();
252  }
253  }
254 
255  public void mouseReleased(MouseEvent e)
256  {
257  super.mouseReleased(e);
258  if (frame.isPickingAvailable(e))
259  {
260  super.mouseReleased(e);
261  int x = super.offScreenX(e.getX());
262  int y = super.offScreenY(e.getY());
263  manageActive(x, y);
264  }
265  }
266 
267  public void setupScrollFromUntilted(int sx, int sy) {
268 
269  // Calculate the offset coordinates for sx and sy
270  int ox = offScreenX(sx);
271  int oy = offScreenY(sy);
272 
273  setupScroll(ox, oy);
274 
275  }
276 }
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
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xmipp.utils.XmippMessage.getOutOfBoundsMsg
static String getOutOfBoundsMsg(Object o)
Definition: XmippMessage.java:56
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.addParticleToAligner
void addParticleToAligner(UntiltedParticle up, boolean recalculateAngles)
Definition: UntiltedMicrograph.java:90
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abstract void refreshActive(PickerParticle p)
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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TiltedMicrograph.java
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1 package xmipp.viewer.particlepicker.tiltpair.model;
2 
3 import java.util.ArrayList;
4 import java.util.List;
5 
6 import xmipp.jni.Particle;
7 import xmipp.viewer.particlepicker.Micrograph;
8 import xmipp.viewer.particlepicker.PickerParticle;
9 
10 public class TiltedMicrograph extends Micrograph
11 {
12 
13  private List<TiltedParticle> particles;
14  private UntiltedMicrograph untiltedmicrograph;
15 
16  public TiltedMicrograph(String file)
17  {
18  super(file, getName(file, 1));
19  particles = new ArrayList<TiltedParticle>();
20  }
21 
22  @Override
23  public boolean hasData()
24  {
25  return !particles.isEmpty();
26  }
27 
28  @Override
29  public List<? extends PickerParticle> getParticleList() {
30  return getParticles();
31  }
32 
33 
34  public List<TiltedParticle> getParticles()
35  {
36  return particles;
37  }
38 
39  public void removeParticle(UntiltedParticle p)
40  {
41  particles.remove(p);
42 
43  }
44 
45  public void addParticle(TiltedParticle p)
46  {
47  particles.add(p);
48 
49  }
50 
51  public TiltedParticle getParticle(int x, int y, int size)
52  {
53  for (TiltedParticle p : particles)
54  if (p.contains(x, y, size))
55  return p;
56  return null;
57  }
58 
59  public void removeParticle(TiltedParticle p)
60  {
61  if (p != null)
62  {
63  particles.remove(p);
64  p.getUntiltedParticle().setTiltedParticle(null);
65  }
66  }
67 
68  public UntiltedMicrograph getUntiltedMicrograph()
69  {
70  return untiltedmicrograph;
71  }
72 
73  public void setUntiltedMicrograph(UntiltedMicrograph untiltedmicrograph)
74  {
75  this.untiltedmicrograph = untiltedmicrograph;
76  }
77 
78  public void removeParticles(int x, int y)
79  {
80  List<TiltedParticle> particles = new ArrayList<TiltedParticle>();
81  for(TiltedParticle p: getParticles())
82  if (p.contains(x, y, p.getParticlePicker().getSize()))
83  particles.add(p);
84  for(TiltedParticle p: particles)
85  removeParticle(p);
86  }
87 
88 
89 
90 }
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xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.setUntiltedMicrograph
void setUntiltedMicrograph(UntiltedMicrograph untiltedmicrograph)
Definition: TiltedMicrograph.java:73
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class  xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle
 
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package  xmipp.viewer.particlepicker.tiltpair.model
 
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1 package xmipp.viewer.particlepicker.tiltpair.model;
2 
3 import xmipp.viewer.particlepicker.training.model.ManualParticle;
4 
5 public class TiltedParticle extends ManualParticle {
6 
7  private UntiltedParticle untiltedparticle;
8 
9  public TiltedParticle(int x, int y, UntiltedParticle untiltedparticle)
10  {
11  super(x, y, untiltedparticle.getParticlePicker(), ((UntiltedMicrograph)untiltedparticle.getMicrograph()).getTiltedMicrograph());
12  this.untiltedparticle = untiltedparticle;
13  }
14 
15  public UntiltedParticle getUntiltedParticle()
16  {
17  return untiltedparticle;
18  }
19 
20 
21 
22 }
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xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle.TiltedParticle
TiltedParticle(int x, int y, UntiltedParticle untiltedparticle)
Definition: TiltedParticle.java:9
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package  xmipp.tomography.alignment
 
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1 package xmipp.tomography.alignment;
2 
3 import ij.ImageStack;
4 
5 import java.awt.Color;
6 import java.io.File;
7 import java.util.ArrayList;
8 import java.util.Date;
9 import java.util.List;
10 import java.util.logging.FileHandler;
11 import java.util.logging.Level;
12 import java.util.logging.Logger;
13 import java.util.logging.SimpleFormatter;
14 
15 import xmipp.jni.MDLabel;
16 import xmipp.jni.MetaData;
17 
18 import xmipp.utils.XmippMessage;
19 
20 public class TomoSerieAligner {
21 
22  public static void main(String[] args)
23  {
24  TomoSerieAligner aligner = new TomoSerieAligner(args[0], args[1], 50, 45);
25  aligner.alignTomographies();
26  }
27 
28  public static Logger getLogger()
29  {
30  try
31  {
32  if (logger == null)
33  {
34  FileHandler fh = new FileHandler("TomoSerieAligner.log", true);
35  fh.setFormatter(new SimpleFormatter());
36  logger = Logger.getLogger("TomoSerieAlignerLogger");
37  logger.addHandler(fh);
38  }
39  return logger;
40  }
41  catch (Exception e)
42  {
43  // TODO Auto-generated catch block
44  e.printStackTrace();
45  }
46  return null;
47  }
48 
49 
50  private static Logger logger;
51  private String tomoseriefile;
52  private String outputdir;
53  private List<Tomography> tomographies;
54  private int dmin;
55  private int dmax;
56 
57  public TomoSerieAligner(String tomoseriefile, String outputdir, int dmin, int dmax)
58  {
59  this.tomoseriefile = tomoseriefile;
60  this.outputdir = outputdir;
61  this.dmin = dmin;
62  this.dmax = dmax;
63  loadTomographies();
64  }
65 
66  public int getDmin() {
67  return dmin;
68  }
69 
70 
71 
72  public int getDmax() {
73  return dmax;
74  }
75 
76 
77 
78  private void loadTomographies()
79  {
80  tomographies = new ArrayList<Tomography>();
81  String file = tomoseriefile;
82  if (!new File(file).exists())
83  throw new IllegalArgumentException(XmippMessage.getNoSuchFieldValueMsg("tomoseriefile", tomoseriefile));
84  Tomography tomography = null, previous;
85  String tomofile;
86  int tiltangle;
87  try
88  {
89  MetaData md = new MetaData(file);
90  long[] ids = md.findObjects();
91  for (long id : ids)
92  {
93  tomofile = md.getValueString(MDLabel.MDL_IMAGE, id);
94 // System.out.println(tomofile);
95  tiltangle = md.getValueInt(MDLabel.MDL_ANGLE_TILT, id);
96  previous = tomography;
97  tomography = new Tomography(tomofile, tiltangle, previous);
98  if(previous != null)
99  previous.setNext(tomography);
100  tomographies.add(tomography);
101  }
102  if (tomographies.isEmpty())
103  throw new IllegalArgumentException(XmippMessage.getEmptyFieldMsg("tomographies"));
104  }
105  catch (Exception e)
106  {
107  getLogger().log(Level.SEVERE, e.getMessage(), e);
108  throw new IllegalArgumentException(e.getMessage());
109  }
110  }
111 
112  public List<Tomography> getTomographies()
113  {
114  return tomographies;
115  }
116 
117  public ImageStack alignTomographies()
118  {
119  System.out.println(new Date());
120  for(Tomography t: tomographies)
121  {
122  if(t.getPrevious() != null)
123  {
124  t.computeAffineTransform();
125  }
126  }
127  System.out.println(new Date());
128  return null;
129  }
130 
131 
132 }
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native long [] findObjects()
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native int getValueInt(int label, long objId)
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native String getValueString(int label, long objId)
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static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
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static String getNoSuchFieldValueMsg(String field, Object value)
Definition: XmippMessage.java:52
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static final int MDL_ANGLE_TILT
< difference between rot angles (double,degrees)
Definition: MDLabel.java:16
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xmipp.utils.XmippMessage.getEmptyFieldMsg
static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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xmipp.tomography.alignment.TomoSerieAligner.TomoSerieAligner
TomoSerieAligner(String tomoseriefile, String outputdir, int dmin, int dmax)
Definition: TomoSerieAligner.java:57
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class  xmipp.tomography.alignment.Tomography
 
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package  xmipp.tomography.alignment
 
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Tomography.java
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1 package xmipp.tomography.alignment;
2 
3 
4 import ij.ImagePlus;
5 
6 import java.awt.Rectangle;
7 import java.awt.geom.AffineTransform;
8 import java.util.Arrays;
9 import java.util.HashMap;
10 import java.util.List;
11 import java.util.Map;
12 
13 import com.labun.surf.Descriptor;
14 import com.labun.surf.Detector;
15 import com.labun.surf.IntegralImage;
16 import com.labun.surf.InterestPoint;
17 import com.labun.surf.Matcher;
18 import com.labun.surf.Params;
19 
20 import xmipp.ij.commons.XmippUtil;
21 
22 public class Tomography {
23 
24  private int tiltangle;
25  private String tomofile;
26  private Tomography previous;
27  private Tomography next;
28  private Matrix atmatrix;
29  private ImagePlus imp;
30  private IntegralImage intimg;
31 
32  public Tomography(String tomofile, int tiltangle)
33  {
34  this.tomofile = tomofile;
35  this.tiltangle = tiltangle;
36  }
37 
38  public Tomography(String tomofile, int tiltangle, Tomography previous) {
39  this(tomofile, tiltangle);
40  setPrevious(previous);
41  }
42 
43 
44  public void setPrevious(Tomography previous)
45  {
46  this.previous = previous;
47  }
48 
49  public void setNext(Tomography next)
50  {
51  this.next = next;
52  }
53 
54 
55  public Tomography getPrevious()
56  {
57  return previous;
58  }
59 
60  public Tomography getNext()
61  {
62  return next;
63  }
64 
65  public void computeAffineTransform()
66  {
67 
68  Map<InterestPoint, InterestPoint> cpm = getCommonPointsMapping();
69  if (cpm == null || cpm.isEmpty())
70  return;//no affine transform
71  System.out.println("Computing affine transform on " + tomofile + " and " + getPrevious().getTomofile());
72 
73  System.out.println(cpm.size());
74  }
75 
76 
77  private String getTomofile() {
78  return tomofile;
79  }
80 
81  public Map<InterestPoint, InterestPoint> getCommonPointsMapping()
82  {
83  if(previous == null)
84  return null;
85 
86  Params pparams = new Params(4, 4, 0.0001f, 2, false, false, false, 1, false);//octaves, layers, threshold, initialStep, upright, ...
87  Params params = new Params(pparams);
88 
89 
90  List<InterestPoint> pipoints = detectAndDescribeInterestPoints(previous.getIntegralImage(), pparams);
91  List<InterestPoint> ipoints = detectAndDescribeInterestPoints(getIntegralImage(), params);
92 
93 
94  Map<InterestPoint, InterestPoint> matchedpoints = Matcher.findMathes(pipoints, ipoints);
95  Map<InterestPoint, InterestPoint> revmatchedpoints = Matcher.findMathes(ipoints, pipoints);
96  // take only those points that matched in the reverse comparison too
97  Map<InterestPoint, InterestPoint> commonpoints = new HashMap<InterestPoint, InterestPoint>();
98  for (InterestPoint ppoint : matchedpoints.keySet()) {
99  InterestPoint point = matchedpoints.get(ppoint);
100  if (ppoint == revmatchedpoints.get(point))
101  commonpoints.put(ppoint, point);
102  }
103 
104  return commonpoints;
105  }
106 
107  public static List<InterestPoint> detectAndDescribeInterestPoints(IntegralImage intImg, Params p) {
108 
109  List<InterestPoint> ipts = Detector.fastHessian(intImg, p);
110 
111 
112  // Describe interest points with SURF-descriptor
113  if (!p.isUpright())
114  for (InterestPoint ipt: ipts)
115  Descriptor.computeAndSetOrientation(ipt, intImg);
116  for (InterestPoint ipt: ipts)
117  Descriptor.computeAndSetDescriptor(ipt, intImg, p);
118 
119  return ipts;
120  }
121 
122  public Matrix getAffineTransform()
123  {
124  return atmatrix;
125  }
126 
127  public Rectangle getOverlappedArea()
128  {
129  return null;
130  }
131 
132  public ImagePlus getImagePlus()
133  {
134  if(imp == null)
135  imp = XmippUtil.getImagePlus(tomofile);
136  return imp;
137  }
138 
139  public IntegralImage getIntegralImage()
140  {
141  if(intimg == null)
142  intimg = new IntegralImage(getImagePlus().getProcessor(), true);
143  return intimg;
144  }
145 
146 
147 
148 
149 }
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xmipp.tomography.alignment.Tomography.Tomography
Tomography(String tomofile, int tiltangle)
Definition: Tomography.java:32
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static ImagePlus getImagePlus(String file)
Definition: XmippUtil.java:55
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xmipp.tomography.alignment.Tomography.getCommonPointsMapping
Map< InterestPoint, InterestPoint > getCommonPointsMapping()
Definition: Tomography.java:81
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xmipp.tomography.alignment.Tomography.Tomography
Tomography(String tomofile, int tiltangle, Tomography previous)
Definition: Tomography.java:38
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xmipp.tomography.alignment.Tomography.detectAndDescribeInterestPoints
static List< InterestPoint > detectAndDescribeInterestPoints(IntegralImage intImg, Params p)
Definition: Tomography.java:107
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xmipp.tomography.alignment.Tomography.setPrevious
void setPrevious(Tomography previous)
Definition: Tomography.java:44
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package  xmipp.ij.commons
 
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1 package xmipp.ij.commons;
2 
3 public enum Tool
4 {
5  IMAGEJ, PICKER, VIEWER;
6 
7 
8  public static Tool getTool(String name)
9  {
10  if (name.equalsIgnoreCase("Particle Picker Tool"))
11  return Tool.PICKER;
12  else if(name.equalsIgnoreCase("Xmipp Micrograph Viewer Tool"))
13  return Tool.VIEWER;
14  return Tool.IMAGEJ;
15  }
16 
17  public static String getTool(Tool tool)
18  {
19  if(tool == Tool.PICKER)
20  return "Particle Picker Tool";
21  else if(tool == Tool.VIEWER)
22  return "Xmipp Micrograph Viewer Tool";
23  return null;
24  }
25 }
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static Tool getTool(String name)
Definition: Tool.java:8
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static String getTool(Tool tool)
Definition: Tool.java:17
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.viewer.particlepicker.training;
8 
9 import java.awt.Rectangle;
10 import java.util.logging.Level;
11 import xmipp.jni.MDRow;
12 import xmipp.jni.Particle;
13 import xmipp.jni.PickingClassifier;
14 import xmipp.utils.XmippDialog;
15 import xmipp.utils.XmippWindowUtil;
16 import xmipp.viewer.particlepicker.ParticlePicker;
17 import xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame;
18 import xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker;
19 import xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph;
20 
25 public class TrainRunnable implements Runnable
26  {
27 
28  protected SupervisedPickerJFrame frame;
29  protected MDRow[] trainInput;
30  protected Rectangle rectangle;
31  protected Particle[] autopickRows;
32  protected SupervisedPickerMicrograph micrograph;
33  protected final SupervisedParticlePicker picker;
34  protected final PickingClassifier classifier;
35 
36  public TrainRunnable(SupervisedPickerJFrame frame, MDRow[] trainInput, SupervisedPickerMicrograph trainmic)
37  {
38  this.frame = frame;
39  this.trainInput = trainInput;
40  this.micrograph = frame.getMicrograph();
41  rectangle = trainmic.getRectangle();
42  if(trainmic != micrograph)
43  trainmic.resetParticlesRectangle();
44  this.picker = frame.getParticlePicker();
45  this.classifier = (PickingClassifier)picker.getClassifier();
46  }
47 
48  public void run()
49  {
50  try
51  {
52  classifier.train(trainInput, (int) rectangle.getX(), (int) rectangle.getY(), (int) rectangle.getWidth(), (int) rectangle.getHeight());// should remove training
53  micrograph.setAutopickpercent(picker.getAutopickpercent());
54  autopickRows = classifier.autopick(micrograph.getFile(), micrograph.getAutopickpercent());
55  picker.loadParticles(micrograph, autopickRows);
56  picker.saveData(micrograph);
57  XmippWindowUtil.releaseGUI(frame.getRootPane());
58  frame.getCanvas().setEnabled(true);
59  frame.getCanvas().repaint();
60  frame.updateMicrographsModel();
61  }
62  catch (Exception e)
63  {
64  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
65  XmippDialog.showError(frame, "Classifier error");
66  }
67  }
68 
69 
70  }
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synchronized native void train(MDRow[] micrographs, int x, int y, int width, int height)
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void loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
Definition: SupervisedParticlePicker.java:1102
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xmipp.utils.XmippWindowUtil.releaseGUI
static void releaseGUI(JRootPane panel)
Definition: XmippWindowUtil.java:242
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TrainRunnable(SupervisedPickerJFrame frame, MDRow[] trainInput, SupervisedPickerMicrograph trainmic)
Definition: TrainRunnable.java:36
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.jni.PickingClassifier.autopick
synchronized native Particle [] autopick(String micrograph, int percent)
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class  Transparent_Image_Overlay
 
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1 import ij.*;
2 import ij.process.*;
3 import ij.gui.*;
4 import java.awt.*;
5 import ij.plugin.*;
6 import java.awt.image.*;
7 
8 public class Transparent_Image_Overlay implements PlugIn {
9 
10  public void run(String arg) {
11  if (IJ.versionLessThan("1.46p"))
12  return;
13  ImagePlus imp = IJ.openImage("http://imagej.nih.gov/ij/images/cardio.dcm.zip");
14  ImageProcessor ip = imp.getProcessor();
15  ip = ip.crop();
16  ip.setRoi(142, 132, 654, 616);
17  int width = ip.getWidth()/2;
18  int height = ip.getHeight()/2;
19  ip = ip.resize(width, height, true);
20  ip.setColor(Color.red);
21  ip.setFont(new Font("SansSerif",Font.PLAIN,28));
22  ip.drawString("Transparent\nImage\nOverlay", 0, 40);
23  ImageRoi imageRoi = new ImageRoi(100, 25, ip);
24  imageRoi.setZeroTransparent(true);
25  ImagePlus boats = IJ.openImage("http://imagej.nih.gov/ij/images/boats.gif");
26  Overlay overlay = new Overlay(imageRoi);
27  boats.setOverlay(overlay);
28  boats.setRoi(imageRoi);
29  boats.show();
30  for (int a=0; a<=360; a++) {
31  imageRoi.setAngle(a);
32  boats.draw();
33  IJ.wait(20);
34  }
35  }
36 
37 }
Transparent_Image_Overlay
Definition: Transparent_Image_Overlay.java:8
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Transparent_Image_Overlay.run
void run(String arg)
Definition: Transparent_Image_Overlay.java:10
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UntiltedMicrographCanvas.java File Reference
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class  xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas
 
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package  xmipp.viewer.particlepicker.tiltpair.gui
 
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UntiltedMicrographCanvas.java
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1 package xmipp.viewer.particlepicker.tiltpair.gui;
2 
3 import java.awt.Color;
4 import java.awt.Graphics2D;
5 import java.awt.event.MouseEvent;
6 
7 import javax.swing.SwingUtilities;
8 
9 import xmipp.jni.Particle;
10 import xmipp.utils.XmippDialog;
11 import xmipp.utils.XmippMessage;
12 import xmipp.utils.XmippMessageDialog;
13 import xmipp.viewer.particlepicker.ParticlePickerCanvas;
14 import xmipp.viewer.particlepicker.PickerParticle;
15 import xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker;
16 import xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle;
17 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph;
18 import xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle;
19 import xmipp.viewer.particlepicker.training.model.ManualParticle;
20 
21 public class UntiltedMicrographCanvas extends ParticlePickerCanvas
22 {
23  // Constructors
24  public UntiltedMicrographCanvas(TiltPairPickerJFrame frame)
25  {
26  super(frame);
27 
28  }
29 
30  // Fields getters and setters
31  @Override
32  public TiltPairPickerJFrame getFrame()
33  {
34  return (TiltPairPickerJFrame)frame;
35  }
36 
37  @Override
38  public UntiltedParticle getActive()
39  {
40  return (UntiltedParticle) active;
41  }
42 
43  @Override
44  public UntiltedMicrograph getMicrograph()
45  {
46  return (UntiltedMicrograph)micrograph;
47  }
48 
49  protected UntiltedParticle getLastParticle()
50  {
51  if (getMicrograph().getParticles().isEmpty())
52  return null;
53  return getMicrograph().getParticles().get(getMicrograph().getParticles().size() - 1);
54  }
55 
56 
57 
58  public TiltedParticle getActiveTiltedParticle()
59  {
60  if (hasActiveParticle()) {
61  return ((UntiltedParticle) active).getTiltedParticle();
62  }else {
63  return null;
64  }
65  }
66 
67 
68 
69  @Override
70  public TiltPairPicker getParticlePicker()
71  {
72  return (TiltPairPicker)picker;
73  }
74 
75  // Methods
76 
77  public void zoomIn(int sx, int sy)
78  {
79  super.zoomIn(sx, sy);
80 
81  if(getParticlePicker().getZoom() != getFrame().getTiltedCanvas().getMagnification())
82  getFrame().getTiltedCanvas().zoomIn(sx, sy);
83  }
84 
85  public void zoomOut(int sx, int sy)
86  {
87  super.zoomOut(sx, sy);
88 
89  if(getParticlePicker().getZoom() != getFrame().getTiltedCanvas().getMagnification())
90  getFrame().getTiltedCanvas().zoomOut(sx, sy);
91  }
92 
93  private void addParticle(int x, int y)
94  {
95  try
96  {
97  if (active != null && getActive().getTiltedParticle() == null)
98  {
99  XmippMessageDialog.showInfo(frame, "Remember to pick tilted particle for each particle");
100  return;
101  }
102  Particle tp = getMicrograph().getAlignedTiltedParticle(x, y);
103  if (getMicrograph().getAddedCount() > UntiltedMicrograph.getAlignmentMin() && !getMicrograph().getTiltedMicrograph().fits(tp.getX(), tp.getY(), getParticlePicker().getSize()))
104  throw new IllegalArgumentException(XmippMessage.getOutOfBoundsMsg("Tilted particle"));
105  UntiltedParticle p = new UntiltedParticle(x, y, getMicrograph(), getParticlePicker());
106 
107  getMicrograph().addParticle(p);
108 
109  if (tp != null)
110  getMicrograph().setAlignedTiltedParticle(p);
111  refreshActive(p);
112  frame.updateMicrographsModel();
113  frame.setChanged(true);
114  }
115  catch (Exception e)
116  {
117  XmippDialog.showInfo(frame, e.getMessage());
118  }
119 
120  }
121 
122 
123  @Override
124  protected void removeParticle(PickerParticle particleToRemove) {
125 
126  UntiltedParticle toRemove = (UntiltedParticle) particleToRemove;
127 
128  getMicrograph().removeParticle(toRemove);
129 
130  if (active != null && active.equals(toRemove))
131  {
132  if (!getMicrograph().getParticles().isEmpty())
133  refreshActive(getMicrograph().getParticles().get(getMicrograph().getParticles().size() - 1));
134  else
135  refreshActive(null);
136  }
137 
138 
139  if (toRemove.isAdded())
140  getMicrograph().initAligner();
141  refresh();
142  getFrame().getTiltedCanvas().repaint();
143  }
144 
145  public void refreshActive(PickerParticle up)
146  {
147 
148  if (up != null)
149  {
150  active = up;
151  TiltedParticle tp = getActive().getTiltedParticle();
152  if (tp != null)
153  {
154  int x = getFrame().getTiltedCanvas().getXOnImage(tp.getX());
155  int y = getFrame().getTiltedCanvas().getYOnImage(tp.getY());
156 
157  if (!micrograph.fits(x, y, getParticlePicker().getSize()))
158  getFrame().getTiltedCanvas().moveTo(tp);
159  }
160  }
161  else
162  active = null;
163  repaint();
164  getFrame().getTiltedCanvas().repaint();
165  }
166 
167  protected void manageActive(int x, int y)
168  {
169 
170  UntiltedParticle activeParticle = getActive();
171 
172  if (!activemoved)
173  return;
174 
175  if (micrograph.fits(x, y, getFrame().getParticleSize()))
176  {
177  moveActiveParticle(x, y);
178 
179  }
180  if (activeParticle.isAdded())// added particle on matrix has been moved. Matrix
181  // changed and tilted particle has to be
182  // recalculated
183  {
184  activeParticle.setAdded(false);
185  getMicrograph().initAligner();
186  }
187  getFrame().getTiltedCanvas().repaint();
188  setActiveMoved(false);
189  }
190 
191  @Override
192  public void customScrollSetup(MouseEvent e){
193 
194  super.customScrollSetup(e);
195  getFrame().getTiltedCanvas().setupScrollFromUntilted(e.getX(),e.getY());
196 
197  }
198  @Override
199  protected void doCustomPaint(Graphics2D g2)
200  {
201  g2.setColor(getFrame().getColor());
202  for (ManualParticle p : getMicrograph().getParticles())
203  {
204  drawShape(g2, p, false);
205  }
206  if (active != null)
207  {
208  g2.setColor(Color.red);
209  drawShape(g2, getActive(), true);
210  }
211  if (getFrame().drawAngles())
212  drawLine(Math.toRadians(getMicrograph().getUntiltedAngle()), g2);
213 
214  }
215 
216  // Event listeners
217 
224  public void mousePressed(MouseEvent e)
225  {
226  super.mousePressed(e);
227  if (frame.isPickingAvailable(e))
228  {
229 
230  if (frame.isEraserMode(e))
231  {
232  erase(e);
233  getFrame().getTiltedCanvas().repaint();
234  return;
235 
236  }
237 
238  UntiltedParticle activeParticle = getActive();
239 
240  if (!isDragImage(e)){
241 
242  int x = super.offScreenX(e.getX());
243  int y = super.offScreenY(e.getY());
244 
245  if (active != null && !activeParticle.isAdded() && activeParticle.getTiltedParticle() != null)
246  getMicrograph().addParticleToAligner(activeParticle, true);
247 
248  UntiltedParticle p = getMicrograph().getParticle(x, y, getParticlePicker().getSize());
249 
250  if(p == null && activeParticle != null && activeParticle.contains(x, y))
251  p = activeParticle;
252  if (p != null)
253  {
254  if (SwingUtilities.isLeftMouseButton(e) && e.isShiftDown())
255  removeParticle(p);
256  else if (SwingUtilities.isLeftMouseButton(e))
257  refreshActive(p);
258  }
259  else if (SwingUtilities.isLeftMouseButton(e))
260  {
261  if (micrograph.fits(x, y, getFrame().getParticleSize()))
262  addParticle(x, y);
263  else
264  XmippMessageDialog.showInfo(frame, XmippMessage.getOutOfBoundsMsg(String
265  .format("Particle centered at %s, %s with size %s", x, y, frame.getParticlePicker().getSize())));
266  }
267  }
268  }
269  }
270 
271 
272 
273  @Override
274  public void mouseDragged(MouseEvent e)
275  {
276  super.mouseDragged(e);
277 
278  // Sync screen view with tilted canvas
279  if (isDragImage(e)){
280  getFrame().getTiltedCanvas().syncWithUntiltedCanvas(e.getX(),e.getY());
281  return;
282  }
283 
284  if (frame.isPickingAvailable(e)){
285 
286  if (frame.isEraserMode(e))
287  {
288  erase(e);
289  return;
290  }
291 
292  int x = super.offScreenX(e.getX());
293  int y = super.offScreenY(e.getY());
294 
295  if (active != null && micrograph.fits(x, y, getFrame().getParticleSize())){
296  setActiveMoved(true);
297  moveActiveParticle(x, y);
298  }
299  frame.setChanged(true);
300  repaint();
301  }
302 
303  }
304 
305 
306  public void mouseReleased(MouseEvent e)
307  {
308  super.mouseReleased(e);
309  if (frame.isPickingAvailable(e))
310  {
311  int x = super.offScreenX(e.getX());
312  int y = super.offScreenY(e.getY());
313  manageActive(x, y);
314  }
315 
316  }
317 }
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abstract void setChanged(boolean changed)
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.utils.XmippMessage.getOutOfBoundsMsg
static String getOutOfBoundsMsg(Object o)
Definition: XmippMessage.java:56
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.addParticleToAligner
void addParticleToAligner(UntiltedParticle up, boolean recalculateAngles)
Definition: UntiltedMicrograph.java:90
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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UntiltedMicrograph.java
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1 package xmipp.viewer.particlepicker.tiltpair.model;
2 
3 import java.util.ArrayList;
4 import java.util.List;
5 import xmipp.jni.Particle;
6 import xmipp.jni.TiltPairAligner;
7 import xmipp.utils.XmippMessage;
8 import xmipp.viewer.particlepicker.Micrograph;
9 import xmipp.viewer.particlepicker.PickerParticle;
10 
11 public class UntiltedMicrograph extends Micrograph
12 {
13 
14  private static int alignmentmin = 4;
15  private TiltedMicrograph tiltedmicrograph;
16  private List<UntiltedParticle> particles;
17  private TiltPairAligner tpa;
18  private int added;
19  private double[] angles;
20 
21  public UntiltedMicrograph(String file, TiltedMicrograph tiltedmicrograph)
22  {
23  super(file, getName(file, 1));
24  this.tiltedmicrograph = tiltedmicrograph;
25  particles = new ArrayList<UntiltedParticle>();
26  tpa = new TiltPairAligner();
27 
28  }
29 
30  public int getAddedCount()
31  {
32  return added;
33  }
34 
35  public TiltedMicrograph getTiltedMicrograph()
36  {
37  return tiltedmicrograph;
38  }
39 
40  public UntiltedParticle getParticle(int x, int y, int size)
41  {
42  for (UntiltedParticle p : particles)
43  if (p.contains(x, y, size))
44  return p;
45  return null;
46 
47  }
48 
49  @Override
50  public boolean hasData()
51  {
52  return !particles.isEmpty();
53  }
54 
55  @Override
56  public List<? extends PickerParticle> getParticleList() {
57  return getParticles();
58  }
59 
60 
61  public void reset(TiltPairPicker picker)
62  {
63  angles = null;
64  for(UntiltedParticle p: particles)
65  p.setTiltedParticle(null);
66  getParticles().clear();
67  getTiltedMicrograph().getParticles().clear();
68  //JMRT: I think is very very dangerous to delete the existing pos files.
69  //new File(picker.getOutputPath(getPosFile())).delete();
70  //new File(picker.getOutputPath(getTiltedMicrograph().getPosFile())).delete();
71  initAligner();
72  }
73 
74  public void removeParticle(UntiltedParticle p)
75  {
76  particles.remove(p);
77  tiltedmicrograph.removeParticle(p.getTiltedParticle());
78  }
79 
80  public void addParticle(UntiltedParticle p)
81  {
82  particles.add(p);
83  }
84 
85  public List<UntiltedParticle> getParticles()
86  {
87  return particles;
88  }
89 
90  public void addParticleToAligner(UntiltedParticle up, boolean recalculateAngles)
91  {
92  if (up.getTiltedParticle() == null)
93  throw new IllegalArgumentException(XmippMessage.getEmptyFieldMsg("TiltedParticle"));
94  tpa.addParticleToAligner(up.getX(), up.getY(), up.getTiltedParticle().getX(), up.getTiltedParticle().getY());
95  up.setAdded(true);
96  added++;
97  if (anglesAvailable() && recalculateAngles)
98  angles = tpa.computeAngles();
99  }
100 
101  public void initAligner()
102  {
103  tpa.clear();
104  added = 0;
105  for (UntiltedParticle p : particles)
106  if (p.getTiltedParticle() != null)
107  addParticleToAligner(p, false);
108  if (anglesAvailable())
109  angles = tpa.computeAngles();
110  }
111 
112  public boolean anglesAvailable()
113  {
114  return !(added < 10);
115  }
116 
117  // public double[] getAngles()
118  // {
119  // return angles;
120  // }
121 
122  public double getUntiltedAngle()
123  {
124  if (angles == null)
125  return 90;
126  return angles[0];
127  }
128 
129  public double getTiltedAngle()
130  {
131  if (angles == null)
132  return 90;
133  return angles[1];
134  }
135 
136  public double getTiltAngle()
137  {
138  if (angles == null)
139  return 0;
140  return angles[2];
141  }
142 
143  public Particle getAlignedTiltedParticle(int x, int y)
144  {
145  if (getAddedCount() < getAlignmentMin())
146  return null;
147  Particle p = tpa.getTiltedParticle(x, y);
148  return p;
149  }
150 
151  public Particle getAlignedUntiltedParticle(int x, int y)
152  {
153  if (getAddedCount() < getAlignmentMin())
154  return null;
155  Particle p = tpa.getUntiltedParticle(x, y);
156  return p;
157  }
158 
159  public void setAlignedTiltedParticle(UntiltedParticle up)
160  {
161  tiltedmicrograph.removeParticle(up.getTiltedParticle());
162  Particle p = getAlignedTiltedParticle(up.getX(), up.getY());
163  if(!tiltedmicrograph.fits(p.getX(), p.getY(), up.getParticlePicker().getSize()))
164  p = null;
165  if (p != null)
166  {
167  TiltedParticle tp = new TiltedParticle(p.getX(), p.getY(), up);
168  getTiltedMicrograph().addParticle(tp);
169  up.setTiltedParticle(tp);
170  }
171  }
172 
173  public void removeParticles(int x, int y)
174  {
175  List<UntiltedParticle> particles = new ArrayList<UntiltedParticle>();
176  for (UntiltedParticle p : getParticles())
177  if (p.contains(x, y, p.getParticlePicker().getSize()))
178  particles.add(p);
179  for (UntiltedParticle p : particles)
180  removeParticle(p);
181  }
182 
183  public static int getAlignmentMin()
184  {
185  return alignmentmin;
186  }
187 
188 }
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.UntiltedMicrograph
UntiltedMicrograph(String file, TiltedMicrograph tiltedmicrograph)
Definition: UntiltedMicrograph.java:21
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xmipp.jni.TiltPairAligner.addParticleToAligner
native void addParticleToAligner(int x1, int y1, int x2, int y2)
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.addParticleToAligner
void addParticleToAligner(UntiltedParticle up, boolean recalculateAngles)
Definition: UntiltedMicrograph.java:90
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xmipp.jni.TiltPairAligner.computeAngles
native double [] computeAngles()
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xmipp.utils.XmippMessage.getEmptyFieldMsg
static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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1 package xmipp.viewer.particlepicker.tiltpair.model;
2 
3 import xmipp.viewer.particlepicker.ParticlePicker;
4 import xmipp.viewer.particlepicker.training.model.ManualParticle;
5 
6 
7 public class UntiltedParticle extends ManualParticle{
8 
9  private TiltedParticle tiltedparticle;
10  private boolean added = false;
11 
12 
13  public boolean isAdded()
14  {
15  return added;
16  }
17 
18  public UntiltedParticle(int x, int y, UntiltedMicrograph micrograph, ParticlePicker picker)
19  {
20  super(x, y, picker, micrograph);
21 
22  }
23 
24  public void setTiltedParticle(TiltedParticle tiltedparticle)
25  {
26  this.tiltedparticle = tiltedparticle;
27  }
28 
29  public TiltedParticle getTiltedParticle()
30  {
31  return tiltedparticle;
32  }
33 
34  public void setAdded(boolean added)
35  {
36  this.added = added;
37  }
38 
39 
40 
41 
42 }
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle.UntiltedParticle
UntiltedParticle(int x, int y, UntiltedMicrograph micrograph, ParticlePicker picker)
Definition: UntiltedParticle.java:18
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package  xmipp.viewer
 
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1 /*
2  * Copyright (c) 1995, 2008, Oracle and/or its affiliates. All rights reserved.
3  *
4  * Redistribution and use in source and binary forms, with or without
5  * modification, are permitted provided that the following conditions
6  * are met:
7  *
8  * - Redistributions of source code must retain the above copyright
9  * notice, this list of conditions and the following disclaimer.
10  *
11  * - Redistributions in binary form must reproduce the above copyright
12  * notice, this list of conditions and the following disclaimer in the
13  * documentation and/or other materials provided with the distribution.
14  *
15  * - Neither the name of Oracle or the names of its
16  * contributors may be used to endorse or promote products derived
17  * from this software without specific prior written permission.
18  *
19  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
20  * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
21  * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
22  * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
23  * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
24  * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
25  * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
26  * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
27  * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
28  * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
29  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
30  */
31 
32 package xmipp.viewer;
33 
34 /*
35  * ToolBarDemo2.java requires the following addditional files:
36  * images/Back24.gif
37  * images/Forward24.gif
38  * images/Up24.gif
39  */
40 
41 import javax.swing.JToolBar;
42 import javax.swing.JButton;
43 import javax.swing.ImageIcon;
44 import javax.swing.JTextField;
45 
46 import javax.swing.JFrame;
47 import javax.swing.JTextArea;
48 import javax.swing.JScrollPane;
49 import javax.swing.JPanel;
50 import javax.swing.UIManager;
51 import javax.swing.SwingUtilities;
52 
53 import java.net.URL;
54 
55 import java.awt.BorderLayout;
56 import java.awt.Dimension;
57 import java.awt.event.ActionEvent;
58 import java.awt.event.ActionListener;
59 
60 public class ViewerTest extends JPanel
61  implements ActionListener {
62  protected JTextArea textArea;
63  protected String newline = "\n";
64  static final private String PREVIOUS = "previous";
65  static final private String UP = "up";
66  static final private String NEXT = "next";
67  static final private String SOMETHING_ELSE = "other";
68  static final private String TEXT_ENTERED = "text";
69 
70  public ViewerTest() {
71  super(new BorderLayout());
72 
73  //Create the toolbar.
74  JToolBar toolBar = new JToolBar("Still draggable");
75  addButtons(toolBar);
76  toolBar.setFloatable(false);
77  toolBar.setRollover(true);
78 
79  //Create the text area used for output. Request
80  //enough space for 5 rows and 30 columns.
81  textArea = new JTextArea(5, 30);
82  textArea.setEditable(false);
83  JScrollPane scrollPane = new JScrollPane(textArea);
84 
85  //Lay out the main panel.
86  setPreferredSize(new Dimension(450, 130));
87  add(toolBar, BorderLayout.PAGE_START);
88  add(scrollPane, BorderLayout.CENTER);
89  }
90 
91  protected void addButtons(JToolBar toolBar) {
92  JButton button = null;
93 
94  //first button
95  button = makeNavigationButton("save", PREVIOUS,
96  "Save something",
97  "Save");
98  toolBar.add(button);
99 
100  //first button
101  button = makeNavigationButton("left", PREVIOUS,
102  "Back to previous something-or-other",
103  "Previous");
104  toolBar.add(button);
105 
106  //second button
107  button = makeNavigationButton("up", UP,
108  "Up to something-or-other",
109  "Up");
110  toolBar.add(button);
111 
112  //third button
113  button = makeNavigationButton("right", NEXT,
114  "Forward to something-or-other",
115  "Next");
116  toolBar.add(button);
117 
118  //separator
119  toolBar.addSeparator();
120 
121  //fourth button
122  button = new JButton("Another button");
123  button.setActionCommand(SOMETHING_ELSE);
124  button.setToolTipText("Something else");
125  button.addActionListener(this);
126  toolBar.add(button);
127 
128  //fifth component is NOT a button!
129  JTextField textField = new JTextField("A text field");
130  textField.setColumns(10);
131  textField.addActionListener(this);
132  textField.setActionCommand(TEXT_ENTERED);
133  toolBar.add(textField);
134  }
135 
136  protected JButton makeNavigationButton(String imageName,
137  String actionCommand,
138  String toolTipText,
139  String altText) {
140  //Look for the image.
141  String imgLocation = "/home/josem/xmipp_current/resources/"
142  + imageName
143  + ".png";
144  //URL imageURL = ViewerTest.class.getResource(imgLocation);
145 
146  //Create and initialize the button.
147  JButton button = new JButton();
148  button.setActionCommand(actionCommand);
149  button.setToolTipText(toolTipText);
150  button.addActionListener(this);
151 
152  //if (imageURL != null) { //image found
153  button.setIcon(new ImageIcon(imgLocation, altText));
154 // } else { //no image found
155 // button.setText(altText);
156 // System.err.println("Resource not found: "
157 // + imgLocation);
158 // }
159 
160  return button;
161  }
162 
163  public void actionPerformed(ActionEvent e) {
164  String cmd = e.getActionCommand();
165  String description = null;
166 
167  // Handle each button.
168  if (PREVIOUS.equals(cmd)) { //first button clicked
169  description = "taken you to the previous <something>.";
170  } else if (UP.equals(cmd)) { // second button clicked
171  description = "taken you up one level to <something>.";
172  } else if (NEXT.equals(cmd)) { // third button clicked
173  description = "taken you to the next <something>.";
174  } else if (SOMETHING_ELSE.equals(cmd)) { // fourth button clicked
175  description = "done something else.";
176  } else if (TEXT_ENTERED.equals(cmd)) { // text field
177  JTextField tf = (JTextField)e.getSource();
178  String text = tf.getText();
179  tf.setText("");
180  description = "done something with this text: "
181  + newline + " \""
182  + text + "\"";
183  }
184 
185  displayResult("If this were a real app, it would have "
186  + description);
187  }
188 
189  protected void displayResult(String actionDescription) {
190  textArea.append(actionDescription + newline);
191  textArea.setCaretPosition(textArea.getDocument().getLength());
192  }
193 
199  static public void createAndShowGUI() {
200  //Create and set up the window.
201  JFrame frame = new JFrame("ToolBarDemo2");
202  frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
203 
204  //Add content to the window.
205  frame.add(new ViewerTest());
206 
207  //Display the window.
208  frame.pack();
209  frame.setLocationRelativeTo(null);
210  frame.setVisible(true);
211  }
212 
213  public static void main(String[] args) {
214  //Schedule a job for the event dispatch thread:
215  //creating and showing this application's GUI.
216  SwingUtilities.invokeLater(new Runnable() {
217  public void run() {
218  //Turn off metal's use of bold fonts
219  UIManager.put("swing.boldMetal", Boolean.FALSE);
220  createAndShowGUI();
221  }
222  });
223  }
224 }
xmipp.viewer.ViewerTest.addButtons
void addButtons(JToolBar toolBar)
Definition: ViewerTest.java:91
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xmipp.viewer.ViewerTest.main
static void main(String[] args)
Definition: ViewerTest.java:213
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xmipp.viewer.ViewerTest.displayResult
void displayResult(String actionDescription)
Definition: ViewerTest.java:189
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xmipp.viewer.ViewerTest.makeNavigationButton
JButton makeNavigationButton(String imageName, String actionCommand, String toolTipText, String altText)
Definition: ViewerTest.java:136
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xmipp.viewer.ViewerTest.actionPerformed
void actionPerformed(ActionEvent e)
Definition: ViewerTest.java:163
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xmipp.viewer.ViewerTest.createAndShowGUI
static void createAndShowGUI()
Definition: ViewerTest.java:199
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1 package xmipp.viewer;
2 
3 import javax.swing.SwingUtilities;
4 import xmipp.utils.DEBUG;
5 import xmipp.utils.Params;
6 import xmipp.utils.StopWatch;
7 
8 import xmipp.viewer.windows.ImagesWindowFactory;
9 
10 public class Viewer
11 {
12  public static void main(String args[])
13  {
14  StopWatch stopWatch = StopWatch.getInstance();
15  stopWatch.printElapsedTime("starting app");
16  // Schedule a job for the event dispatch thread:
17  // creating and showing this application's GUI.
18  final String[] myargs = args;
19  SwingUtilities.invokeLater(new Runnable()
20  {
21  public void run()
22  {
23  Params parameters = new Params(myargs);
24  try
25  {
26  if (parameters.debug)
27  DEBUG.enableDebug(true);
28 
29  if (parameters.files != null)
30  {
31  // DEBUG.enableDebug(true);
32  openFiles(parameters);
33  }
34  }
35  catch (Exception e)
36  {
37  e.printStackTrace();
38  }
39 
40  }
41  });
42  }
43 
44 
45 
46  static void openFiles(Params parameters) throws Exception
47  {
48  ImagesWindowFactory.openFilesAsDefault(parameters.files, parameters);
49  }
50 
51 
52 }
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void printElapsedTime(String comment)
Definition: StopWatch.java:43
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static void openFilesAsDefault(String filenames[], Params parameters)
Definition: ImagesWindowFactory.java:47
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static StopWatch getInstance()
Definition: StopWatch.java:26
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String files[]
Definition: Params.java:58
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xmipp.viewer.Viewer.main
static void main(String args[])
Definition: Viewer.java:12
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Definition: DEBUG.java:14
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.viewer.models;
27 
28 import ij.ImagePlus;
29 import xmipp.ij.commons.ImagePlusLoader;
30 import xmipp.ij.commons.XmippImageConverter;
31 import xmipp.jni.Filename;
32 import xmipp.jni.ImageGeneric;
33 import xmipp.utils.DEBUG;
34 import xmipp.utils.XmippPopupMenuCreator;
35 import xmipp.viewer.ImageDimension;
36 import xmipp.viewer.windows.ImagesWindowFactory;
37 
38 
39 
40 public class VolumeGalleryTableModel extends ImageGalleryTableModel {
41 
42  protected String volFn;
43  protected long volNumber;
44  ImageGeneric volume;
45 
46  public VolumeGalleryTableModel(GalleryData data) throws Exception {
47  super(data, null);
48  data.normalize = true; // volumes are displayed with global
49  // normalization by default
50  selection = new boolean[n];
51  calculateMinAndMax();
52  }
53 
54  private static final long serialVersionUID = 1L;
55 
56  // Load initial dimensions
57  protected ImageDimension loadDimension() throws Exception {
58  volFn = Filename.getFilename(data.selectedVolFn);
59  DEBUG.printFormat("loading volFn: %s", volFn);
60  volNumber = Filename.getNimage(data.selectedVolFn);
61  volume = new ImageGeneric(data.selectedVolFn); // read image header
62  volume.read(volNumber);
63  if (data.resliceView != ImageGeneric.Z_NEG)
64  volume.reslice(data.resliceView);
65  ImageDimension dim = new ImageDimension(volume);
66  n = dim.getZDim();
67  image_width = dim.getXDim();
68  image_height = dim.getYDim();
69  return dim;
70  }
71 
72  // @Override
73  // protected void setZoomValue(int z) {
74  // super.setZoomValue(z);
75  // try {
76  // volume.read(thumb_width, thumb_height, volNumber);
77  // } catch (Exception e) {
78  // e.printStackTrace();
79  // }
80  // }
81 
82  @Override
83  protected double[] getMinAndMax() {
84  try {
85  // ImageGeneric image = new ImageGeneric(volFn);
86  // image.read(volNumber);
87  double[] stats = volume.getStatistics();
88  // image.destroy();
89  return stats;
90  } catch (Exception ex) {
91  ex.printStackTrace();
92  }
93  return null;
94  }
95 
96  @Override
97  public String getItemKey(int index) throws Exception {
98  return String.format("%d_(%d,%d)", index, thumb_width, thumb_height);
99  }
100 
101  @Override
102  public String getTitle() {
103  return String.format("Volume: %s (%d x %d x %d)", data.selectedVolFn,
104  image_width, image_height, n);
105  }
106 
107  @Override
108  protected ImageItem createItem(int index, String key, ColumnInfo ci) throws Exception {
109  ImageGeneric preview = new ImageGeneric();
110  volume.getPreview(preview, thumb_width, thumb_height, index + 1,
111  ImageGeneric.FIRST_IMAGE);
112  ImagePlus imp = new ImagePlusLoader(preview, data.inverty).getImagePlus();
113  ImageItem item = new ImageItem(index, imp);
114  //item.setImagePlus(imp);
115  return item;
116  }
117 
118  @Override
119  public boolean handleDoubleClick(int row, int col) {
120  try {
121  int index = getIndex(row, col);
122  //ImagePlus imp = XmippImageConverter.convertToImagePlus(volume, ImageGeneric.FIRST_IMAGE, index + 1);
123  ImagePlusLoader loader = new ImagePlusLoader(index + 1, volume, data.inverty);
124  ImagesWindowFactory.openXmippImageWindow(loader, data.parameters);
125  return true;
126  } catch (Exception e) {
127  e.printStackTrace();
128  }
129  return false;
130  }// function handleDoubleClick
131 
132  @Override
133  public String getLabel(int row, int col) {
134  int index = getIndex(row, col);
135  return String.format("slice %d", index + 1);
136  }
137 
138  @Override
139  public ImagePlusLoader getImageLoader() {
140  try {
141  ImagePlusLoader loader = new ImagePlusLoader(data.selectedVolFn, data.inverty);
142  if(data.normalize)
143  loader.setNormalize(normalize_min, normalize_max);
144  return loader;
145  } catch (Exception e) {
146  e.printStackTrace();
147  }
148  return null;
149  }
150 
151  @Override
152  public boolean handleRightClick(int row, int col,
153  XmippPopupMenuCreator xpopup) {
154  return false;
155  }
156 
157  @Override
158  public boolean showLabels() {
159  return false;
160  }
161 
162 
163 
164 }// class VolumeGallery
xmipp.jni.ImageGeneric.reslice
native void reslice(int view)
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void setNormalize(double normalize_min, double normalize_max)
Definition: ImagePlusLoader.java:97
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static void printFormat(String format, Object...objects)
Definition: DEBUG.java:24
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Definition: ImageGeneric.java:126
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static final int Z_NEG
Definition: ImageGeneric.java:35
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Definition: Filename.java:320
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static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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static XmippIJWindow openXmippImageWindow(ImagePlus imp, Params params)
Definition: ImagesWindowFactory.java:134
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static String getFilename(String filename)
Definition: Filename.java:302
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ImageItem createItem(int index, String key, ColumnInfo ci)
Definition: VolumeGalleryTableModel.java:108
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boolean handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)
Definition: VolumeGalleryTableModel.java:152
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native void getPreview(ImageGeneric imgOut, int xdim, int ydim, int select_slice, long select_image)
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1 /*
2  * To change this license header, choose License Headers in Project Properties.
3  * To change this template file, choose Tools | Templates
4  * and open the template in the editor.
5  */
6 
7 package xmipp.viewer.windows;
8 
9 import ij.ImagePlus;
10 import java.util.ArrayList;
11 import xmipp.ij.commons.ImagePlusLoader;
12 import xmipp.ij.commons.XmippImageConverter;
13 import xmipp.ij.commons.XmippImageWindow;
14 import xmipp.jni.ImageGeneric;
15 import xmipp.jni.MDLabel;
16 import xmipp.jni.MDRow;
17 import xmipp.jni.MetaData;
18 import xmipp.utils.XmippDialog;
19 import xmipp.utils.XmippWindowUtil;
20 
25 public class Worker implements Runnable
26  {
27  public static final int STATS = 0;
28  public static final int PCA = 1;
29  public static final int FSC = 2;
30  public String message;
32  private int op; // store operation
33  private MetaData imagesmd;
34  private GalleryJFrame frame = null;
35 
36  public Worker(int operation, boolean selected, GalleryJFrame frame)
37  {
38  this.frame = frame;
39 
40  op = operation;
41  imagesmd = frame.data.getImagesMd(frame.gallery.getSelection(), selected);
42  if (imagesmd.size() == 0)
43  throw new IllegalArgumentException("No images available");
44  }
45 
46  public void run()
47  {
48  try
49  {
50  switch (op)
51  {
52  case STATS:
53  computeStatsImages();
54  break;
55  case PCA:
56  pca();
57  break;
58  case FSC:
59  fsc();
60  break;
61  }
62  }
63  catch (Exception e)
64  {
65  XmippWindowUtil.releaseGUI(frame.getRootPane());
66  XmippDialog.showException(frame, e);
67  return;
68 
69  }
70  XmippWindowUtil.releaseGUI(frame.getRootPane());
71  }
72 
73  public String getMessage()
74  {
75  switch (op)
76  {
77  case STATS:
78  return "Computing average and std images...";
79  case PCA:
80  return "Computing PCA...";
81  case FSC:
82  return "Computing FSC...";
83  }
84  return "";
85  }
86 
87  private void computeStatsImages() throws Exception
88  {
89  ImageGeneric imgAvg = new ImageGeneric();
90  ImageGeneric imgStd = new ImageGeneric();
91 
92  imagesmd.getStatsImages(imgAvg, imgStd, frame.data.useGeo(), frame.data.isWrap(), MDLabel.MDL_IMAGE);
93  ImagePlus impAvg = XmippImageConverter.convertToImagePlus(imgAvg);
94  ImagePlus impStd = XmippImageConverter.convertToImagePlus(imgStd);
95  imgAvg.destroy();
96  imgStd.destroy();
97 
98  XmippImageWindow winAvg = new XmippImageWindow(new ImagePlusLoader(impAvg), "AVG:", frame.data.parameters);
99  XmippWindowUtil.setLocation(0.2f, 0.5f, winAvg, frame);
100  winAvg.setVisible(true);
101  XmippImageWindow winStd = new XmippImageWindow(new ImagePlusLoader(impStd), "STD:", frame.data.parameters);
102 
103  XmippWindowUtil.setLocation(0.8f, 0.5f, winStd, frame);
104  winStd.setVisible(true);
105  }
106 
107  public void pca() throws Exception
108  {
109  ImageGeneric image = new ImageGeneric();
110  imagesmd.getPCAbasis(image, MDLabel.MDL_IMAGE);
111  ImagePlus imp = XmippImageConverter.convertToImagePlus(image);
112  imp.setTitle("PCA: " + frame.data.getFileName());
113  ImagesWindowFactory.openXmippImageWindow(imp, frame.data.parameters);
114 
115  }
116 
117  public void fsc() throws Exception
118  {
119  FSCJFrame fscframe = new FSCJFrame(frame.data, imagesmd, MDLabel.MDL_IMAGE);
120  XmippWindowUtil.centerWindows(fscframe, frame);
121  fscframe.setVisible(true);
122  }
123 
124 
125 
126 
127  public MDRow[] getImagesMd(MetaData md, int idlabel) {
128 
129  MDRow mdRow;
130  ArrayList<MDRow> imagesmd = new ArrayList<MDRow>();
131  int index = 0;
132  String imagepath;
133  for (long id : md.findObjects()) {
134  if (frame.data.isEnabled(index)) {
135  imagepath = md.getValueString(idlabel, id, true);
136  System.out.println(imagepath);
137  if (imagepath != null && ImageGeneric.exists(imagepath)) {
138  mdRow = new MDRow();
139  if (frame.data.useGeo())
140  md.getRow(mdRow, id);//copy geo info in mdRow
141  mdRow.setValueString(idlabel, imagepath);
142  imagesmd.add(mdRow);
143  }
144  }
145  index++;
146  }
147  return imagesmd.toArray(new MDRow[]{});
148  }
149 
150  }
151 
152 
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native boolean setValueString(int label, String value)
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xmipp.jni.ImageGeneric.destroy
synchronized native void destroy()
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xmipp.viewer.windows.Worker.Worker
Worker(int operation, boolean selected, GalleryJFrame frame)
Definition: Worker.java:36
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xmipp.viewer.windows.Worker.FSC
static final int FSC
Definition: Worker.java:29
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xmipp.jni.MetaData.getPCAbasis
native void getPCAbasis(ImageGeneric basis, int label)
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xmipp.jni.ImageGeneric.exists
static boolean exists(String imagepath)
Definition: ImageGeneric.java:291
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xmipp.jni.MetaData.getRow
native void getRow(MDRow mdRow, long objId)
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xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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boolean showException(Exception e)
Definition: XmippDialog.java:217
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xmipp.viewer.windows.Worker.STATS
static final int STATS
Definition: Worker.java:27
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xmipp.utils.XmippWindowUtil.centerWindows
static void centerWindows(Window w)
Definition: XmippWindowUtil.java:94
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xmipp.viewer.windows.Worker.PCA
static final int PCA
Definition: Worker.java:28
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native long [] findObjects()
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native int size()
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static void releaseGUI(JRootPane panel)
Definition: XmippWindowUtil.java:242
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native String getValueString(int label, long objId)
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native void getStatsImages(ImageGeneric imageAvg, ImageGeneric imageStd, boolean applyGeo, boolean wrap, int label)
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static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
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static XmippIJWindow openXmippImageWindow(ImagePlus imp, Params params)
Definition: ImagesWindowFactory.java:134
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MDRow [] getImagesMd(MetaData md, int idlabel)
Definition: Worker.java:127
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1 package xmipp.ij.commons;
2 
3 
4 
5 public class XmippApplication
6 {
7 
8  private static short instances = 0;
9  private static short ijwindows = 0;
10  private static boolean isscipion = false;
11 
12 
13  public static short getInstances()
14  {
15  return instances;
16  }
17 
18  public static void addInstance(boolean isijwindow)
19  {
20  instances ++;
21  if(isijwindow)
22  ijwindows ++;
23  //System.out.printf("instances:%s\n", instances);
24  }
25 
26 
27 
28  public static void removeInstance(boolean isijwindow)
29  {
30  instances --;
31  if(isijwindow)
32  {
33  ijwindows --;
34  if(XmippUtil.getXmippImageJ() != null && ijwindows == 0)
35  XmippUtil.getXmippImageJ().setVisible(false);//if ImageJ is not shared hide it
36  }
37  //System.out.printf("instances %s\n", instances);
38  if (instances == 0)
39  System.exit(0);
40 
41  }
42 
43  public static boolean isScipion()
44  {
45  return isscipion;
46  }
47 
48  public static void setIsScipion(boolean isscipion)
49  {
50  XmippApplication.isscipion = isscipion;
51  }
52 
53 
54 }
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Definition: XmippApplication.java:48
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static XmippImageJ getXmippImageJ()
Definition: XmippUtil.java:49
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Definition: XmippApplication.java:28
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Definition: XmippApplication.java:18
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 import java.awt.BorderLayout;
29 import java.awt.Container;
30 import java.awt.Dialog;
31 import java.awt.FlowLayout;
32 import java.awt.Window;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.ActionListener;
35 import java.awt.event.KeyEvent;
36 
37 import javax.swing.*;
38 
45 public class XmippDialog extends JDialog implements ActionListener {
46  private static final long serialVersionUID = 1L;
47  protected Window parent;
48  protected boolean result;
49  protected JPanel panel;
50  protected JButton btnCancel;
51  protected JButton btnOk;
52  protected String btnOkText = "Ok";
53  protected String btnCancelText = "Cancel";
54  protected boolean btnCancelDisplay = true;
55  protected JPanel panelBtn;
56  protected boolean disposeOnClose = true;
57  protected boolean closeOnAction = true;
58 
59 
60 
61  public XmippDialog(JFrame parent, String title, boolean modal) {
62  super(parent, title, modal);
63  this.parent = parent;
64  }
65 
66  public XmippDialog(Dialog parent, String title, boolean modal) {
67  super(parent, title, modal);
68  this.parent = parent;
69  }
70 
75  protected void initComponents() {
76  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
77  Container content = getContentPane();
78  panel = new JPanel();
79  createContent(panel);
80  content.add(panel, BorderLayout.CENTER);
81  createButtons();
82  content.add(panelBtn, BorderLayout.PAGE_END);
83 
84  pack();
85  if (parent != null)
86  XmippWindowUtil.centerWindows(this, parent);
87  else
88  XmippWindowUtil.centerWindows(this);
89  }
90 
91  protected void registerHotKeys(final JButton btn, int keyStroke){
92  // Associate the escape with cancel
93  KeyStroke stroke = KeyStroke.getKeyStroke(keyStroke, 0);
94 
95  panel.registerKeyboardAction(
96  new ActionListener() {
97  @Override
98  public void actionPerformed(ActionEvent e) {
99  btn.doClick();
100  }
101  }, stroke, JComponent.WHEN_IN_FOCUSED_WINDOW);
102 
103  }
104 
105  protected JButton addButton(String text) {
106  return addButton(text, 0);
107  }
108  protected JButton addButton(String text, int keyStroke) {
109  JButton btn = XmippWindowUtil.getTextButton(text, this);
110  panelBtn.add(btn);
111 
112  if (keyStroke != 0){
113  registerHotKeys(btn, keyStroke);
114  }
115  return btn;
116  }
117 
118  protected void createButtons() {
119  // Create panel for Ok and Cancel buttons
120  panelBtn = new JPanel(new FlowLayout(FlowLayout.TRAILING));
121  btnOk = addButton(btnOkText, KeyEvent.VK_ENTER);
122  if (btnCancelDisplay)
123  btnCancel = addButton(btnCancelText, KeyEvent.VK_ESCAPE);
124  }
125 
127  public boolean showDialog() {
128  setVisible(true);
129 
130  return result;
131  }
132 
137  protected void createContent(JPanel panel) {
138 
139  }
140 
144  public void handleActionPerformed(ActionEvent evt) {
145 
146  }
147 
151  public void handleOk() {
152  }
153 
157  public void handleCancel() {
158  }
159 
160 
161 
162  @Override
163  public void actionPerformed(ActionEvent evt) {
164  Object obj = evt.getSource();
165  if (obj == btnOk) {
166  close(true);
167  } else if (obj == btnCancel) {
168  close(false);
169  } else
170  handleActionPerformed(evt);
171  }
172 
174  protected void close(boolean result) {
175  if (result)
176  handleOk();
177  else
178  handleCancel();
179 
180  if (closeOnAction) {
181  this.result = result;
182  setVisible(false);
183  if (disposeOnClose)
184  dispose();
185  }
186  }// function close
187 
189  public void setDisposeOnClose(boolean value) {
190  disposeOnClose = value;
191  }
192 
194  public void setCloseOnOk(boolean value) {
195  closeOnAction = value;
196  }
197 
199  public boolean showInfo(String message) {
200  XmippMessageDialog dlg = new XmippMessageDialog(this, "INFO", message,
201  "info.gif");
202  return dlg.showDialog();
203  }
204 
205  public boolean showWarning(String message) {
206  XmippMessageDialog dlg = new XmippMessageDialog(this, "WARNING",
207  message, "warning.gif");
208  return dlg.showDialog();
209  }
210 
211  public boolean showError(String message) {
212  XmippMessageDialog dlg = new XmippMessageDialog(this, "ERROR", message,
213  "error.gif");
214  return dlg.showDialog();
215  }
216 
217  public boolean showException(Exception e) {
218  XmippMessageDialog dlg = new XmippMessageDialog(this, "ERROR",
219  e.getMessage(), "error.gif");
220  // TODO: Integrate the stack trace into the dialog
221  e.printStackTrace();
222  return dlg.showDialog();
223  }
224 
226  public static boolean showInfo(JFrame parent, String message) {
227  XmippMessageDialog dlg = new XmippMessageDialog(parent, "INFO",
228  message, "info.gif");
229  dlg.btnCancel.setVisible(false);
230  return dlg.showDialog();
231  }
232 
233  public static boolean showWarning(JFrame parent, String message) {
234  XmippMessageDialog dlg = new XmippMessageDialog(parent, "WARNING",
235  message, "warning.gif");
236  dlg.btnCancel.setVisible(false);
237  return dlg.showDialog();
238  }
239 
240  public static boolean showError(JFrame parent, String message) {
241  if(message == null || message.isEmpty())
242  message = XmippMessage.getUnexpectedErrorMsg();
243  XmippMessageDialog dlg = new XmippMessageDialog(parent, "ERROR",
244  message, "error.gif");
245  dlg.btnCancel.setVisible(false);
246  return dlg.showDialog();
247  }
248 
249  public static boolean showException(JFrame parent, Exception e) {
250  XmippMessageDialog dlg = new XmippMessageDialog(parent, "ERROR",
251  e.getMessage(), "error.gif");
252  dlg.btnCancel.setVisible(false);
253  // TODO: Integrate the stack trace into the dialog
254  e.printStackTrace();
255  return dlg.showDialog();
256  }
257 
258  public static boolean showQuestion(JFrame parent, String message) {
259  XmippMessageDialog dlg = new XmippQuestionDialog(parent, message);
260  return dlg.showDialog();
261  }
262 
263  public static boolean showYesNoQuestion(JFrame parent, String message) {
264  XmippMessageDialog dlg = new XmippQuestionDialog(parent, message, false);
265  return dlg.showDialog();
266  }
267 
268 
269  public static boolean showQuestion(JDialog parent, String message) {
270  XmippMessageDialog dlg = new XmippQuestionDialog(parent, message);
271  return dlg.showDialog();
272  }
273 
274  public static int showQuestionYesNoCancel(JFrame parent, String message) {
275  XmippQuestionDialog dlg = new XmippQuestionDialog(parent, message);
276  dlg.setVisible(true);
277  return dlg.getOption();
278  }
279 
280  public static String removeColors(String message) {
281  if (message == null)
282  return null;
283  String redPrefix = String.format("%c[%d;%dm", 0x1B, 1, 31);
284  String redSuffix = String.format("%c[0m", 0x1B);
285  return message.replace(redPrefix, "").replace(redSuffix, "");
286  }
287 
288 
289 
290 }// class XmippDialog
291 
xmipp.utils.XmippDialog.showException
static boolean showException(JFrame parent, Exception e)
Definition: XmippDialog.java:249
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void setDisposeOnClose(boolean value)
Definition: XmippDialog.java:189
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xmipp.utils.XmippDialog.XmippDialog
XmippDialog(JFrame parent, String title, boolean modal)
Definition: XmippDialog.java:61
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xmipp.utils.XmippDialog.registerHotKeys
void registerHotKeys(final JButton btn, int keyStroke)
Definition: XmippDialog.java:91
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xmipp.utils.XmippDialog.handleActionPerformed
void handleActionPerformed(ActionEvent evt)
Definition: XmippDialog.java:144
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xmipp.utils.XmippDialog.showException
boolean showException(Exception e)
Definition: XmippDialog.java:217
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xmipp.utils.XmippDialog.removeColors
static String removeColors(String message)
Definition: XmippDialog.java:280
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xmipp.utils.XmippWindowUtil.centerWindows
static void centerWindows(Window w)
Definition: XmippWindowUtil.java:94
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xmipp.utils.XmippDialog.setCloseOnOk
void setCloseOnOk(boolean value)
Definition: XmippDialog.java:194
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xmipp.utils.XmippDialog.showQuestion
static boolean showQuestion(JDialog parent, String message)
Definition: XmippDialog.java:269
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xmipp.utils.XmippDialog.showQuestion
static boolean showQuestion(JFrame parent, String message)
Definition: XmippDialog.java:258
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xmipp.utils.XmippDialog.showWarning
static boolean showWarning(JFrame parent, String message)
Definition: XmippDialog.java:233
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xmipp.utils.XmippDialog.createContent
void createContent(JPanel panel)
Definition: XmippDialog.java:137
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xmipp.utils.XmippDialog.addButton
JButton addButton(String text)
Definition: XmippDialog.java:105
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xmipp.utils.XmippDialog.showError
static boolean showError(JFrame parent, String message)
Definition: XmippDialog.java:240
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xmipp.utils.XmippMessage.getUnexpectedErrorMsg
static String getUnexpectedErrorMsg()
Definition: XmippMessage.java:84
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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void close(boolean result)
Definition: XmippDialog.java:174
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xmipp.utils.XmippDialog.actionPerformed
void actionPerformed(ActionEvent evt)
Definition: XmippDialog.java:163
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xmipp.utils.XmippWindowUtil.getTextButton
static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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xmipp.utils.XmippDialog.showInfo
static boolean showInfo(JFrame parent, String message)
Definition: XmippDialog.java:226
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xmipp.utils.XmippDialog.addButton
JButton addButton(String text, int keyStroke)
Definition: XmippDialog.java:108
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xmipp.utils.XmippDialog.showYesNoQuestion
static boolean showYesNoQuestion(JFrame parent, String message)
Definition: XmippDialog.java:263
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xmipp.utils.XmippDialog.showWarning
boolean showWarning(String message)
Definition: XmippDialog.java:205
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xmipp.utils.XmippDialog.showQuestionYesNoCancel
static int showQuestionYesNoCancel(JFrame parent, String message)
Definition: XmippDialog.java:274
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.utils.XmippDialog.XmippDialog
XmippDialog(Dialog parent, String title, boolean modal)
Definition: XmippDialog.java:66
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XmippError.java
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1 package xmipp.jni;
2 
3 public class XmippError {
4  public static final int ERR_FIRST_LABEL = 0;
5  public static final int ERR_ARG_BADCMDLINE = 1;
6  public static final int ERR_ARG_INCORRECT = 2;
7  public static final int ERR_ARG_MISSING = 3;
8  public static final int ERR_ARG_DEPENDENCE = 4;
9  public static final int ERR_PROG_NOTDEF = 5;
10  public static final int ERR_DEBUG_TEST = 6;
11  public static final int ERR_DEBUG_IMPOSIBLE = 7;
12  public static final int ERR_DOCFILE = 8;
13  public static final int ERR_GPU_MEMORY = 9;
14  public static final int ERR_GRID = 10;
15  public static final int ERR_GRID_SIZE = 11;
16  public static final int ERR_IMG_NOREAD = 12;
17  public static final int ERR_IMG_NOWRITE = 13;
18  public static final int ERR_IMG_UNKNOWN = 14;
19  public static final int ERR_INDEX_OUTOFBOUNDS = 15;
20  public static final int ERR_IO = 16;
21  public static final int ERR_IO_NOCLOSED = 17;
22  public static final int ERR_IO_NOTEXIST = 18;
23  public static final int ERR_IO_NOTOPEN = 19;
24  public static final int ERR_IO_NOPERM = 20;
25  public static final int ERR_IO_NOREAD = 21;
26  public static final int ERR_IO_NOWRITE = 22;
27  public static final int ERR_IO_NOTFILE = 23;
28  public static final int ERR_IO_NOTDIR = 24;
29  public static final int ERR_IO_NOPATH = 25;
30  public static final int ERR_IO_LOCKED = 26;
31  public static final int ERR_IO_SIZE = 27;
32  public static final int ERR_LOGIC_ERROR = 28;
33  public static final int ERR_MATRIX = 29;
34  public static final int ERR_MATRIX_DIM = 30;
35  public static final int ERR_MATRIX_EMPTY = 31;
36  public static final int ERR_MATRIX_SIZE = 32;
37  public static final int ERR_MD = 33;
38  public static final int ERR_MD_NOACTIVE = 34;
39  public static final int ERR_MD_NOOBJ = 35;
40  public static final int ERR_MD_BADLABEL = 36;
41  public static final int ERR_MD_MISSINGLABEL = 37;
42  public static final int ERR_MD_SQL = 38;
43  public static final int ERR_MD_OBJECTNUMBER = 39;
44  public static final int ERR_MD_BADTYPE = 40;
45  public static final int ERR_MD_UNDEFINED = 41;
46  public static final int ERR_MD_BADBLOCK = 42;
47  public static final int ERR_MEM_BADREQUEST = 43;
48  public static final int ERR_MEM_NOTENOUGH = 44;
49  public static final int ERR_MEM_NOTDEALLOC = 45;
50  public static final int ERR_MEM_NULLPOINTER = 46;
51  public static final int ERR_MMAP = 47;
52  public static final int ERR_MMAP_NOTADDR = 48;
53  public static final int ERR_MULTIDIM_DIM = 49;
54  public static final int ERR_MULTIDIM_SIZE = 50;
55  public static final int ERR_MULTIDIM_EMPTY = 51;
56  public static final int ERR_NOT_IMPLEMENTED = 52;
57  public static final int ERR_NUMERICAL = 53;
58  public static final int ERR_PARAM_INCORRECT = 54;
59  public static final int ERR_PARAM_MISSING = 55;
60  public static final int ERR_PLANS_NOCREATE = 56;
61  public static final int ERR_SELFILE = 57;
62  public static final int ERR_THREADS_NOTINIT = 58;
63  public static final int ERR_TYPE_INCORRECT = 59;
64  public static final int ERR_UNCLASSIFIED = 60;
65  public static final int ERR_VALUE_EMPTY = 61;
66  public static final int ERR_VALUE_INCORRECT = 62;
67  public static final int ERR_VALUE_NOTSET = 63;
68  public static final int ERR_LAST_LABEL = 64;
69 }
xmipp.jni.XmippError.ERR_INDEX_OUTOFBOUNDS
static final int ERR_INDEX_OUTOFBOUNDS
< Unknown image type
Definition: XmippError.java:19
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xmipp.jni.XmippError.ERR_MATRIX_DIM
static final int ERR_MATRIX_DIM
< Matrix error.
Definition: XmippError.java:34
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xmipp.jni.XmippError.ERR_UNCLASSIFIED
static final int ERR_UNCLASSIFIED
< Incorrect type received.
Definition: XmippError.java:64
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xmipp.jni.XmippError.ERR_ARG_BADCMDLINE
static final int ERR_ARG_BADCMDLINE
Definition: XmippError.java:5
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xmipp.jni.XmippError.ERR_MULTIDIM_EMPTY
static final int ERR_MULTIDIM_EMPTY
< Incorrect MultidimArray size
Definition: XmippError.java:55
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xmipp.jni.XmippError.ERR_FIRST_LABEL
static final int ERR_FIRST_LABEL
Definition: XmippError.java:4
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xmipp.jni.XmippError.ERR_NOT_IMPLEMENTED
static final int ERR_NOT_IMPLEMENTED
< MultidimArray is empty.
Definition: XmippError.java:56
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xmipp.jni.XmippError.ERR_MD_NOACTIVE
static final int ERR_MD_NOACTIVE
< MetaData error.
Definition: XmippError.java:38
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xmipp.jni.XmippError.ERR_MATRIX_SIZE
static final int ERR_MATRIX_SIZE
< The matrix is empty.
Definition: XmippError.java:36
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xmipp.jni.XmippError.ERR_MD_SQL
static final int ERR_MD_SQL
< Missing expected label
Definition: XmippError.java:42
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xmipp.jni.XmippError.ERR_PLANS_NOCREATE
static final int ERR_PLANS_NOCREATE
< Parameter missing.
Definition: XmippError.java:60
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xmipp.jni.XmippError.ERR_MD_BADLABEL
static final int ERR_MD_BADLABEL
< No exist requested object.
Definition: XmippError.java:40
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xmipp.jni.XmippError.ERR_VALUE_INCORRECT
static final int ERR_VALUE_INCORRECT
< Empty value.
Definition: XmippError.java:66
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xmipp.jni.XmippError.ERR_MD_MISSINGLABEL
static final int ERR_MD_MISSINGLABEL
< Unexpected label.
Definition: XmippError.java:41
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xmipp.jni.XmippError.ERR_PARAM_INCORRECT
static final int ERR_PARAM_INCORRECT
< Error related to numerical calculation.
Definition: XmippError.java:58
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xmipp.jni.XmippError.ERR_MMAP_NOTADDR
static final int ERR_MMAP_NOTADDR
< Global mmap error.
Definition: XmippError.java:52
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xmipp.jni.XmippError.ERR_TYPE_INCORRECT
static final int ERR_TYPE_INCORRECT
< Threads cannot be initiated.
Definition: XmippError.java:63
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xmipp.jni.XmippError.ERR_THREADS_NOTINIT
static final int ERR_THREADS_NOTINIT
< Error in docfile format
Definition: XmippError.java:62
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xmipp.jni.XmippError.ERR_MD_NOOBJ
static final int ERR_MD_NOOBJ
< No active object in MetaData.
Definition: XmippError.java:39
-
xmipp.jni.XmippError.ERR_IO_NOWRITE
static final int ERR_IO_NOWRITE
< Couldn&#39;t read from file.
Definition: XmippError.java:26
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xmipp.jni.XmippError.ERR_IO_NOTOPEN
static final int ERR_IO_NOTOPEN
< File or directory does not exist.
Definition: XmippError.java:23
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xmipp.jni.XmippError.ERR_MEM_BADREQUEST
static final int ERR_MEM_BADREQUEST
< This block does not exist.
Definition: XmippError.java:47
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xmipp.jni.XmippError.ERR_IO_NOPERM
static final int ERR_IO_NOPERM
< File cannot be open.
Definition: XmippError.java:24
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xmipp.jni.XmippError.ERR_MEM_NOTDEALLOC
static final int ERR_MEM_NOTDEALLOC
< There is not enough memory for allocation.
Definition: XmippError.java:49
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xmipp.jni.XmippError.ERR_DEBUG_TEST
static final int ERR_DEBUG_TEST
< Required function not implemented
Definition: XmippError.java:10
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xmipp.jni.XmippError.ERR_DOCFILE
static final int ERR_DOCFILE
< Just for debugging, situation that can&#39;t happens
Definition: XmippError.java:12
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xmipp.jni.XmippError.ERR_ARG_MISSING
static final int ERR_ARG_MISSING
< Incorrect argument received.
Definition: XmippError.java:7
-
xmipp.jni.XmippError.ERR_ARG_DEPENDENCE
static final int ERR_ARG_DEPENDENCE
< Argument missing.
Definition: XmippError.java:8
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xmipp.jni.XmippError.ERR_NUMERICAL
static final int ERR_NUMERICAL
< Case or algorithm not implemented yet.
Definition: XmippError.java:57
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xmipp.jni.XmippError.ERR_SELFILE
static final int ERR_SELFILE
< FFT Plan cannot be created.
Definition: XmippError.java:61
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xmipp.jni.XmippError.ERR_IO_NOREAD
static final int ERR_IO_NOREAD
< Insufficient permissions to perform operation.
Definition: XmippError.java:25
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xmipp.jni.XmippError.ERR_LOGIC_ERROR
static final int ERR_LOGIC_ERROR
< Incorrect file size.
Definition: XmippError.java:32
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xmipp.jni.XmippError.ERR_DEBUG_IMPOSIBLE
static final int ERR_DEBUG_IMPOSIBLE
< Just an error for debugging purpose.
Definition: XmippError.java:11
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xmipp.jni.XmippError.ERR_VALUE_NOTSET
static final int ERR_VALUE_NOTSET
< Incorrect value received.
Definition: XmippError.java:67
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xmipp.jni.XmippError.ERR_MEM_NOTENOUGH
static final int ERR_MEM_NOTENOUGH
< Bad amount of memory requested.
Definition: XmippError.java:48
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xmipp.jni.XmippError.ERR_MEM_NULLPOINTER
static final int ERR_MEM_NULLPOINTER
< Memory has not been deallocated.
Definition: XmippError.java:50
-
xmipp.jni.XmippError.ERR_PROG_NOTDEF
static final int ERR_PROG_NOTDEF
< Error with some arguments dependencies
Definition: XmippError.java:9
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xmipp.jni.XmippError.ERR_MD
static final int ERR_MD
< Problem with matrix size.
Definition: XmippError.java:37
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xmipp.jni.XmippError.ERR_MD_UNDEFINED
static final int ERR_MD_UNDEFINED
< Bad label type.
Definition: XmippError.java:45
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xmipp.jni.XmippError.ERR_MATRIX_EMPTY
static final int ERR_MATRIX_EMPTY
< Problem with matrix dimensions.
Definition: XmippError.java:35
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xmipp.jni.XmippError.ERR_IMG_NOREAD
static final int ERR_IMG_NOREAD
< Incorrect number of GRID volumes or shapes
Definition: XmippError.java:16
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xmipp.jni.XmippError.ERR_VALUE_EMPTY
static final int ERR_VALUE_EMPTY
< Just to locate unclassified errors.
Definition: XmippError.java:65
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xmipp.jni.XmippError.ERR_MULTIDIM_DIM
static final int ERR_MULTIDIM_DIM
< Map addressing of file has failed.
Definition: XmippError.java:53
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xmipp.jni.XmippError.ERR_MATRIX
static final int ERR_MATRIX
< Some logical error in the pipeline
Definition: XmippError.java:33
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xmipp.jni.XmippError.ERR_MD_BADTYPE
static final int ERR_MD_BADTYPE
< Incorrect number of objects in Metadata
Definition: XmippError.java:44
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xmipp.jni.XmippError.ERR_IMG_UNKNOWN
static final int ERR_IMG_UNKNOWN
< Cannot write image to file.
Definition: XmippError.java:18
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xmipp.jni.XmippError.ERR_MMAP
static final int ERR_MMAP
< Null pointer passed as parameter
Definition: XmippError.java:51
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xmipp.jni.XmippError.ERR_GPU_MEMORY
static final int ERR_GPU_MEMORY
< Error in docfile format
Definition: XmippError.java:13
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xmipp.jni.XmippError.ERR_MD_OBJECTNUMBER
static final int ERR_MD_OBJECTNUMBER
< Error in SQL of MetaData operations.
Definition: XmippError.java:43
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xmipp.jni.XmippError.ERR_LAST_LABEL
static final int ERR_LAST_LABEL
< Value has not been set.
Definition: XmippError.java:68
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xmipp.jni.XmippError.ERR_IMG_NOWRITE
static final int ERR_IMG_NOWRITE
< Cannot read image from file.
Definition: XmippError.java:17
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xmipp.jni.XmippError.ERR_IO_NOCLOSED
static final int ERR_IO_NOCLOSED
< Input/Output general error.
Definition: XmippError.java:21
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xmipp.jni.XmippError.ERR_GRID
static final int ERR_GRID
< GPU memory related issues
Definition: XmippError.java:14
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xmipp.jni.XmippError.ERR_IO
static final int ERR_IO
< Index out of bounds.
Definition: XmippError.java:20
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xmipp.jni.XmippError.ERR_ARG_INCORRECT
static final int ERR_ARG_INCORRECT
< Errors on command line parameters.
Definition: XmippError.java:6
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xmipp.jni.XmippError.ERR_PARAM_MISSING
static final int ERR_PARAM_MISSING
< Parameter incorrect.
Definition: XmippError.java:59
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xmipp.jni.XmippError.ERR_MD_BADBLOCK
static final int ERR_MD_BADBLOCK
< Undefined label.
Definition: XmippError.java:46
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xmipp.jni.XmippError.ERR_MULTIDIM_SIZE
static final int ERR_MULTIDIM_SIZE
< Incorrect MultidimArray dimensions
Definition: XmippError.java:54
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xmipp.jni.XmippError.ERR_IO_NOTEXIST
static final int ERR_IO_NOTEXIST
< File cannot be closed.
Definition: XmippError.java:22
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xmipp.jni.XmippError.ERR_IO_NOTDIR
static final int ERR_IO_NOTDIR
< It is not a file.
Definition: XmippError.java:28
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xmipp.jni.XmippError.ERR_IO_NOPATH
static final int ERR_IO_NOPATH
< It is not a directory.
Definition: XmippError.java:29
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xmipp.jni.XmippError.ERR_GRID_SIZE
static final int ERR_GRID_SIZE
< Grid general error.
Definition: XmippError.java:15
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xmipp.jni.XmippError.ERR_IO_NOTFILE
static final int ERR_IO_NOTFILE
< Couldn&#39;t write to file.
Definition: XmippError.java:27
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xmipp.jni.XmippError.ERR_IO_SIZE
static final int ERR_IO_SIZE
< Error when locking/unloking a file.
Definition: XmippError.java:31
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xmipp.jni.XmippError.ERR_IO_LOCKED
static final int ERR_IO_LOCKED
< Environment PATH cannot be read.
Definition: XmippError.java:30
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 import java.io.File;
29 import javax.swing.JFileChooser;
30 
31 import xmipp.jni.Filename;
32 
33 
35 @SuppressWarnings("serial")
36 public class XmippFileChooser extends JFileChooser {
37 
39  public XmippFileChooser(){
40  this(new File(Filename.getCurrentDir()));
41  }
42 
43  public XmippFileChooser(File f){
44  super(f);
45  init();
46  }
47 
48  public XmippFileChooser(String path) {
49  this(new File(path));
50  }
51 
53  private void init(){
54  //Add custom icons for file types.
55  setFileView(new XmippFileView());
56 
57  //Add the preview pane.
58  setAccessory(new XmippFilePreview(this));
59  }
60 
62  public String getSelectedPath(){
63  return getSelectedFile().getPath();
64  }
65 
66 }
-
xmipp.jni.Filename.getCurrentDir
static String getCurrentDir()
Definition: Filename.java:390
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 import java.awt.Dimension;
29 import java.awt.Graphics;
30 import java.awt.image.BufferedImage;
31 import java.beans.PropertyChangeEvent;
32 import java.beans.PropertyChangeListener;
33 import java.io.File;
34 
35 import javax.swing.ImageIcon;
36 import javax.swing.JComponent;
37 
38 import xmipp.jni.Filename;
39 import xmipp.jni.ImageGeneric;
40 import xmipp.jni.MetaData;
41 
42 /* ImagePreview.java by FileChooserDemo2.java. */
43 public class XmippFilePreview extends JComponent implements
44  PropertyChangeListener {
45  ImageIcon thumbnail = null;
46  File file = null;
47 
48  public XmippFilePreview(XmippFileChooser fc) {
49  setPreferredSize(new Dimension(128, 128));
50  fc.addPropertyChangeListener(this);
51  }
52 
53  private void loadImage(String filename) throws Exception{
54  try{
55  ImageGeneric image;
56  image = new ImageGeneric(filename);
57  image.read(128, 128, ImageGeneric.MID_SLICE, ImageGeneric.FIRST_IMAGE);
58  image.convert2Datatype(ImageGeneric.UChar);
59  BufferedImage bimg = new BufferedImage(image.getXDim(), image.getYDim(),
60  BufferedImage.TYPE_BYTE_GRAY);
61  bimg.getRaster().setDataElements(0, 0, image.getXDim(), image.getYDim(),
62  image.getArrayByte(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE));
63  thumbnail = new ImageIcon(bimg);
64  } catch (Exception e){
65  thumbnail = null;
66  }
67  }
68 
69  public void loadImage() {
70  if (file == null) {
71  thumbnail = null;
72  return;
73  }
74 
75  try {
76  String filename = file.getPath();
77  if (!file.exists() || file.isDirectory()){
78  thumbnail = null;
79  return;
80  }
81  if(filename.endsWith(".pos"))
82  return;// no image on it
83  if (Filename.isSingleImageExt(filename) ||
84  Filename.isStackExt(filename) ||
85  Filename.isVolumeExt(filename))
86  loadImage(filename);
87  else if (Filename.isMetadataExt(filename)){
88  MetaData md = new MetaData(filename);
89  int[] labels = md.getActiveLabels();
90  for (int l: labels)
91  if (MetaData.isImage(l))
92  loadImage(md.getValueString(l, md.firstObject()));
93  md.destroy();
94  }
95 
96 
97  } catch (Exception e) {
98  // TODO Auto-generated catch block
99  e.printStackTrace();
100  }
101  }
102 
103  public void propertyChange(PropertyChangeEvent e) {
104  boolean update = false;
105  String prop = e.getPropertyName();
106 
107  // If the directory changed, don't show an image.
108  if (XmippFileChooser.DIRECTORY_CHANGED_PROPERTY.equals(prop)) {
109  file = null;
110  update = true;
111 
112  // If a file became selected, find out which one.
113  } else if (XmippFileChooser.SELECTED_FILE_CHANGED_PROPERTY.equals(prop)) {
114  file = (File) e.getNewValue();
115  update = true;
116  }
117 
118  // Update the preview accordingly.
119  if (update) {
120  thumbnail = null;
121  if (isShowing()) {
122  loadImage();
123  repaint();
124  }
125  }
126  }
127 
128  protected void paintComponent(Graphics g) {
129  if (thumbnail == null) {
130  loadImage();
131  }
132  if (thumbnail != null) {
133  int x = getWidth() / 2 - thumbnail.getIconWidth() / 2;
134  int y = getHeight() / 2 - thumbnail.getIconHeight() / 2;
135 
136  if (y < 0) {
137  y = 0;
138  }
139 
140  if (x < 5) {
141  x = 5;
142  }
143  thumbnail.paintIcon(this, g, x, y);
144  }
145  }
146 }
xmipp.jni.Filename.isSingleImageExt
static boolean isSingleImageExt(String filename)
Definition: Filename.java:126
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xmipp.jni.ImageGeneric.FIRST_SLICE
static final int FIRST_SLICE
Definition: ImageGeneric.java:9
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xmipp.jni.ImageGeneric.convert2Datatype
final native void convert2Datatype(int dataType)
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xmipp.jni.Filename.isStackExt
static boolean isStackExt(String filename)
Definition: Filename.java:161
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xmipp.jni.Filename.isMetadataExt
static boolean isMetadataExt(String filename)
Definition: Filename.java:175
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xmipp.jni.ImageGeneric.getYDim
native int getYDim()
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xmipp.jni.Filename.isVolumeExt
static boolean isVolumeExt(String filename)
Definition: Filename.java:146
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.jni.ImageGeneric.getXDim
native int getXDim()
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xmipp.jni.MetaData.getActiveLabels
native int [] getActiveLabels()
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xmipp.jni.ImageGeneric.UChar
static final int UChar
Definition: ImageGeneric.java:16
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.jni.MetaData.firstObject
native long firstObject()
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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xmipp.jni.ImageGeneric.getArrayByte
native byte [] getArrayByte(long select_image, int slice)
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xmipp.utils.XmippFilePreview.propertyChange
void propertyChange(PropertyChangeEvent e)
Definition: XmippFilePreview.java:103
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xmipp.jni.ImageGeneric.MID_SLICE
static final int MID_SLICE
Definition: ImageGeneric.java:12
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xmipp.jni.MetaData.isImage
static native boolean isImage(int label)
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xmipp.utils.XmippFilePreview.XmippFilePreview
XmippFilePreview(XmippFileChooser fc)
Definition: XmippFilePreview.java:48
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 import java.io.File;
29 import javax.swing.*;
30 import javax.swing.filechooser.*;
31 
32 import xmipp.jni.Filename;
33 import xmipp.jni.ImageGeneric;
34 
35 /* This class implements the abstract FileView to personalize
36  * the default icons and file info displayed on XmippFileChooser */
37 public class XmippFileView extends FileView {
38 
39  public String getName(File f) {
40  return null; // let the L&F FileView figure this out
41  }
42 
43  public String getDescription(File f) {
44  try {
45  if (!f.isDirectory()) {
46  String filename = f.getPath();
47  if (Filename.isSingleImageExt(filename)
48  || Filename.isStackExt(filename)
49  || Filename.isVolumeExt(filename)) {
50  ImageGeneric image = new ImageGeneric(filename);
51  String desc = String.format("<Image dimensions: %d x %d",
52  image.getXDim(), image.getYDim());
53  return desc;
54  }
55  }
56  } catch (Exception e) {
57  e.printStackTrace();
58  }
59  return null; // let the L&F FileView figure this out
60  }
61 
62  public Boolean isTraversable(File f) {
63  return null; // let the L&F FileView figure this out
64  }
65 
66  public String getTypeDescription(File f) {
67  String type = null;
68  return type;
69  }
70 
71  public Icon getIcon(File f) {
72  Icon icon = null;
73  try {
74  String filename = f.getPath();
75  // if (Filename.exists(filename))
76  {
77  String iconString = "generic_file.gif";
78  if (f.isDirectory())
79  iconString = "folderopen.gif";
80  else if (Filename.isSingleImageExt(filename))
81  iconString = "image.gif";
82  else if (Filename.isMetadataExt(filename))
83  iconString = "md.gif";
84  else if (Filename.isVolumeExt(filename))
85  iconString = "vol.gif";
86  else if (Filename.isStackExt(filename))
87  iconString = "stack.gif";
88  else if (filename.endsWith(Filename.EXT_ERR))
89  iconString = "err.gif";
90  else if (filename.endsWith(Filename.EXT_OUT))
91  iconString = "out.gif";
92  else if (filename.endsWith(Filename.EXT_LOG))
93  iconString = "log.gif";
94  else if (filename.endsWith(Filename.EXT_PY))
95  iconString = "python_file.gif";
96  return XmippResource.getIcon(iconString);
97  }
98  } catch (Exception e) {
99  e.printStackTrace();
100  }
101  return icon;
102  }
103 }
xmipp.jni.Filename.isSingleImageExt
static boolean isSingleImageExt(String filename)
Definition: Filename.java:126
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xmipp.utils.XmippFileView.getTypeDescription
String getTypeDescription(File f)
Definition: XmippFileView.java:66
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xmipp.jni.Filename.EXT_ERR
static final String EXT_ERR
Definition: Filename.java:49
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xmipp.jni.Filename.isStackExt
static boolean isStackExt(String filename)
Definition: Filename.java:161
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xmipp.jni.Filename.isMetadataExt
static boolean isMetadataExt(String filename)
Definition: Filename.java:175
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xmipp.jni.ImageGeneric.getYDim
native int getYDim()
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xmipp.jni.Filename.isVolumeExt
static boolean isVolumeExt(String filename)
Definition: Filename.java:146
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xmipp.utils.XmippFileView.getDescription
String getDescription(File f)
Definition: XmippFileView.java:43
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xmipp.jni.ImageGeneric.getXDim
native int getXDim()
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xmipp.utils.XmippResource.getIcon
static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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xmipp.jni.Filename.EXT_LOG
static final String EXT_LOG
Definition: Filename.java:47
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Definition: Filename.java:48
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static final String EXT_PY
Definition: Filename.java:50
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Definition: XmippFileView.java:62
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1 package xmipp.ij.commons;
2 
3 import xmipp.utils.Params;
4 
5 
6 public interface XmippIJWindow
7 {
8  public void loadData();
9 
10  public void saveData() throws Exception;
11 
12  public void saveDataAs(String file) throws Exception;
13 
14  public ImagePlusLoader getImagePlusLoader();
15 
16  public boolean isVolume();
17 
18  public boolean isStack();
19 
20  public void openMaskToolbar();
21 
22  public XmippImageCanvas getCanvas();
23 
24 
25  public Params getParams();
26 
27 
28 
29 }
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1 package xmipp.ij.commons;
2 
3 import ij.IJ;
4 import ij.ImagePlus;
5 import ij.gui.ImageCanvas;
6 import ij.gui.ImageWindow;
7 import java.awt.Rectangle;
8 import java.awt.event.*;
9 import javax.swing.SwingUtilities;
10 
11 
12 public class XmippImageCanvas extends ImageCanvas implements MouseWheelListener, KeyListener
13 {
14 
15  private boolean invertx;
16  private boolean inverty;
17  boolean[] keys = new boolean[1024];
18 
19  public Tool getTool()
20  {
21 
22  if (IJ.getInstance() == null || !IJ.getInstance().isVisible())
23  return Tool.PICKER;
24  return Tool.getTool(IJ.getToolName());
25  }
26 
27  public XmippImageCanvas(ImagePlus imp)
28  {
29  super(imp);
30  addMouseWheelListener(this);
31 
32 
33  }
34 
35  public void mousePressed(MouseEvent e)
36  {
37  if (getTool() == Tool.IMAGEJ)
38  {
39  super.mousePressed(e);
40  return;
41  }
42  if (isDragImage(e))
43  {
44  customScrollSetup(e);
45  return;
46  }
47  if(e.isControlDown())
48  {
49  if (SwingUtilities.isLeftMouseButton(e))
50  zoomIn(e.getX(), e.getY());
51  if (SwingUtilities.isRightMouseButton(e))
52  zoomOut(e.getX(), e.getY());
53  }
54  }
55  public void customScrollSetup(MouseEvent e){
56 
57  int x = super.offScreenX(e.getX());
58  int y = super.offScreenY(e.getY());
59 
60  setupScroll(x, y);
61 
62  }
63 
64  protected boolean isDragImage(MouseEvent e)
65  {
66  return (SwingUtilities.isRightMouseButton(e) && !e.isControlDown());
67  }
68 
69  public void mouseDragged(MouseEvent e)
70  {
71 
72  if (getTool() == Tool.IMAGEJ)
73  {
74  super.mouseDragged(e);
75  return;
76  }
77  if (isDragImage(e))
78  {
79  scroll(e.getX(), e.getY());
80  return;
81  }
82  }
83 
84 
85 
86 
87  public void mouseReleased(MouseEvent e)
88  {
89  if (getTool() == Tool.IMAGEJ)// do nothing for ImageJ tool is mine is selected
90  {
91  super.mouseReleased(e);
92  return;
93  }
94 
95  }
96 
97  public int getXOnImage(int x)
98  {
99  int x0 = (int) getSrcRect().getX();
100  return (int) ((x - x0) * magnification);
101  }
102 
103  public int getYOnImage(int y)
104  {
105  int y0 = (int) getSrcRect().getY();
106  return (int) ((y - y0) * magnification);
107  }
108 
109  @Override
110  public void mouseWheelMoved(MouseWheelEvent e)
111  {
112  if (!e.isShiftDown())
113  return;
114 
115  int x = e.getX();
116  int y = e.getY();
117  int rotation = e.getWheelRotation();
118  if (rotation < 0)
119  zoomIn(x, y);
120  else
121  zoomOut(x, y);
122 
123 
124  }
125 
126  public void mouseMoved(MouseEvent e)
127  {
128  int x = offScreenX(e.getX());
129  int y = offScreenY(e.getY());
130 
131  if(getParent() instanceof XmippImageWindow)
132  {
133  int[] pixels = imp.getPixel(x, y);
134  if(pixels != null)
135  ((XmippImageWindow)getParent()).showPixels(x, y, pixels);
136  }
137  if (getTool() == Tool.IMAGEJ)
138  super.mouseMoved(e);
139 
140  imp.mouseMoved(x, y);
141  imp.updateStatusbarValue();
142 
143  }
144 
145  public int offScreenX(int x)
146  {
147  x = super.offScreenX(x);
148  if(invertx)
149  x = imp.getWidth() - x;
150  return x;
151  }
152 
153  public int offScreenY(int y)
154  {
155  y = super.offScreenY(y);
156  if(inverty)
157  y = imp.getHeight() - y;
158  return y;
159  }
160 
161  public void loadData(XmippIJWindow xiw)
162  {
163  double currmagnif = getMagnification();
164  Rectangle rect = getSrcRect();
165  imp = xiw.getImagePlusLoader().loadImagePlus();
166  imp.setTitle(xiw.getImagePlusLoader().getName());
167  ImageWindow iw = (ImageWindow) xiw;
168  iw.setImage(getImage());
169  iw.updateImage(getImage());
170 
171  setSourceRect(rect);
172  double prefmagnif = getPreferredMagnification();
173  if (currmagnif < prefmagnif)
174  setMagnification(prefmagnif);
175  else
176  setMagnification(currmagnif);
177  setDrawingSize((int) (rect.getWidth() * magnification), (int) (rect.getHeight() * magnification));
178 
179  repaint();
180  iw.pack();
181 
182  }
183 
184  public double getPreferredMagnification()
185  {
186  double magnification = getMagnification();
187  int min = 200;
188  while (Math.min(getSrcRect().getWidth() * magnification, getSrcRect().getHeight() * magnification) < min)
189  {
190  magnification = 2 * magnification;
191  }
192  return magnification;
193  }
194 
195  public void adjustMagnification()// for micrographs will not happen
196  {
197  double currmagnif = getMagnification();
198  double prefmagnif = getPreferredMagnification();
199  if (currmagnif < prefmagnif)
200  {
201  setMagnification(prefmagnif);
202  setDrawingSize((int) (getSrcRect().getWidth() * magnification), (int) (getSrcRect().getHeight() * magnification));
203  repaint();
204  if (getParent() != null)
205  {
206  ImageWindow iw = (ImageWindow) getParent();
207  iw.pack();
208  }
209  }
210  }
211 
212  public void setInvertX(boolean value)
213  {
214  invertx = value;
215  }
216 
217  public void setInvertY(boolean value)
218  {
219  inverty = value;
220  }
221 
222  @Override
223  public void keyTyped(KeyEvent keyEvent) {
224 
225  }
226 
227  @Override
228  public void keyPressed(KeyEvent keyEvent) {
229 
230  keys[keyEvent.getKeyCode()] = true;
231  }
232 
233  @Override
234  public void keyReleased(KeyEvent keyEvent) {
235  keys[keyEvent.getKeyCode()] = false;
236  }
237 
238  protected boolean isKeyPressed(int keyCode){
239  if (keyCode < keys.length){
240  return keys[keyCode];
241  }
242  return false;
243  }
244 
245 
246 }
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xmipp.ij.commons.Tool.getTool
static Tool getTool(String name)
Definition: Tool.java:8
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xmipp.ij.commons.XmippIJWindow.getImagePlusLoader
ImagePlusLoader getImagePlusLoader()
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xmipp.ij.commons.XmippImageCanvas.keyReleased
void keyReleased(KeyEvent keyEvent)
Definition: XmippImageCanvas.java:234
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xmipp.ij.commons.XmippImageCanvas.keyPressed
void keyPressed(KeyEvent keyEvent)
Definition: XmippImageCanvas.java:228
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xmipp.ij.commons.XmippImageCanvas.mouseWheelMoved
void mouseWheelMoved(MouseWheelEvent e)
Definition: XmippImageCanvas.java:110
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class  xmipp.ij.commons.XmippImageConverter
 
class  xmipp.ij.commons.ProcessorCreator
 
class  xmipp.ij.commons.ProcessorCreatorByte
 
class  xmipp.ij.commons.ProcessorCreatorShort
 
class  xmipp.ij.commons.ProcessorCreatorFloat
 
class  xmipp.ij.commons.DataSetter
 
class  xmipp.ij.commons.DataSetterByte
 
class  xmipp.ij.commons.DataSetterShort
 
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1 
2 /***************************************************************************
3  * Authors: Juanjo Vega
4  * J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
5  *
6  *
7  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
8  *
9  * This program is free software; you can redistribute it and/or modify
10  * it under the terms of the GNU General Public License as published by
11  * the Free Software Foundation; either version 2 of the License, or
12  * (at your option) any later version.
13  *
14  * This program is distributed in the hope that it will be useful,
15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17  * GNU General Public License for more details.
18  *
19  * You should have received a copy of the GNU General Public License
20  * along with this program; if not, write to the Free Software
21  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
22  * 02111-1307 USA
23  *
24  * All comments concerning this program package may be sent to the
25  * e-mail address 'xmipp@cnb.csic.es'
26  ***************************************************************************/
27 
28 package xmipp.ij.commons;
29 
30 import ij.IJ;
31 import ij.ImagePlus;
32 import ij.ImageStack;
33 import ij.io.FileInfo;
34 import ij.process.ByteProcessor;
35 import ij.process.FloatProcessor;
36 import ij.process.ImageProcessor;
37 import ij.process.ShortProcessor;
38 import ij.process.StackStatistics;
39 
40 import java.io.File;
41 import java.util.LinkedList;
42 
43 import xmipp.jni.Filename;
44 import xmipp.jni.ImageGeneric;
45 import xmipp.jni.MetaData;
46 
47 public class XmippImageConverter {
48 
49  public static ImagePlus loadImage(String filename) throws Exception {
50  return loadImage(filename, 100);
51  }
52 
53  public static ImagePlus loadImage(String filename, int zoom)
54  throws Exception {
55  ImageGeneric image = new ImageGeneric(filename);
56 
57  double scale = zoom / 100.0;
58  int w = (int) (image.getXDim() * scale);
59  int h = (int) (image.getYDim() * scale);
60 
61  ImagePlus imp;
62  /*
63  * if (Filename.hasPrefix(filename)) { String name =
64  * Filename.getFilename(filename); long nimage =
65  * Filename.getNimage(filename);
66  *
67  * image = new ImageGeneric(name); imp = convertToImageJ(image, nimage);
68  * } else {
69  */
70  long select_image = Filename.getNimage(filename);
71  imp = readToImagePlus(image, w, h, select_image);
72  // }
73 
74  image.destroy();
75  return imp;
76  }
77 
82  public static ImagePlus readToImagePlus(ImageGeneric image)
83  throws Exception {
84  return readToImagePlus(image, ImageGeneric.ALL_SLICES);
85  }
86 
87  public static ImagePlus readToImagePlus(ImageGeneric image, int nslice)
88  throws Exception {
89  return readToImagePlus(image, image.getXDim(), image.getYDim(), nslice);
90  }
91 
92  public static ImagePlus readToImagePlus(ImageGeneric image, long nimage, int nslice)
93  throws Exception {
94  return readToImagePlus(image, image.getXDim(), image.getYDim(), nslice, nimage);
95  }
96 
97  public static ImagePlus readToImagePlus(ImageGeneric image, long nimage)
98  throws Exception {
99  return readToImagePlus(image, image.getXDim(), image.getYDim(), nimage);
100  }
101 
102  public static ImagePlus readToImagePlus(ImageGeneric image, int width,
103  int height) throws Exception {
104  return readToImagePlus(image, width, height, ImageGeneric.ALL_SLICES,
105  ImageGeneric.ALL_IMAGES);
106  }
107 
108  public static ImagePlus readToImagePlus(ImageGeneric image, int width,
109  int height, int nslice) throws Exception {
110  return readToImagePlus(image, width, height, nslice,
111  ImageGeneric.ALL_IMAGES);
112  }
113 
114  public static ImagePlus readToImagePlus(ImageGeneric image, int width,
115  int height, long nimage) throws Exception {
116  return readToImagePlus(image, width, height, ImageGeneric.ALL_SLICES,
117  nimage);
118  }
119 
124  public static ImagePlus readToImagePlus(ImageGeneric image, int width,
125  int height, int slice, long select_image) throws Exception {
126  ImageStack is = new ImageStack(width, height);
127  ProcessorCreator pc = createProcessorCreator(image);
128  long lastImage = select_image;
129 
130  if (select_image == ImageGeneric.ALL_IMAGES) {
131  select_image = ImageGeneric.FIRST_IMAGE;
132  lastImage = image.getNDim();
133  }
134  else if (select_image == -1)
135  select_image = lastImage = image.getNDim()/2;
136  for (; select_image <= lastImage; select_image++) {
137  image.read(width, height, select_image);
138  addSlicesToStack(image, ImageGeneric.FIRST_IMAGE, slice, is, pc);
139  }
140 
141  return buildImagePlus(image.getFilename(), is);
142  }
143 
148  public static ImagePlus convertToImagePlus(ImageGeneric image)
149  throws Exception {
150  return convertToImagePlus(image, ImageGeneric.ALL_IMAGES,
151  ImageGeneric.ALL_SLICES);
152  }
153 
158  public static ImagePlus convertToImagePlus(ImageGeneric image,
159  long select_image) throws Exception {
160  return convertToImagePlus(image, select_image, ImageGeneric.ALL_SLICES);
161  }
162 
163  public static ImagePlus convertToImagePlus(ImageGeneric image,
164  long select_image, int slice) throws Exception {
165  int width = image.getXDim();
166  int height = image.getYDim();
167 
168  ImageStack is = new ImageStack(width, height);
169  ProcessorCreator pc = createProcessorCreator(image);
170  long lastImage = select_image;
171 
172  if (select_image == ImageGeneric.ALL_IMAGES) {
173  select_image = ImageGeneric.FIRST_IMAGE;
174  lastImage = image.getNDim();
175  }
176  for (; select_image <= lastImage; select_image++) {
177  addSlicesToStack(image, select_image, slice, is, pc);
178  }
179  return buildImagePlus(image.getFilename(), is);
180  }
181 
183  private static void addSlicesToStack(ImageGeneric image, long select_image,
184  int slice, ImageStack is, ProcessorCreator pc) throws Exception {
185  if (image.isPSD()) {
186  image.convertPSD(image.getUseLogarithm());
187  }
188  int lastSlice = slice;
189  if (slice == ImageGeneric.ALL_SLICES) {
190  slice = ImageGeneric.FIRST_SLICE;
191  lastSlice = image.getZDim();
192  }
193 
194  for (; slice <= lastSlice; slice++)
195  is.addSlice("", pc.getProcessor(image, select_image, slice));
196  }
197 
198  public static ImagePlus readMdRowToImagePlus(String fn, MetaData md,
199  long objId, int width, int height, boolean useGeo, boolean wrap)
200  throws Exception {
201  ImageGeneric image = new ImageGeneric();
202  if (useGeo)
203  image.readApplyGeo(fn, md, objId, width, height, wrap);
204  else
205  image.read(fn, width, height);
206 
207  ImagePlus ip = convertToImagePlus(image);
208 
209  image.destroy();
210  return ip;
211  }
212 
213  public static ImagePlus readMdRowToImagePlus(String fn, MetaData md,
214  long objId, boolean useGeo, boolean wrap) throws Exception {
215  ImageGeneric image = new ImageGeneric();
216  if (useGeo)
217  image.readApplyGeo(fn, md, objId, wrap);
218  else
219  image.read(fn, true);
220  ImagePlus ip = convertToImagePlus(image, ImageGeneric.ALL_IMAGES);
221  image.destroy();
222  return ip;
223  }
224 
226  public static ImagePlus readMetadataToImagePlus(int label, MetaData md,
227  boolean useGeo, boolean wrap, boolean inverty) throws Exception {
228  LinkedList<String> missing = new LinkedList<String>();
229  ImagePlus imp = null;
230 
231  if (md.containsLabel(label)) {
232  ImageStack is = null;
233  long ids[] = md.findObjects();
234 
235  for (long id : ids) {
236  String filename = md.getValueString(label, id, true);
237 
238  try {
239  ImagePlus slice = readMdRowToImagePlus(filename, md, id, useGeo, wrap);
240  if(inverty)
241  slice = new ImagePlusLoader(slice, inverty).getImagePlus();
242  if (is == null)
243  is = new ImageStack(slice.getWidth(), slice.getHeight());
244  is.addSlice(filename, slice.getProcessor());
245  } catch (Exception ex) {
246  ex.printStackTrace(System.err);
247  missing.add(filename);
248  }
249  }
250  imp = buildImagePlus(md.getFilename(), is);
251  }
252  // Tells user about missing files.
253  if (!missing.isEmpty()) {
254  String message = "There are missing files:\n";
255  for (int i = 0; i < missing.size(); i++) {
256  message += missing.get(i) + "\n";
257  }
258  IJ.error(message);
259  }
260 
261  return imp;
262  }//function readMetadataToImagePlus
263 
264  public static ImagePlus buildImagePlus(String filename, ImageStack is) {
265  ImagePlus imp = new ImagePlus(filename, is);
266 
267  if (filename != null) {
268  // Sets associated file info.
269  File f = new File(filename);
270  FileInfo fi = new FileInfo();
271  String absPath = f.getAbsolutePath();
272  fi.directory = absPath.substring(0,
273  absPath.lastIndexOf(File.separator));
274  fi.fileName = f.getName();
275  imp.setFileInfo(fi);
276  }
277 
278  return imp;
279  }
280 
281  public static void normalizeImagePlus(ImagePlus imp) {
282  StackStatistics ss = new StackStatistics(imp);
283  imp.getProcessor().setMinAndMax(ss.min, ss.max);
284  }
285 
286  public static void revert(ImagePlus imp, String path) throws Exception {
287  ImagePlus imp2 = XmippImageConverter.loadImage(path);
288  imp2.setTitle("Revert!!: " + System.currentTimeMillis());
289  imp2.show();
290  imp.setStack(imp.getTitle(), imp2.getImageStack());
291  }
292 
297  public static ImageGeneric convertToImageGeneric(ImagePlus imp)
298  throws Exception {
299  ImageGeneric image = new ImageGeneric();
300  DataSetter ds = createDataSetter(image, imp.getType());
301  image.resize(imp.getWidth(), imp.getHeight(), imp.getStackSize());
302 
303  ImageStack is = imp.getStack();
304  for (int nslice = ImageGeneric.FIRST_SLICE; nslice <= is.getSize(); nslice++) {
305  ds.setArray(image, is.getProcessor(nslice).getPixels(),
306  ImageGeneric.FIRST_IMAGE, nslice);
307  }
308 
309  return image;
310  }
311 
312  public static boolean writeImagePlus(ImagePlus imp, String filename)
313  throws Exception {
314  ImageGeneric image = new ImageGeneric();
315 
316  int width = imp.getWidth();
317  int height = imp.getHeight();
318  int depth = imp.getStackSize();
319  int image_index = 1;
320 
321  boolean storeAllImages = Filename.hasStackExtension(filename);
322  boolean storeAllSlices = !storeAllImages;// =
323  // Filename.hasVolumeExtension(filename);
324 
325  // TODO: Add support for hyperstacks and remove this "if".
326  if (storeAllImages) {
327  image_index = depth;
328  depth = 1;
329  }
330 
331  DataSetter ds = createDataSetter(image, imp.getType());
332 
333  for (long nimage = ImageGeneric.FIRST_IMAGE; nimage <= image_index; nimage++) {
334  image.mapFile2Write(width, height, depth, filename, nimage);
335 
336  // Store volume.
337  for (int nslice = ImageGeneric.FIRST_SLICE; nslice <= depth; nslice++) {
338  Object data = imp.getStack()
339  .getProcessor((int) nimage * nslice).getPixels();
340 
341  // image.setData...
342  ds.setArray(image, data, ImageGeneric.FIRST_IMAGE, nslice);
343 
344  // If just one image, breaks loop.
345  if (!storeAllSlices) {
346  break;
347  }
348  }
349 
350  image.write(filename);
351 
352  // If just one image, breaks loop.
353  if (!storeAllImages) {
354  break;
355  }
356  }
357 
358  image.destroy();
359  return true;
360  }
361 
362  static ProcessorCreator createProcessorCreator(ImageGeneric image)
363  throws Exception {
364  ProcessorCreator pc = null;
365  switch (image.getDataType()) {
366  case ImageGeneric.Float:
367  case ImageGeneric.Double:
368  pc = new ProcessorCreatorFloat();
369  break;
370  case ImageGeneric.Short:
371  case ImageGeneric.UShort:
372  pc = new ProcessorCreatorShort();
373  break;
374  case ImageGeneric.UHalfByte:
375  case ImageGeneric.SChar:
376  case ImageGeneric.UChar:
377  pc = new ProcessorCreatorByte();
378  break;
379  default:
380  pc = new ProcessorCreatorFloat();
381  }
382 
383  return pc;
384  }
385 
386  static DataSetter createDataSetter(ImageGeneric image, int dataType)
387  throws Exception {
388 
389  // Creates a DataSetter according to dataType.
390  DataSetter ds = null;
391  boolean setDataType = image.getDataType() == ImageGeneric.Unknown_Type;
392 
393  switch (dataType) {
394  case ImagePlus.GRAY32:
395  if (setDataType) {
396  image.setDataType(ImageGeneric.Float);
397  }
398  ds = new DataSetterFloat();
399  break;
400  case ImagePlus.GRAY16:
401  if (setDataType) {
402  image.setDataType(ImageGeneric.UShort);
403  }
404  ds = new DataSetterShort();
405  break;
406  case ImagePlus.GRAY8:
407  if (setDataType) {
408  image.setDataType(ImageGeneric.UChar);
409  }
410  ds = new DataSetterByte();
411  break;
412  default:
413  throw new Exception("Format not supported: " + dataType);
414  }
415 
416  return ds;
417  }
418 }
419 
420 abstract class ProcessorCreator {
421 
422  public abstract ImageProcessor getProcessor(ImageGeneric image,
423  long select_image, int slice) throws Exception;
424 }
425 
426 class ProcessorCreatorByte extends ProcessorCreator {
427 
428  @Override
429  public ImageProcessor getProcessor(ImageGeneric image, long select_image,
430  int slice) throws Exception {
431  return new ByteProcessor(image.getXDim(), image.getYDim(),
432  image.getArrayByte(select_image, slice), null);
433  }
434 }
435 
436 class ProcessorCreatorShort extends ProcessorCreator {
437 
438  @Override
439  public ImageProcessor getProcessor(ImageGeneric image, long select_image,
440  int slice) throws Exception {
441  return new ShortProcessor(image.getXDim(), image.getYDim(),
442  image.getArrayShort(select_image, slice), null);
443  }
444 }
445 
446 class ProcessorCreatorFloat extends ProcessorCreator {
447 
448  @Override
449  public ImageProcessor getProcessor(ImageGeneric image, long select_image,
450  int slice) throws Exception {
451  return new FloatProcessor(image.getXDim(), image.getYDim(),
452  image.getArrayFloat(select_image, slice), null);
453  }
454 }
455 
456 abstract class DataSetter {
457 
458  public abstract void setArray(ImageGeneric image, Object data,
459  long select_image, int slice) throws Exception;
460 }
461 
462 class DataSetterByte extends DataSetter {
463 
464  @Override
465  public void setArray(ImageGeneric image, Object data, long select_image,
466  int slice) throws Exception {
467  image.setArrayByte((byte[]) data, select_image, slice);
468  }
469 }
470 
471 class DataSetterShort extends DataSetter {
472 
473  @Override
474  public void setArray(ImageGeneric image, Object data, long select_image,
475  int slice) throws Exception {
476  image.setArrayShort((short[]) data, select_image, slice);
477  }
478 }
479 
480 class DataSetterFloat extends DataSetter {
481 
482  @Override
483  public void setArray(ImageGeneric image, Object data, long select_image,
484  int slice) throws Exception {
485  image.setArrayFloat((float[]) data, select_image, slice);
486  }
487 }
xmipp.jni.ImageGeneric.SChar
static final int SChar
Definition: ImageGeneric.java:17
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xmipp.ij.commons.XmippImageConverter.normalizeImagePlus
static void normalizeImagePlus(ImagePlus imp)
Definition: XmippImageConverter.java:281
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xmipp.jni.ImageGeneric.FIRST_SLICE
static final int FIRST_SLICE
Definition: ImageGeneric.java:9
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xmipp.jni.ImageGeneric.mapFile2Write
native void mapFile2Write(int xDim, int yDim, int zDim, String filename, long nimage)
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image, int width, int height, long nimage)
Definition: XmippImageConverter.java:114
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xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(String filename, MetaData metadata, long id)
Definition: ImageGeneric.java:168
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xmipp.ij.commons.XmippImageConverter.buildImagePlus
static ImagePlus buildImagePlus(String filename, ImageStack is)
Definition: XmippImageConverter.java:264
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xmipp.jni.ImageGeneric.destroy
synchronized native void destroy()
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xmipp.jni.Filename.hasStackExtension
static native boolean hasStackExtension(String filename)
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xmipp.ij.commons.XmippImageConverter.readMetadataToImagePlus
static ImagePlus readMetadataToImagePlus(int label, MetaData md, boolean useGeo, boolean wrap, boolean inverty)
Definition: XmippImageConverter.java:226
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xmipp.ij.commons.XmippImageConverter.readMdRowToImagePlus
static ImagePlus readMdRowToImagePlus(String fn, MetaData md, long objId, int width, int height, boolean useGeo, boolean wrap)
Definition: XmippImageConverter.java:198
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xmipp.ij.commons.XmippImageConverter.convertToImageGeneric
static ImageGeneric convertToImageGeneric(ImagePlus imp)
Definition: XmippImageConverter.java:297
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xmipp.jni.ImageGeneric.ALL_SLICES
static final int ALL_SLICES
Definition: ImageGeneric.java:11
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image, long nimage, int nslice)
Definition: XmippImageConverter.java:92
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xmipp.jni.ImageGeneric.getArrayShort
native short [] getArrayShort(long select_image, int slice)
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xmipp.ij.commons.XmippImageConverter.loadImage
static ImagePlus loadImage(String filename)
Definition: XmippImageConverter.java:49
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xmipp.jni.ImageGeneric.write
native void write(String filename)
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xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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xmipp.ij.commons.XmippImageConverter.writeImagePlus
static boolean writeImagePlus(ImagePlus imp, String filename)
Definition: XmippImageConverter.java:312
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xmipp.jni.ImageGeneric.convertPSD
native void convertPSD(boolean useLogarithm)
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xmipp.jni.ImageGeneric.setArrayShort
native void setArrayShort(short data[], long select_image, int slice)
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xmipp.jni.ImageGeneric.getYDim
native int getYDim()
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image, int nslice)
Definition: XmippImageConverter.java:87
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xmipp.ij.commons.XmippImageConverter.revert
static void revert(ImagePlus imp, String path)
Definition: XmippImageConverter.java:286
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xmipp.jni.ImageGeneric.getDataType
native int getDataType()
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xmipp.jni.ImageGeneric.setArrayFloat
native void setArrayFloat(float data[], long select_image, int slice)
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image, int width, int height, int slice, long select_image)
Definition: XmippImageConverter.java:124
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xmipp.jni.ImageGeneric.getXDim
native int getXDim()
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xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image, long select_image, int slice)
Definition: XmippImageConverter.java:163
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image, int width, int height, int nslice)
Definition: XmippImageConverter.java:108
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xmipp.jni.ImageGeneric.UShort
static final int UShort
Definition: ImageGeneric.java:18
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xmipp.jni.ImageGeneric.Unknown_Type
static final int Unknown_Type
Definition: ImageGeneric.java:15
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xmipp.ij.commons.XmippImageConverter.readMdRowToImagePlus
static ImagePlus readMdRowToImagePlus(String fn, MetaData md, long objId, boolean useGeo, boolean wrap)
Definition: XmippImageConverter.java:213
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xmipp.jni.ImageGeneric.UChar
static final int UChar
Definition: ImageGeneric.java:16
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.ImageGeneric.setArrayByte
native void setArrayByte(byte data[], long select_image, int slice)
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xmipp.jni.ImageGeneric.resize
void resize(int w, int h)
Definition: ImageGeneric.java:90
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xmipp.jni.ImageGeneric.setDataType
final native void setDataType(int dataType)
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xmipp.ij.commons.XmippImageConverter.loadImage
static ImagePlus loadImage(String filename, int zoom)
Definition: XmippImageConverter.java:53
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image, long nimage)
Definition: XmippImageConverter.java:97
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xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image, long select_image)
Definition: XmippImageConverter.java:158
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xmipp.jni.ImageGeneric.ALL_IMAGES
static final long ALL_IMAGES
Definition: ImageGeneric.java:10
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xmipp.jni.Filename.getNimage
static long getNimage(String filename)
Definition: Filename.java:320
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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xmipp.jni.ImageGeneric.UHalfByte
static final int UHalfByte
Definition: ImageGeneric.java:31
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xmipp.jni.ImageGeneric.getArrayByte
native byte [] getArrayByte(long select_image, int slice)
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xmipp.jni.ImageGeneric.getZDim
native int getZDim()
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xmipp.jni.ImageGeneric.Short
static final int Short
Definition: ImageGeneric.java:19
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xmipp.jni.ImageGeneric.getArrayFloat
native float [] getArrayFloat(long select_image, int slice)
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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xmipp.jni.ImageGeneric.Double
static final int Double
Definition: ImageGeneric.java:25
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xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image, int width, int height)
Definition: XmippImageConverter.java:102
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xmipp.jni.ImageGeneric.Float
static final int Float
Definition: ImageGeneric.java:24
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1 package xmipp.ij.commons;
2 
3 import ij.ImageJ;
4 
5 import java.awt.event.WindowEvent;
6 
7 public class XmippImageJ extends ImageJ
8 {
9 
10  public static final String duplicateFilter = "Duplicate";
11  public static final String bandPassFilter = "Bandpass Filter...";
12  public static final String anisotropicDiffFilter = "Anisotropic Diffusion...";
13  public static final String substractBackgroundFilter = "Subtract Background...";
14  public static final String gaussianBlurFilter = "Gaussian Blur...";
15  public static final String brightnessContrastFilter = "Brightness/Contrast...";
16  public static final String invertLUTFilter = "Invert LUT";
17  public static final String enhanceContrastFilter = "Enhance Contrast...";
18 
19 
20  public void windowClosing(WindowEvent e) {
21  setVisible(false);
22  }
23 
24 
25 }
xmipp.ij.commons.XmippImageJ.bandPassFilter
static final String bandPassFilter
Definition: XmippImageJ.java:11
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xmipp.ij.commons.XmippImageJ.brightnessContrastFilter
static final String brightnessContrastFilter
Definition: XmippImageJ.java:15
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static final String substractBackgroundFilter
Definition: XmippImageJ.java:13
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static final String invertLUTFilter
Definition: XmippImageJ.java:16
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void windowClosing(WindowEvent e)
Definition: XmippImageJ.java:20
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xmipp.ij.commons.XmippImageJ.anisotropicDiffFilter
static final String anisotropicDiffFilter
Definition: XmippImageJ.java:12
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static final String duplicateFilter
Definition: XmippImageJ.java:10
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xmipp.ij.commons.XmippImageJ.gaussianBlurFilter
static final String gaussianBlurFilter
Definition: XmippImageJ.java:14
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Definition: XmippImageJ.java:17
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1 package xmipp.ij.commons;
2 
3 import ij.IJ;
4 import ij.ImagePlus;
5 import ij.WindowManager;
6 import ij.gui.ImageCanvas;
7 import ij.gui.ImageWindow;
8 
9 import java.awt.Label;
10 import java.awt.MenuItem;
11 import java.awt.event.ActionEvent;
12 import java.awt.event.ActionListener;
13 import java.awt.event.ComponentEvent;
14 import java.awt.event.MouseEvent;
15 import java.awt.event.MouseListener;
16 import java.awt.event.WindowEvent;
17 
18 import javax.swing.SwingUtilities;
19 
20 import xmipp.ij.commons.XmippMenuBar.IJRequirement;
21 import xmipp.utils.Params;
22 import xmipp.utils.XmippWindowUtil;
23 
24 public class XmippImageWindow extends ImageWindow implements XmippIJWindow
25 {
26 
27  protected XmippMenuBar menu;
28  protected ImagePlusLoader ipl;
29  protected Label pixelslb;
30  private DesignMaskJFrame maskfr;
31  protected Params params;
32  protected boolean closing = false;
33 
34 
35  public XmippImageWindow(ImagePlusLoader ipl, Params params)
36  {
37  this(ipl, ipl.getName(), params);
38  }
39 
40  public XmippImageWindow(ImagePlus imp, Params params)
41  {
42  this(imp, new XmippImageCanvas(imp), params);
43  }
44 
45  public XmippImageWindow(ImagePlus imp, ImageCanvas canvas, Params params)
46  {
47  super(imp, canvas);
48  this.ipl = new ImagePlusLoader(imp);
49  this.params = params;
50  XmippApplication.addInstance(true);
51  initComponents();
52  XmippWindowUtil.setScipionImageIcon(this);
53  }
54 
55 
56  public XmippImageWindow(ImagePlusLoader ipl, String title, Params params)
57  {
58  super(ipl.getImagePlus(), new XmippImageCanvas(ipl.getImagePlus()));
59  this.ipl = ipl;
60  imp.setTitle(title);
61  this.params = params;
62  XmippApplication.addInstance(true);
63  initComponents();
64  XmippWindowUtil.setScipionImageIcon(this);
65  }
66 
67  protected void initComponents()
68  {
69 
70  menu = new XmippMenuBar(this);
71  if(params != null)//otherwise is picker window
72  {
73  setMenuBar(menu);
74  if(XmippApplication.isScipion())
75  {
76  MenuItem createMaskmi = new MenuItem("Design Mask");
77  createMaskmi.addActionListener(new ActionListener() {
78 
79  @Override
80  public void actionPerformed(ActionEvent ae) {
81  loadMaskFrame();
82  }
83  });
84  menu.advancedmn.add(createMaskmi);
85  if(params!= null && params.isMask())
86  loadMaskFrame();
87  }
88  }
89  pixelslb = new Label(" ");
90  add(pixelslb);
91 
92 
93  }
94 
95  @Override
96  public void openMaskToolbar()
97  {
98  menu.runCommand("Masks Tool Bar", new IJRequirement[] { IJRequirement.IMAGEJ });
99  }
100 
101  @Override
102  public void loadData()
103  {
104  getCanvas().loadData(this);
105  if(params != null)//otherwise is picker window
106  menu.applyFilters();
107  }
108 
109  @Override
110  public void saveDataAs(String file) throws Exception
111  {
112  XmippImageConverter.writeImagePlus(imp, file);
113  }
114 
115  @Override
116  public void saveData() throws Exception
117  {
118  saveDataAs(imp.getTitle());
119  }
120 
121  @Override
122  public ImagePlusLoader getImagePlusLoader()
123  {
124  return ipl;
125  }
126 
127  @Override
128  public boolean isVolume()
129  {
130  return false;
131  }
132 
133  @Override
134  public boolean isStack()
135  {
136  return false;
137  }
138 
139  //overwriting ImageJ event to avoid switching menu
140  @Override
141  public void windowActivated(WindowEvent e)
142  {
143  // if (IJ.isMacintosh())
144  // this.setMenuBar(Menus.getMenuBar());
145 
146  if (!closed)
147  {
148  //ic.requestFocus();
149  WindowManager.setCurrentWindow(this);
150  }
151  }
152 
153  @Override
154  public XmippImageCanvas getCanvas()
155  {
156  return ((XmippImageCanvas) super.getCanvas());
157  }
158 
159  public void showPixels(int x, int y, int[] pixels)
160  {
161  if(pixelslb == null)//avoid error running showPixels before initialization
162  return;
163  pixelslb.setText(pixelsToString(imp, x, y, pixels));
164 
165  }
166 
167  public static String pixelsToString(ImagePlus imp, int x, int y, int[] pixels)
168  {
169  String text = "";
170  String value = "";
171  switch (imp.getType())
172  {
173  case ImagePlus.GRAY8:
174  case ImagePlus.GRAY16:
175  double cValue = imp.getCalibration().getCValue(pixels[0]);
176  if (cValue == pixels[0])
177  value = String.valueOf(pixels[0]);
178  else
179  value = IJ.d2s(cValue) + " (" + pixels[0] + ")";
180  text = String.format("x=%s, y=%s, value=%-5s", x, y, value);
181  break;
182  case ImagePlus.GRAY32:
183  text = String.format("x=%s, y=%s, value=%.2f", x, y, Float.intBitsToFloat(pixels[0]));
184  break;
185  case ImagePlus.COLOR_256:
186  case ImagePlus.COLOR_RGB:
187  value = pixels[0] + "," + pixels[1] + "," + pixels[2];
188  text = String.format("x=%s, y=%s, value=%-15s", x, y, value);
189  break;
190  }
191  return text;
192 
193  }
194 
195 
196  @Override
197  public void windowClosing(WindowEvent e) {
198 
199  super.windowClosing(e);
200  myClose();
201  imp.flush();
202  }
203 
204  public synchronized void myClose()
205  {
206  closing = true;
207  XmippApplication.removeInstance(true);
208  if(maskfr != null)
209  {
210  maskfr.setVisible(false);
211  maskfr.dispose();
212 
213  }
214  }
215 
216 
217  @Override
218  public boolean close()
219  {
220  boolean result = super.close();
221  myClose();
222  return result;
223  }
224 
225 
226  public Params getParams()
227  {
228  return params;
229  }
230 
231 
232  protected void loadMaskFrame()
233  {
234  if(maskfr == null || !maskfr.isVisible())
235  {
236  SwingUtilities.invokeLater(new Runnable() {
237 
238  @Override
239  public void run() {
240  maskfr = new DesignMaskJFrame(XmippImageWindow.this);
241  XmippWindowUtil.setLocation(0.2f, 0.5f, XmippImageWindow.this);
242  XmippWindowUtil.setLocation(0.6f, 0.5f, maskfr);
243  }
244  });
245 
246  imp.getCanvas().addMouseListener(new MouseListener() {
247 
248  @Override
249  public void mouseClicked(MouseEvent me) {
250  }
251 
252  @Override
253  public void mousePressed(MouseEvent me) {
254  }
255 
256  @Override
257  public void mouseReleased(MouseEvent me) {
258  maskfr.refreshMask();
259  }
260 
261  @Override
262  public void mouseEntered(MouseEvent me) {
263  }
264 
265  @Override
266  public void mouseExited(MouseEvent me) {
267  }
268  });
269  imp.getCanvas().addComponentListener(new java.awt.event.ComponentAdapter()
270  {
271  @Override
272  public void componentResized(ComponentEvent e)
273  {
274  maskfr.refreshMask();
275  }
276  });
277 
278  }
279  }
280 
281 
282  public synchronized boolean isClosing()
283  {
284  // TODO Auto-generated method stub
285  return closing;
286  }
287 
288 
289 
290 
291 
292 }// class XmippImageWindow
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xmipp.ij.commons.XmippImageWindow.XmippImageWindow
XmippImageWindow(ImagePlus imp, Params params)
Definition: XmippImageWindow.java:40
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xmipp.ij.commons.XmippImageWindow.showPixels
void showPixels(int x, int y, int[] pixels)
Definition: XmippImageWindow.java:159
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xmipp.ij.commons.XmippImageWindow.XmippImageWindow
XmippImageWindow(ImagePlusLoader ipl, String title, Params params)
Definition: XmippImageWindow.java:56
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xmipp.ij.commons.XmippImageConverter.writeImagePlus
static boolean writeImagePlus(ImagePlus imp, String filename)
Definition: XmippImageConverter.java:312
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xmipp.utils.Params.isMask
boolean isMask()
Definition: Params.java:328
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xmipp.ij.commons.XmippImageWindow.pixelsToString
static String pixelsToString(ImagePlus imp, int x, int y, int[] pixels)
Definition: XmippImageWindow.java:167
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xmipp.utils.XmippWindowUtil.setScipionImageIcon
static void setScipionImageIcon(Window w)
Definition: XmippWindowUtil.java:389
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xmipp.ij.commons.XmippImageWindow.XmippImageWindow
XmippImageWindow(ImagePlusLoader ipl, Params params)
Definition: XmippImageWindow.java:35
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xmipp.ij.commons.XmippMenuBar.runCommand
void runCommand(String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:666
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static void removeInstance(boolean isijwindow)
Definition: XmippApplication.java:28
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xmipp.ij.commons.XmippImageWindow.XmippImageWindow
XmippImageWindow(ImagePlus imp, ImageCanvas canvas, Params params)
Definition: XmippImageWindow.java:45
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static void addInstance(boolean isijwindow)
Definition: XmippApplication.java:18
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.utils;
6 
11 public class XmippLabel {
12 
13  public final static String APP_NAME = "XmippJ";
14  public final static String MESAGE_ABOUT = "About " + APP_NAME;
15  public final static String TITLE_ABOUT = "About " + APP_NAME;
16  //public final static String TITLE_XMIPP_BROWSER = "Xmipp Browser";
17  //public final static String TITLE_XMIPP_FILE_SELECTOR_ANY = "Select...";
18  //public final static String TITLE_XMIPP_FILE_SELECTOR_FILE = "Select file(s)";
19  //public final static String TITLE_XMIPP_FILE_SELECTOR_DIR = "Select dir(s)";
20  //public final static String TITLE_WIZARD_PSD = "Wizard PSD";
21  //public final static String TITLE_WIZARD_MEASURE_FREQS = "Wizard Measure Freqs.";
22  //public final static String TITLE_WIZARD_BAD_PIXELS_FILTER = "Wizard Bad Pixels Filter";
23  //public final static String TITLE_WIZARD_BAND_PASS_FILTER = "Wizard Band Pass Filter";
24  //public final static String TITLE_WIZARD_GAUSSIAN_FILTER = "Wizard Gaussian Filter";
25  //public final static String TITLE_WIZARD_MASK_DESIGN = "Wizard Mask Design";
26  public final static String TITLE_ERROR = "Memory error";
27  public final static String TITLE_GO_TO_SLICE = "Go to slice";
28  public final static String TITLE_PREVIEW = "Preview:";
29  //public final static String TITLE_PREVIEW_FILTER = "Filter:";
30  public final static String TITLE_SEND2WINDOW = "Send image to window";
31  public final static String TITLE_FSC = "FSC: ";
32  public final static String TITLE_UNTITLED = "Untitled";
33 
37  public final static String BUTTON_IMAGE_STATS = "Mean & Std";
38  public final static String BUTTON_CANCEL = "Cancel";
39  //public final static String BUTTON_CAPTURE_WINDOW = "Capture";
40  public final static String BUTTON_INVERT_SELECTION = "Invert Selection";
41  public final static String BUTTON_NORMALIZE = "Normalize";
42  //public final static String BUTTON_OPEN_AS_IMAGE = "Open as Image";
43  //public final static String BUTTON_OPEN_AS_GALLERY = "Open as gallery";
44  public final static String OPERATION_OPEN_AS_3D_VOLUME = "3D Volume";
45  public final static String OPERATION_OPEN_AS_METADATA = "Metadata";
46  public final static String OPERATION_OPEN_AS_STACK = "Stack";
47  public final static String BUTTON_OK = "Ok";
48  public final static String BUTTON_CLOSE = "Close";
49  //public final static String BUTTON_PARENT_DIRECTORY = "Parent";
50  public final static String BUTTON_RELOAD_GALLERY = "Reload";
51  public final static String BUTTON_REFRESH = "Refresh";
52  //public final static String BUTTON_REFRESH_DIRECTORY = "Refresh";
53  public final static String BUTTON_SAVE = "Save";
54  public final static String BUTTON_SELECT_ALL = "Select All";
55  public final static String BUTTON_STD_DEVIATION = "Std. Deviation";
56  public final static String BUTTON_PCA = "PCA";
57  public final static String BUTTON_FSC = "FSC";
58  public final static String BUTTON_TO_STACK = "To Stack";
59  public final static String BUTTON_EXPORT_PROFILE = "Export Profiles";
60  public final static String BUTTON_EXPORT_RADIAL_AVERAGE = "Export Radial AVG.";
61  public final static String CB_PLOT_PROFILE = "Profile";
62  public final static String CB_PLOT_BGNOISE = "Log(BGNoise)";
63  public final static String CB_PLOT_ENVELOPE = "Log(Envelope)";
64  public final static String CB_PLOT_PSD = "PSD";
65  public final static String CB_PLOT_CTF = "CTF";
66  public final static String CB_PLOT_DIFFERENCE = "Difference";
67 // public final static String SAMPLING_DIRECT = "A";
68 // public final static String SAMPLING_INVERSE = "1/A";
72  public final static String OPERATION_MENU_TRANSFORM = "Transform";
73  public final static String OPERATION_TO_GALLERY = "To Gallery";
74  public final static String OPERATION_MENU_FLIP = "Flip";
75  public final static String OPERATION_MENU_ROTATE = "Rotate";
76  public final static String OPERATION_CROP = "Crop";
77  public final static String OPERATION_MENU_DENOISING = "Denoising";
78  public final static String OPERATION_MENU_OPEN_WITH = "Open with...";
79  public final static String OPERATION_MENU_THRESHOLDING = "Thresholding";
80  public final static String OPERATION_MENU_BINARY = "Binary";
81  public final static String OPERATION_MENU_INFO = "Info";
82  public final static String OPERATION_MENU_PROCESS = "Process";
83  //public final static String OPERATION_MENU_RESLICE = "Reslice";
84  public final static String OPERATION_MENU_GO_TO = "Go to";
85  public final static String OPERATION_MENU_THRESHOLD = "Threshold";
86  public final static String OPERATION_MENU_DRAW = "Draw";
87  public final static String OPERATION_FLIP_VERTICAL = "Flip Vertical";
88  public final static String OPERATION_FLIP_HORIZONTAL = "Flip Horizontal";
89  public final static String OPERATION_ROTATE_LEFT = "Rotate Left";
90  public final static String OPERATION_ROTATE_RIGHT = "Rotate Right";
91  public final static String OPERATION_HISTOGRAM = "Histogram";
92  public final static String OPERATION_PLOT_PROFILE = "Plot Profile";
93  public final static String OPERATION_MEASUREMENTS = "Measurements";
94  public final static String OPERATION_BC = "Bright&Contrast";
95  public final static String OPERATION_ENHANCE_CONTRAST = "Enhance Contrast";
96  public final static String OPERATION_THRESHOLD = "Threshold";
97  public final static String OPERATION_SUBTRACTBG = "Subtract Background";
98  public final static String OPERATION_GAUSSIAN_BLUR = "Gaussian Blur";
99  public final static String OPERATION_CONVOLVE = "Convolve";
100  public final static String OPERATION_MEDIAN = "Median";
101  public final static String OPERATION_MEAN = "Mean";
102  public final static String OPERATION_FFT = "FFT";
103  public final static String OPERATION_FFT_BAND_PASS_FILTER = "FFT Band Pass Filter";
104  public final static String OPERATION_RESLICE_TOP = "Reslice Top";
105  public final static String OPERATION_RESLICE_RIGHT = "Reslice Right";
106  public final static String OPERATION_STACK_SLICER = "StackSlicer (dynamic orthogonal views)";
107  public final static String OPERATION_RADIAL_RESLICE = "Radial Reslice (orthogonal reconstructions)";
108  public final static String OPERATION_STRAIGHTEN_CURVED_OBJECTS = "Straighten Curved Objects";
109  public final static String OPERATION_UNTILT_STACK = "Untilt Stack (removes tilt from a stack of images)";
110  public final static String OPERATION_TRANSFORMJ = "TransformJ";
111  public final static String OPERATION_TJABOUT = "TJ About";
112  public final static String OPERATION_TJAFFINE = "TJ Affine";
113  public final static String OPERATION_TJCROP = "TJ Crop";
114  public final static String OPERATION_TJEMBED = "TJ Embed";
115  public final static String OPERATION_TJMIRROR = "TJ Mirror";
116  public final static String OPERATION_TJOPTIONS = "TJ Options";
117  public final static String OPERATION_TJPANEL = "TJ Panel";
118  public final static String OPERATION_TJROTATE = "TJ Rotate";
119  public final static String OPERATION_TJSCALE = "TJ Scale";
120  public final static String OPERATION_TJSHIFT = "TJ Shift";
121  public final static String OPERATION_TJTURN = "TJ Turn";
122  public final static String OPERATION_TJWEBSITE = "TJ Website";
123  public final static String OPERATION_SURFACEJ = "SurfaceJ";
124  public final static String OPERATION_OPEN_AS_3D = "3D Viewer";
125  public final static String OPERATION_POLL = "Poll";
126  public final static String OPERATION_DUPLICATE = "Duplicate";
127  public final static String OPERATION_GO_TO_SLICE = "Go to slice";
128  public final static String OPERATION_SUBSTACK_MAKER = "Substack Maker";
129  public final static String OPERATION_ANISOTROPIC_DIFFUSION = "Anisotropic Diffusion";
130  public final static String OPERATION_MEAN_SHIFT_FILTER = "Mean Shift Filter";
131  public final static String OPERATION_VOLUME_VIEWER_3D_SLICER = "Volume Viewer/3D-Slicer";
132  public final static String OPERATION_VOLUMEJ = "VolumeJ";
133  public final static String OPERATION_AUTOCORRELATION = "Autocorrelation";
134  public final static String OPERATION_CONCENTRIC_CIRCLES = "Concentric Circles";
135  public final static String OPERATION_LINE_ANALYZER = "Line Analyzer";
136  public final static String OPERATION_OVAL_PROFILER_PLOT = "Oval Profile Plot";
137  public final static String OPERATION_RADIAL_PROFILE_PLOT_ANGLE = "Radial Profile Plot Angle";
138  public final static String OPERATION_RADIAL_PROFILE_PLOT_HEIGHT = "Radial Profile Plot Height";
139  public final static String OPERATION_CONTOUR_PLOTTER = "Contour Plotter";
140  public final static String OPERATION_FEATUREJ = "FeatureJ";
141  public final static String OPERATION_SYNC_WINDOWS = "Sync Windows";
142  public final static String OPERATION_SYNC_MEASURE_3D = "Sync Measure 3D";
143  public final static String OPERATION_OTSU_THRESHOLDING = "Otsu Thresholding";
144  public final static String OPERATION_MULTI_OTSU_THRESHOLDING = "Multi Otsu Threshold";
145  public final static String OPERATION_MIXTURE_MODELING_THRESHOLDING = "Mixture Modeling Thresholding";
146  public final static String OPERATION_MAXIMUM_ENTROPY_THRESHOLDING = "Maximum Entropy Thresholding";
147  public final static String OPERATION_MULTI_THRESHOLDER = "MultiThresholder";
148  public final static String OPERATION_SIOX = "SIOX Simple Interactive Object Extraction";
149  public final static String OPERATION_RATS = "RATS Robust Automatic Threshold Selection";
150  public final static String OPERATION_VOXEL_COUNTER = "Voxel Counter";
151  public final static String OPERATION_ERODE = "Erode";
152  public final static String OPERATION_DILATE = "Dilate";
153  public final static String OPERATION_OPEN = "Open";
154  public final static String OPERATION_CLOSE = "Close";
155  public final static String OPERATION_FLOAT_MORPHOLOGY = "Float Morphology";
156  public final static String OPERATION_OUTLINE = "Outline";
157  public final static String OPERATION_FILL_HOLES = "Fill holes";
158  public final static String OPERATION_SKELETONIZE = "Skeletonize";
159  public final static String OPERATION_DISTANCE_MAP = "Distance map";
160  public final static String OPERATION_ULTIMATE_POINTS = "Ultimate points";
161  public final static String OPERATION_WATERSHED = "Watershed";
162  public final static String OPERATION_VORONOI = "Voronoi";
163  public final static String OPERATION_OPTIONS = "Options";
164  public final static String OPERATION_CLAHE = "CLAHE Contrast Limited Adaptive Histogram Equalization";
165  public final static String OPERATION_PCA = "PCA Principal Component Analysis";
166  public final static String OPERATION_POLAR_TRANSFORMER = "Polar Transformer convert to polar coordinates";
167  public final static String OPERATION_DOTTED_AND_DASHED_LINES = "Dotted and Dashed Lines";
168  public final static String OPERATION_RADIAL_GRID = "Radial Grid";
169  public final static String OPERATION_TEMPLATE_MATCHING = "Template Matching";
170  public final static String OPERATION_MENU_MASKS = "Masks";
171  public final static String OPERATION_MASKS_TOOLBAR = "Masks Tool Bar";
172  //public final static String OPERATION_FLOWJ = "FlowJ";
173  //public final static String OPERATION_FLOW3J = "Flow3J";
174  //public final static String OPERATION_OBJECTJ = "ObjectJ";
175  public final static String LABEL_SHOW_CTF_INFO = "Show CTF info";
176  public final static String LABEL_EXTRACT_COLUMN_ENABLED = "Extract Column (enabled)";
177  public final static String LABEL_EXTRACT_COLUMN_ALL = "Extract Column (all)";
178  public final static String LABEL_RECALCULATE_CTF = "Recalculate CTF";
179  public final static String LABEL_VIEW_CTF_PROFILE = "View CTF Profile";
183  public final static String LABEL_DIGITAL_FREQUENCY = "Digital frequency";
184  public final static String LABEL_AUTO_AJUST_COLS = "Auto adjust columns";
185  public final static String LABEL_SHOW_LABELS = "Show label: ";
186  public final static String LABEL_ROTSPECTRA_SHOW_NIMAGES = "Show #images";
187  public final static String LABEL_SORT_BY_LABEL = "Sort by label";
188  public final static String LABEL_USE_GEOMETRY = "Use geometry";
189  //public final static String LABEL_FILTER = "Filter: ";
190  public final static String LABEL_WIDTH = "Width: ";
191  public final static String LABEL_HEIGHT = "Height: ";
192  public final static String LABEL_DEPTH = "Depth: ";
193  public final static String LABEL_NIMAGES = "#Images: ";
194  public final static String LABEL_LOAD_PREVIEW = "Load preview";
195  public final static String LABEL_GALLERY_DISABLE = "Disable";
196  public final static String LABEL_GALLERY_ENABLE = "Enable";
197  public final static String LABEL_GALLERY_ENABLE_ALL = "Enable All";
198  public final static String LABEL_GALLERY_ENABLE_FROM = "Enable from here";
199  public final static String LABEL_GALLERY_ENABLE_TO = "Enable to here";
200  public final static String LABEL_GALLERY_HIDE_DISABLED = "Hide disabled";
201  public final static String LABEL_GALLERY_DISABLE_ALL = "Disable All";
202  public final static String LABEL_GALLERY_DISABLE_FROM = "Disable from here";
203  public final static String LABEL_GALLERY_DISABLE_TO = "Disable to here";
204  public final static String LABEL_GALLERY_FILE = "File";
205  public final static String LABEL_GALLERY_SAVE = "Save";
206  public final static String LABEL_GALLERY_SAVEAS = "Save as";
207  public final static String LABEL_GALLERY_EXIT = "Exit";
208  public final static String LABEL_VIEW_MD = "Go to TABLE view";
209  public final static String LABEL_VIEW_GALLERY = "Go to GALLERY view";
210  //public final static String LABEL_GALLERY_SAVE_AS_IMAGES = "Save as images";
211  public final static String LABEL_GALLERY_SAVE_AS_METADATA = "Save as metadata";
212  public final static String LABEL_GALLERY_SAVE_SELECTION_AS_METADATA = "Save selection as metadata";
213  public final static String LABEL_GALLERY_SAVE_AS_IMAGE = "Save as image";
214  public final static String LABEL_GALLERY_SAVE_SELECTION_AS_IMAGE = "Save selection as image";
215  public final static String LABEL_RESLICE = "Reslice";
216  public final static String LABEL_RESLICE_TOP = "Reslice Top (Y)";
217  public final static String LABEL_RESLICE_RIGHT = "Reslice Right (X)";
218  public final static String LABEL_CTF = "CTF";
219  public final static String LABEL_PSD = "Log(PSD)";
220  public final static String LABEL_SAMPLING = "1/A";
221  public final static String LABEL_PROFILES = "Profiles";
222  public final static String LABEL_RADIAL_AVERAGE = "Radial Average";
223  //public final static String LABEL_RADIAL_FREQ_DIRECT = "freq. (A)";
224  //public final static String LABEL_RADIAL_FREQ_INVERSE = "freq. (1/A)";
225  public final static String LABEL_RADIAL_AVG = "Radial Average";
226  public final static String LABEL_TAB_PROFILE = "Profiles";
227  public final static String LABEL_TAB_RADIAL_AVERAGE = "Radial Average";
228  public final static String LABEL_ZOOM = "Zoom (%): ";
229  public final static String LABEL_ROWS = " Rows";
230  public final static String LABEL_COLUMNS = " Cols";
231  public final static String LABEL_BLOCK = " Block";
232  public final static String LABEL_VOLUME = " Volume";
233  public final static String LABEL_GOTO_ITEM = "Go to item";
234  //public final static String LABEL_FLIP = "Flip: ";
235  //public final static String LABEL_ROTATE = "Rotate: ";
236  //public final static String LABEL_INFO = "Info: ";
237  //public final static String LABEL_PROCESS = "Process: ";
238  //public final static String LABEL_RESLICE = "Reslice: ";
239  //public final static String LABEL_OPEN_AS = "Open as: ";
240  public final static String LABEL_UNKNOWN = "Unknown label";
241  //public final static String LABEL_SAMPLING = "Sampling: ";
242  //public final static String LABEL_DOWNSAMPLING = "Downsampling: ";
243  //public final static String LABEL_BAD_PIXELS_FACTOR = "Bad pixels factor: ";
244  //public final static String LABEL_W1 = "W1: ";
245  //public final static String LABEL_W2 = "W2: ";
246  //public final static String LABEL_RAISED_W = "Raised W: ";
247  public final static String MENU_STATS = "Statistics";
248  public final static String MENU_OPEN_WITH = "Open with...";
249  public final static String MENU_OPEN_WITH_CHIMERA = "UCSF Chimera";
250  public final static String MENU_OPEN_WITH_IJ = "ImageJ";
251 //
252 // public static String LABEL_FILES_SHOWING(int elements, int total) {
253 // return total != elements ? " Showing " + elements + " / " + total + " elements." : "";
254 // }
255 //
256 // public static String MESSAGE_MEMORY_ERROR(long fileSize, long maxMemory) {
257 // return "File size (" + FileBrowser.getFileSizeString(fileSize) + ") is bigger than available memory (" + FileBrowser.getFileSizeString(maxMemory) + ")";
258 // }
259  public final static String MSG_NO_ITEMS_SELECTED = "No items selected (or not enabled)";
260  //public final static String FILE_SELECTED_OUTPUT_PREFIX = "File selected: ";
261  public final static String MESSAGE_OVERWRITE_FILE = "Overwrite existing file?";
262  public final static String MESSAGE_OVERWRITE_FILE_TITLE = "Confirm Overwrite";
263  public final static String MESSAGE_FILE_SAVED = "File saved: ";
264  public final static String MESSAGE_FILE_SAVED_TITLE = "Saved!";
265  public final static String MSG_NORMALIZE = "Global normalization";
266  public final static String MSG_APPLY_GEO = "Apply geometry";
267  public final static String MSG_SHOW_LABEL = "Show labels";
268  public final static String MSG_RENDER_IMG = "Render images";
269  public final static String MSG_ADJUST_COLS = "Adjust columns when resizing";
270 }
xmipp.utils.XmippLabel.OPERATION_CROP
static final String OPERATION_CROP
Definition: XmippLabel.java:76
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xmipp.utils.XmippLabel.OPERATION_TJABOUT
static final String OPERATION_TJABOUT
Definition: XmippLabel.java:111
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xmipp.utils.XmippLabel.OPERATION_MIXTURE_MODELING_THRESHOLDING
static final String OPERATION_MIXTURE_MODELING_THRESHOLDING
Definition: XmippLabel.java:145
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xmipp.utils.XmippLabel.OPERATION_HISTOGRAM
static final String OPERATION_HISTOGRAM
Definition: XmippLabel.java:91
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xmipp.utils.XmippLabel.LABEL_WIDTH
static final String LABEL_WIDTH
Definition: XmippLabel.java:190
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xmipp.utils.XmippLabel.OPERATION_VORONOI
static final String OPERATION_VORONOI
Definition: XmippLabel.java:162
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xmipp.utils.XmippLabel.LABEL_DEPTH
static final String LABEL_DEPTH
Definition: XmippLabel.java:192
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xmipp.utils.XmippLabel.OPERATION_MULTI_THRESHOLDER
static final String OPERATION_MULTI_THRESHOLDER
Definition: XmippLabel.java:147
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xmipp.utils.XmippLabel.LABEL_USE_GEOMETRY
static final String LABEL_USE_GEOMETRY
Definition: XmippLabel.java:188
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xmipp.utils.XmippLabel.LABEL_GALLERY_HIDE_DISABLED
static final String LABEL_GALLERY_HIDE_DISABLED
Definition: XmippLabel.java:200
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xmipp.utils.XmippLabel.BUTTON_REFRESH
static final String BUTTON_REFRESH
Definition: XmippLabel.java:51
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xmipp.utils.XmippLabel.BUTTON_PCA
static final String BUTTON_PCA
Definition: XmippLabel.java:56
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xmipp.utils.XmippLabel.LABEL_GALLERY_DISABLE_ALL
static final String LABEL_GALLERY_DISABLE_ALL
Definition: XmippLabel.java:201
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xmipp.utils.XmippLabel.CB_PLOT_ENVELOPE
static final String CB_PLOT_ENVELOPE
Definition: XmippLabel.java:63
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xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE_AS_IMAGE
static final String LABEL_GALLERY_SAVE_AS_IMAGE
Definition: XmippLabel.java:213
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xmipp.utils.XmippLabel.LABEL_HEIGHT
static final String LABEL_HEIGHT
Definition: XmippLabel.java:191
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xmipp.utils.XmippLabel.LABEL_GALLERY_ENABLE_FROM
static final String LABEL_GALLERY_ENABLE_FROM
Definition: XmippLabel.java:198
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xmipp.utils.XmippLabel.BUTTON_NORMALIZE
static final String BUTTON_NORMALIZE
Definition: XmippLabel.java:41
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xmipp.utils.XmippLabel.OPERATION_DOTTED_AND_DASHED_LINES
static final String OPERATION_DOTTED_AND_DASHED_LINES
Definition: XmippLabel.java:167
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xmipp.utils.XmippLabel.MSG_ADJUST_COLS
static final String MSG_ADJUST_COLS
Definition: XmippLabel.java:269
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xmipp.utils.XmippLabel.LABEL_TAB_RADIAL_AVERAGE
static final String LABEL_TAB_RADIAL_AVERAGE
Definition: XmippLabel.java:227
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xmipp.utils.XmippLabel.LABEL_LOAD_PREVIEW
static final String LABEL_LOAD_PREVIEW
Definition: XmippLabel.java:194
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xmipp.utils.XmippLabel.MESSAGE_FILE_SAVED
static final String MESSAGE_FILE_SAVED
Definition: XmippLabel.java:263
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xmipp.utils.XmippLabel.OPERATION_TJMIRROR
static final String OPERATION_TJMIRROR
Definition: XmippLabel.java:115
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xmipp.utils.XmippLabel.OPERATION_DISTANCE_MAP
static final String OPERATION_DISTANCE_MAP
Definition: XmippLabel.java:159
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xmipp.utils.XmippLabel.LABEL_RECALCULATE_CTF
static final String LABEL_RECALCULATE_CTF
Definition: XmippLabel.java:178
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xmipp.utils.XmippLabel.OPERATION_FLIP_VERTICAL
static final String OPERATION_FLIP_VERTICAL
Definition: XmippLabel.java:87
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xmipp.utils.XmippLabel.LABEL_GALLERY_DISABLE_TO
static final String LABEL_GALLERY_DISABLE_TO
Definition: XmippLabel.java:203
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xmipp.utils.XmippLabel.LABEL_SAMPLING
static final String LABEL_SAMPLING
Definition: XmippLabel.java:220
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xmipp.utils.XmippLabel.OPERATION_MEAN_SHIFT_FILTER
static final String OPERATION_MEAN_SHIFT_FILTER
Definition: XmippLabel.java:130
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xmipp.utils.XmippLabel.BUTTON_CLOSE
static final String BUTTON_CLOSE
Definition: XmippLabel.java:48
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xmipp.utils.XmippLabel.OPERATION_GO_TO_SLICE
static final String OPERATION_GO_TO_SLICE
Definition: XmippLabel.java:127
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xmipp.utils.XmippLabel.OPERATION_FFT
static final String OPERATION_FFT
Definition: XmippLabel.java:102
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xmipp.utils.XmippLabel.LABEL_VIEW_GALLERY
static final String LABEL_VIEW_GALLERY
Definition: XmippLabel.java:209
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xmipp.utils.XmippLabel.OPERATION_SYNC_MEASURE_3D
static final String OPERATION_SYNC_MEASURE_3D
Definition: XmippLabel.java:142
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xmipp.utils.XmippLabel.MESSAGE_OVERWRITE_FILE
static final String MESSAGE_OVERWRITE_FILE
Definition: XmippLabel.java:261
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xmipp.utils.XmippLabel.OPERATION_TO_GALLERY
static final String OPERATION_TO_GALLERY
Definition: XmippLabel.java:73
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xmipp.utils.XmippLabel.OPERATION_FILL_HOLES
static final String OPERATION_FILL_HOLES
Definition: XmippLabel.java:157
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xmipp.utils.XmippLabel.LABEL_GALLERY_ENABLE
static final String LABEL_GALLERY_ENABLE
Definition: XmippLabel.java:196
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xmipp.utils.XmippLabel.OPERATION_MAXIMUM_ENTROPY_THRESHOLDING
static final String OPERATION_MAXIMUM_ENTROPY_THRESHOLDING
Definition: XmippLabel.java:146
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xmipp.utils.XmippLabel.OPERATION_RADIAL_PROFILE_PLOT_HEIGHT
static final String OPERATION_RADIAL_PROFILE_PLOT_HEIGHT
Definition: XmippLabel.java:138
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xmipp.utils.XmippLabel.LABEL_GALLERY_SAVEAS
static final String LABEL_GALLERY_SAVEAS
Definition: XmippLabel.java:206
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xmipp.utils.XmippLabel.OPERATION_THRESHOLD
static final String OPERATION_THRESHOLD
Definition: XmippLabel.java:96
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xmipp.utils.XmippLabel.CB_PLOT_CTF
static final String CB_PLOT_CTF
Definition: XmippLabel.java:65
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xmipp.utils.XmippLabel.OPERATION_TJWEBSITE
static final String OPERATION_TJWEBSITE
Definition: XmippLabel.java:122
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xmipp.utils.XmippLabel.LABEL_GALLERY_EXIT
static final String LABEL_GALLERY_EXIT
Definition: XmippLabel.java:207
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xmipp.utils.XmippLabel.OPERATION_STACK_SLICER
static final String OPERATION_STACK_SLICER
Definition: XmippLabel.java:106
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xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE
static final String LABEL_GALLERY_SAVE
Definition: XmippLabel.java:205
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xmipp.utils.XmippLabel.OPERATION_POLAR_TRANSFORMER
static final String OPERATION_POLAR_TRANSFORMER
Definition: XmippLabel.java:166
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xmipp.utils.XmippLabel.OPERATION_TJTURN
static final String OPERATION_TJTURN
Definition: XmippLabel.java:121
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xmipp.utils.XmippLabel.OPERATION_RESLICE_RIGHT
static final String OPERATION_RESLICE_RIGHT
Definition: XmippLabel.java:105
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xmipp.utils.XmippLabel.BUTTON_OK
static final String BUTTON_OK
Definition: XmippLabel.java:47
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xmipp.utils.XmippLabel.OPERATION_TJCROP
static final String OPERATION_TJCROP
Definition: XmippLabel.java:113
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xmipp.utils.XmippLabel.LABEL_VIEW_CTF_PROFILE
static final String LABEL_VIEW_CTF_PROFILE
Definition: XmippLabel.java:179
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xmipp.utils.XmippLabel.OPERATION_LINE_ANALYZER
static final String OPERATION_LINE_ANALYZER
Definition: XmippLabel.java:135
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xmipp.utils.XmippLabel.CB_PLOT_DIFFERENCE
static final String CB_PLOT_DIFFERENCE
Definition: XmippLabel.java:66
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xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE_AS_METADATA
static final String LABEL_GALLERY_SAVE_AS_METADATA
Definition: XmippLabel.java:211
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xmipp.utils.XmippLabel.OPERATION_MENU_BINARY
static final String OPERATION_MENU_BINARY
Definition: XmippLabel.java:80
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xmipp.utils.XmippLabel.OPERATION_SKELETONIZE
static final String OPERATION_SKELETONIZE
Definition: XmippLabel.java:158
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xmipp.utils.XmippLabel.OPERATION_MASKS_TOOLBAR
static final String OPERATION_MASKS_TOOLBAR
Definition: XmippLabel.java:171
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xmipp.utils.XmippLabel.OPERATION_MENU_THRESHOLDING
static final String OPERATION_MENU_THRESHOLDING
Definition: XmippLabel.java:79
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xmipp.utils.XmippLabel.OPERATION_PLOT_PROFILE
static final String OPERATION_PLOT_PROFILE
Definition: XmippLabel.java:92
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xmipp.utils.XmippLabel.TITLE_GO_TO_SLICE
static final String TITLE_GO_TO_SLICE
Definition: XmippLabel.java:27
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xmipp.utils.XmippLabel.OPERATION_FFT_BAND_PASS_FILTER
static final String OPERATION_FFT_BAND_PASS_FILTER
Definition: XmippLabel.java:103
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xmipp.utils.XmippLabel.TITLE_PREVIEW
static final String TITLE_PREVIEW
Definition: XmippLabel.java:28
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xmipp.utils.XmippLabel.MESSAGE_FILE_SAVED_TITLE
static final String MESSAGE_FILE_SAVED_TITLE
Definition: XmippLabel.java:264
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xmipp.utils.XmippLabel.MENU_OPEN_WITH_IJ
static final String MENU_OPEN_WITH_IJ
Definition: XmippLabel.java:250
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xmipp.utils.XmippLabel.OPERATION_TJPANEL
static final String OPERATION_TJPANEL
Definition: XmippLabel.java:117
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xmipp.utils.XmippLabel.APP_NAME
static final String APP_NAME
Definition: XmippLabel.java:13
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xmipp.utils.XmippLabel.LABEL_BLOCK
static final String LABEL_BLOCK
Definition: XmippLabel.java:231
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xmipp.utils.XmippLabel.OPERATION_UNTILT_STACK
static final String OPERATION_UNTILT_STACK
Definition: XmippLabel.java:109
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xmipp.utils.XmippLabel.LABEL_EXTRACT_COLUMN_ENABLED
static final String LABEL_EXTRACT_COLUMN_ENABLED
Definition: XmippLabel.java:176
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xmipp.utils.XmippLabel.OPERATION_TJAFFINE
static final String OPERATION_TJAFFINE
Definition: XmippLabel.java:112
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xmipp.utils.XmippLabel.CB_PLOT_PSD
static final String CB_PLOT_PSD
Definition: XmippLabel.java:64
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xmipp.utils.XmippLabel.MSG_NORMALIZE
static final String MSG_NORMALIZE
Definition: XmippLabel.java:265
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xmipp.utils.XmippLabel.OPERATION_MENU_OPEN_WITH
static final String OPERATION_MENU_OPEN_WITH
Definition: XmippLabel.java:78
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xmipp.utils.XmippLabel.LABEL_ZOOM
static final String LABEL_ZOOM
Definition: XmippLabel.java:228
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xmipp.utils.XmippLabel.OPERATION_TJSCALE
static final String OPERATION_TJSCALE
Definition: XmippLabel.java:119
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xmipp.utils.XmippLabel.OPERATION_MENU_FLIP
static final String OPERATION_MENU_FLIP
Definition: XmippLabel.java:74
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xmipp.utils.XmippLabel.OPERATION_SUBTRACTBG
static final String OPERATION_SUBTRACTBG
Definition: XmippLabel.java:97
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xmipp.utils.XmippLabel.OPERATION_OVAL_PROFILER_PLOT
static final String OPERATION_OVAL_PROFILER_PLOT
Definition: XmippLabel.java:136
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xmipp.utils.XmippLabel.MESAGE_ABOUT
static final String MESAGE_ABOUT
Definition: XmippLabel.java:14
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xmipp.utils.XmippLabel.BUTTON_INVERT_SELECTION
static final String BUTTON_INVERT_SELECTION
Definition: XmippLabel.java:40
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xmipp.utils.XmippLabel.OPERATION_OPEN_AS_3D_VOLUME
static final String OPERATION_OPEN_AS_3D_VOLUME
Definition: XmippLabel.java:44
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xmipp.utils.XmippLabel.OPERATION_TJEMBED
static final String OPERATION_TJEMBED
Definition: XmippLabel.java:114
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xmipp.utils.XmippLabel.TITLE_SEND2WINDOW
static final String TITLE_SEND2WINDOW
Definition: XmippLabel.java:30
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xmipp.utils.XmippLabel.OPERATION_SYNC_WINDOWS
static final String OPERATION_SYNC_WINDOWS
Definition: XmippLabel.java:141
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xmipp.utils.XmippLabel.OPERATION_CLOSE
static final String OPERATION_CLOSE
Definition: XmippLabel.java:154
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xmipp.utils.XmippLabel.LABEL_UNKNOWN
static final String LABEL_UNKNOWN
Definition: XmippLabel.java:240
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xmipp.utils.XmippLabel.OPERATION_MENU_DENOISING
static final String OPERATION_MENU_DENOISING
Definition: XmippLabel.java:77
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xmipp.utils.XmippLabel.MSG_APPLY_GEO
static final String MSG_APPLY_GEO
Definition: XmippLabel.java:266
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xmipp.utils.XmippLabel.OPERATION_ENHANCE_CONTRAST
static final String OPERATION_ENHANCE_CONTRAST
Definition: XmippLabel.java:95
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xmipp.utils.XmippLabel.OPERATION_RATS
static final String OPERATION_RATS
Definition: XmippLabel.java:149
-
xmipp.utils.XmippLabel.BUTTON_TO_STACK
static final String BUTTON_TO_STACK
Definition: XmippLabel.java:58
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xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE_SELECTION_AS_IMAGE
static final String LABEL_GALLERY_SAVE_SELECTION_AS_IMAGE
Definition: XmippLabel.java:214
-
xmipp.utils.XmippLabel.OPERATION_STRAIGHTEN_CURVED_OBJECTS
static final String OPERATION_STRAIGHTEN_CURVED_OBJECTS
Definition: XmippLabel.java:108
-
xmipp.utils.XmippLabel.LABEL_PROFILES
static final String LABEL_PROFILES
Definition: XmippLabel.java:221
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xmipp.utils.XmippLabel.OPERATION_GAUSSIAN_BLUR
static final String OPERATION_GAUSSIAN_BLUR
Definition: XmippLabel.java:98
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xmipp.utils.XmippLabel.OPERATION_MULTI_OTSU_THRESHOLDING
static final String OPERATION_MULTI_OTSU_THRESHOLDING
Definition: XmippLabel.java:144
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xmipp.utils.XmippLabel.LABEL_TAB_PROFILE
static final String LABEL_TAB_PROFILE
Definition: XmippLabel.java:226
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xmipp.utils.XmippLabel.LABEL_RESLICE_TOP
static final String LABEL_RESLICE_TOP
Definition: XmippLabel.java:216
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xmipp.utils.XmippLabel.BUTTON_RELOAD_GALLERY
static final String BUTTON_RELOAD_GALLERY
Definition: XmippLabel.java:50
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xmipp.utils.XmippLabel.BUTTON_EXPORT_RADIAL_AVERAGE
static final String BUTTON_EXPORT_RADIAL_AVERAGE
Definition: XmippLabel.java:60
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xmipp.utils.XmippLabel.MENU_OPEN_WITH
static final String MENU_OPEN_WITH
Definition: XmippLabel.java:248
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xmipp.utils.XmippLabel.OPERATION_RESLICE_TOP
static final String OPERATION_RESLICE_TOP
Definition: XmippLabel.java:104
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xmipp.utils.XmippLabel.TITLE_UNTITLED
static final String TITLE_UNTITLED
Definition: XmippLabel.java:32
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xmipp.utils.XmippLabel.OPERATION_BC
static final String OPERATION_BC
Definition: XmippLabel.java:94
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xmipp.utils.XmippLabel.LABEL_NIMAGES
static final String LABEL_NIMAGES
Definition: XmippLabel.java:193
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xmipp.utils.XmippLabel.LABEL_RESLICE
static final String LABEL_RESLICE
Definition: XmippLabel.java:215
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xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE_SELECTION_AS_METADATA
static final String LABEL_GALLERY_SAVE_SELECTION_AS_METADATA
Definition: XmippLabel.java:212
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xmipp.utils.XmippLabel.BUTTON_SAVE
static final String BUTTON_SAVE
Definition: XmippLabel.java:53
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xmipp.utils.XmippLabel.TITLE_ABOUT
static final String TITLE_ABOUT
Definition: XmippLabel.java:15
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xmipp.utils.XmippLabel.LABEL_DIGITAL_FREQUENCY
static final String LABEL_DIGITAL_FREQUENCY
Definition: XmippLabel.java:183
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xmipp.utils.XmippLabel.OPERATION_ROTATE_LEFT
static final String OPERATION_ROTATE_LEFT
Definition: XmippLabel.java:89
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xmipp.utils.XmippLabel.OPERATION_FLOAT_MORPHOLOGY
static final String OPERATION_FLOAT_MORPHOLOGY
Definition: XmippLabel.java:155
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xmipp.utils.XmippLabel.OPERATION_CONTOUR_PLOTTER
static final String OPERATION_CONTOUR_PLOTTER
Definition: XmippLabel.java:139
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xmipp.utils.XmippLabel.LABEL_AUTO_AJUST_COLS
static final String LABEL_AUTO_AJUST_COLS
Definition: XmippLabel.java:184
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xmipp.utils.XmippLabel.OPERATION_OUTLINE
static final String OPERATION_OUTLINE
Definition: XmippLabel.java:156
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xmipp.utils.XmippLabel.OPERATION_PCA
static final String OPERATION_PCA
Definition: XmippLabel.java:165
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xmipp.utils.XmippLabel.OPERATION_MENU_PROCESS
static final String OPERATION_MENU_PROCESS
Definition: XmippLabel.java:82
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xmipp.utils.XmippLabel.OPERATION_CONCENTRIC_CIRCLES
static final String OPERATION_CONCENTRIC_CIRCLES
Definition: XmippLabel.java:134
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xmipp.utils.XmippLabel.OPERATION_ROTATE_RIGHT
static final String OPERATION_ROTATE_RIGHT
Definition: XmippLabel.java:90
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xmipp.utils.XmippLabel.LABEL_VIEW_MD
static final String LABEL_VIEW_MD
Definition: XmippLabel.java:208
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xmipp.utils.XmippLabel.OPERATION_TJOPTIONS
static final String OPERATION_TJOPTIONS
Definition: XmippLabel.java:116
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xmipp.utils.XmippLabel.LABEL_RADIAL_AVG
static final String LABEL_RADIAL_AVG
Definition: XmippLabel.java:225
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xmipp.utils.XmippLabel.LABEL_CTF
static final String LABEL_CTF
Definition: XmippLabel.java:218
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xmipp.utils.XmippLabel.OPERATION_DUPLICATE
static final String OPERATION_DUPLICATE
Definition: XmippLabel.java:126
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xmipp.utils.XmippLabel.LABEL_GALLERY_DISABLE
static final String LABEL_GALLERY_DISABLE
Definition: XmippLabel.java:195
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xmipp.utils.XmippLabel.OPERATION_VOXEL_COUNTER
static final String OPERATION_VOXEL_COUNTER
Definition: XmippLabel.java:150
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xmipp.utils.XmippLabel.OPERATION_OTSU_THRESHOLDING
static final String OPERATION_OTSU_THRESHOLDING
Definition: XmippLabel.java:143
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xmipp.utils.XmippLabel.OPERATION_TJSHIFT
static final String OPERATION_TJSHIFT
Definition: XmippLabel.java:120
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xmipp.utils.XmippLabel.OPERATION_MENU_INFO
static final String OPERATION_MENU_INFO
Definition: XmippLabel.java:81
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xmipp.utils.XmippLabel.CB_PLOT_BGNOISE
static final String CB_PLOT_BGNOISE
Definition: XmippLabel.java:62
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xmipp.utils.XmippLabel.OPERATION_MENU_TRANSFORM
static final String OPERATION_MENU_TRANSFORM
Definition: XmippLabel.java:72
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xmipp.utils.XmippLabel.LABEL_COLUMNS
static final String LABEL_COLUMNS
Definition: XmippLabel.java:230
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xmipp.utils.XmippLabel.LABEL_ROWS
static final String LABEL_ROWS
Definition: XmippLabel.java:229
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xmipp.utils.XmippLabel.MESSAGE_OVERWRITE_FILE_TITLE
static final String MESSAGE_OVERWRITE_FILE_TITLE
Definition: XmippLabel.java:262
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xmipp.utils.XmippLabel.OPERATION_MEASUREMENTS
static final String OPERATION_MEASUREMENTS
Definition: XmippLabel.java:93
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xmipp.utils.XmippLabel.OPERATION_ERODE
static final String OPERATION_ERODE
Definition: XmippLabel.java:151
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xmipp.utils.XmippLabel.MENU_OPEN_WITH_CHIMERA
static final String MENU_OPEN_WITH_CHIMERA
Definition: XmippLabel.java:249
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xmipp.utils.XmippLabel.OPERATION_RADIAL_RESLICE
static final String OPERATION_RADIAL_RESLICE
Definition: XmippLabel.java:107
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xmipp.utils.XmippLabel.LABEL_RADIAL_AVERAGE
static final String LABEL_RADIAL_AVERAGE
Definition: XmippLabel.java:222
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xmipp.utils.XmippLabel.OPERATION_SUBSTACK_MAKER
static final String OPERATION_SUBSTACK_MAKER
Definition: XmippLabel.java:128
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xmipp.utils.XmippLabel.LABEL_SORT_BY_LABEL
static final String LABEL_SORT_BY_LABEL
Definition: XmippLabel.java:187
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xmipp.utils.XmippLabel.OPERATION_MEAN
static final String OPERATION_MEAN
Definition: XmippLabel.java:101
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xmipp.utils.XmippLabel.OPERATION_POLL
static final String OPERATION_POLL
Definition: XmippLabel.java:125
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xmipp.utils.XmippLabel.OPERATION_MENU_MASKS
static final String OPERATION_MENU_MASKS
Definition: XmippLabel.java:170
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xmipp.utils.XmippLabel.LABEL_GALLERY_ENABLE_TO
static final String LABEL_GALLERY_ENABLE_TO
Definition: XmippLabel.java:199
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xmipp.utils.XmippLabel.OPERATION_MENU_ROTATE
static final String OPERATION_MENU_ROTATE
Definition: XmippLabel.java:75
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xmipp.utils.XmippLabel.OPERATION_TJROTATE
static final String OPERATION_TJROTATE
Definition: XmippLabel.java:118
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xmipp.utils.XmippLabel.OPERATION_CLAHE
static final String OPERATION_CLAHE
Definition: XmippLabel.java:164
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xmipp.utils.XmippLabel.LABEL_SHOW_CTF_INFO
static final String LABEL_SHOW_CTF_INFO
Definition: XmippLabel.java:175
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xmipp.utils.XmippLabel.OPERATION_RADIAL_PROFILE_PLOT_ANGLE
static final String OPERATION_RADIAL_PROFILE_PLOT_ANGLE
Definition: XmippLabel.java:137
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xmipp.utils.XmippLabel.OPERATION_TRANSFORMJ
static final String OPERATION_TRANSFORMJ
Definition: XmippLabel.java:110
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xmipp.utils.XmippLabel.MSG_NO_ITEMS_SELECTED
static final String MSG_NO_ITEMS_SELECTED
Definition: XmippLabel.java:259
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xmipp.utils.XmippLabel.LABEL_GALLERY_DISABLE_FROM
static final String LABEL_GALLERY_DISABLE_FROM
Definition: XmippLabel.java:202
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xmipp.utils.XmippLabel.MSG_SHOW_LABEL
static final String MSG_SHOW_LABEL
Definition: XmippLabel.java:267
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xmipp.utils.XmippLabel.LABEL_EXTRACT_COLUMN_ALL
static final String LABEL_EXTRACT_COLUMN_ALL
Definition: XmippLabel.java:177
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xmipp.utils.XmippLabel.OPERATION_CONVOLVE
static final String OPERATION_CONVOLVE
Definition: XmippLabel.java:99
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xmipp.utils.XmippLabel.BUTTON_STD_DEVIATION
static final String BUTTON_STD_DEVIATION
Definition: XmippLabel.java:55
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xmipp.utils.XmippLabel.LABEL_RESLICE_RIGHT
static final String LABEL_RESLICE_RIGHT
Definition: XmippLabel.java:217
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xmipp.utils.XmippLabel.LABEL_GOTO_ITEM
static final String LABEL_GOTO_ITEM
Definition: XmippLabel.java:233
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xmipp.utils.XmippLabel.BUTTON_EXPORT_PROFILE
static final String BUTTON_EXPORT_PROFILE
Definition: XmippLabel.java:59
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xmipp.utils.XmippLabel.TITLE_FSC
static final String TITLE_FSC
Definition: XmippLabel.java:31
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xmipp.utils.XmippLabel.OPERATION_SIOX
static final String OPERATION_SIOX
Definition: XmippLabel.java:148
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xmipp.utils.XmippLabel.BUTTON_FSC
static final String BUTTON_FSC
Definition: XmippLabel.java:57
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xmipp.utils.XmippLabel.BUTTON_SELECT_ALL
static final String BUTTON_SELECT_ALL
Definition: XmippLabel.java:54
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xmipp.utils.XmippLabel.OPERATION_MENU_GO_TO
static final String OPERATION_MENU_GO_TO
Definition: XmippLabel.java:84
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xmipp.utils.XmippLabel.OPERATION_OPEN
static final String OPERATION_OPEN
Definition: XmippLabel.java:153
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xmipp.utils.XmippLabel.OPERATION_MENU_DRAW
static final String OPERATION_MENU_DRAW
Definition: XmippLabel.java:86
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xmipp.utils.XmippLabel.OPERATION_OPEN_AS_METADATA
static final String OPERATION_OPEN_AS_METADATA
Definition: XmippLabel.java:45
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xmipp.utils.XmippLabel.CB_PLOT_PROFILE
static final String CB_PLOT_PROFILE
Definition: XmippLabel.java:61
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xmipp.utils.XmippLabel.LABEL_GALLERY_ENABLE_ALL
static final String LABEL_GALLERY_ENABLE_ALL
Definition: XmippLabel.java:197
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xmipp.utils.XmippLabel.LABEL_ROTSPECTRA_SHOW_NIMAGES
static final String LABEL_ROTSPECTRA_SHOW_NIMAGES
Definition: XmippLabel.java:186
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xmipp.utils.XmippLabel.OPERATION_VOLUME_VIEWER_3D_SLICER
static final String OPERATION_VOLUME_VIEWER_3D_SLICER
Definition: XmippLabel.java:131
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xmipp.utils.XmippLabel.OPERATION_AUTOCORRELATION
static final String OPERATION_AUTOCORRELATION
Definition: XmippLabel.java:133
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xmipp.utils.XmippLabel.OPERATION_OPEN_AS_3D
static final String OPERATION_OPEN_AS_3D
Definition: XmippLabel.java:124
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xmipp.utils.XmippLabel.OPERATION_FEATUREJ
static final String OPERATION_FEATUREJ
Definition: XmippLabel.java:140
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xmipp.utils.XmippLabel.OPERATION_FLIP_HORIZONTAL
static final String OPERATION_FLIP_HORIZONTAL
Definition: XmippLabel.java:88
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xmipp.utils.XmippLabel.OPERATION_RADIAL_GRID
static final String OPERATION_RADIAL_GRID
Definition: XmippLabel.java:168
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xmipp.utils.XmippLabel.OPERATION_TEMPLATE_MATCHING
static final String OPERATION_TEMPLATE_MATCHING
Definition: XmippLabel.java:169
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xmipp.utils.XmippLabel.LABEL_VOLUME
static final String LABEL_VOLUME
Definition: XmippLabel.java:232
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xmipp.utils.XmippLabel.OPERATION_VOLUMEJ
static final String OPERATION_VOLUMEJ
Definition: XmippLabel.java:132
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xmipp.utils.XmippLabel.OPERATION_ANISOTROPIC_DIFFUSION
static final String OPERATION_ANISOTROPIC_DIFFUSION
Definition: XmippLabel.java:129
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xmipp.utils.XmippLabel.MSG_RENDER_IMG
static final String MSG_RENDER_IMG
Definition: XmippLabel.java:268
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xmipp.utils.XmippLabel.TITLE_ERROR
static final String TITLE_ERROR
Definition: XmippLabel.java:26
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xmipp.utils.XmippLabel.LABEL_GALLERY_FILE
static final String LABEL_GALLERY_FILE
Definition: XmippLabel.java:204
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xmipp.utils.XmippLabel.OPERATION_ULTIMATE_POINTS
static final String OPERATION_ULTIMATE_POINTS
Definition: XmippLabel.java:160
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xmipp.utils.XmippLabel.BUTTON_CANCEL
static final String BUTTON_CANCEL
Definition: XmippLabel.java:38
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xmipp.utils.XmippLabel.OPERATION_MEDIAN
static final String OPERATION_MEDIAN
Definition: XmippLabel.java:100
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xmipp.utils.XmippLabel.MENU_STATS
static final String MENU_STATS
Definition: XmippLabel.java:247
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xmipp.utils.XmippLabel.OPERATION_DILATE
static final String OPERATION_DILATE
Definition: XmippLabel.java:152
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xmipp.utils.XmippLabel.OPERATION_OPTIONS
static final String OPERATION_OPTIONS
Definition: XmippLabel.java:163
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xmipp.utils.XmippLabel.BUTTON_IMAGE_STATS
static final String BUTTON_IMAGE_STATS
Definition: XmippLabel.java:37
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xmipp.utils.XmippLabel.OPERATION_MENU_THRESHOLD
static final String OPERATION_MENU_THRESHOLD
Definition: XmippLabel.java:85
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xmipp.utils.XmippLabel.OPERATION_OPEN_AS_STACK
static final String OPERATION_OPEN_AS_STACK
Definition: XmippLabel.java:46
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xmipp.utils.XmippLabel.LABEL_PSD
static final String LABEL_PSD
Definition: XmippLabel.java:219
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xmipp.utils.XmippLabel.OPERATION_WATERSHED
static final String OPERATION_WATERSHED
Definition: XmippLabel.java:161
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xmipp.utils.XmippLabel.OPERATION_SURFACEJ
static final String OPERATION_SURFACEJ
Definition: XmippLabel.java:123
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xmipp.utils.XmippLabel.LABEL_SHOW_LABELS
static final String LABEL_SHOW_LABELS
Definition: XmippLabel.java:185
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 import javax.swing.JMenu;
29 import javax.swing.JMenuBar;
30 
31 public abstract class XmippMenuBarCreator extends XmippMenuCreator {
32 
33  public XmippMenuBarCreator() {
34  super(new JMenuBar());
35  }
36 
37  public JMenuBar getMenuBar(){
38  return (JMenuBar)menu;
39  }
40 
41  public void addSeparator(String key) {
42  JMenu menu = (JMenu) items.get(key);
43  menu.addSeparator();
44  }
45 
46 }
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xmipp.utils.XmippMenuCreator.items
Map< String, JMenuItem > items
Definition: XmippMenuCreator.java:24
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1 /*
2 cd * To change this template, choose Tools | Templates
3  * and openTableFileImageItem the template in the editor.
4  */
5 package xmipp.ij.commons;
6 
7 import ij.CommandListener;
8 import ij.Executer;
9 import ij.IJ;
10 import ij.ImageListener;
11 import ij.ImagePlus;
12 import ij.plugin.frame.Recorder;
13 import ij.process.StackConverter;
14 import ij3d.Content;
15 import ij3d.Image3DUniverse;
16 
17 import java.awt.CheckboxMenuItem;
18 import java.awt.Frame;
19 import java.awt.Menu;
20 import java.awt.MenuBar;
21 import java.awt.MenuItem;
22 import java.awt.MenuShortcut;
23 import java.awt.event.ActionEvent;
24 import java.awt.event.ActionListener;
25 import java.awt.event.ItemEvent;
26 import java.awt.event.ItemListener;
27 import java.awt.event.KeyEvent;
28 import java.io.File;
29 import java.util.ArrayList;
30 import java.util.Collections;
31 import java.util.LinkedHashMap;
32 import java.util.List;
33 import java.util.Map;
34 
35 import javax.vecmath.Color3f;
36 
37 import xmipp.utils.QuickHelpJDialog;
38 import xmipp.utils.XmippDialog;
39 import xmipp.utils.XmippFileChooser;
40 import xmipp.utils.XmippWindowUtil;
41 
46 public class XmippMenuBar extends MenuBar
47 {
48 
49  protected final XmippIJWindow xw;
50  protected Menu filemn;
51  protected Menu imagemn;
52  protected Menu advancedmn;
53  protected MenuItem savemi;
54  protected MenuItem saveasmi;
55  protected MenuItem openwith3dmi;
56  protected Menu infomn;
57 // protected Menu adjustmn;
58  protected Menu transformmn;
59 // protected Menu filtersmn;
60  protected Menu thresholdingmn;
61  protected Menu binarymn;
62  protected Menu processmn;
63  protected Menu drawmn;
64  protected MenuItem imagejmi;
65  protected Menu profilemn;
66  protected CheckboxMenuItem pollmi;
67  protected Object timer;
68  protected PollTimer polltimer;
69  protected MenuItem refreshmi;
70  protected CheckboxMenuItem wrapmi;
71  protected CheckboxMenuItem ugmi;
72  protected MenuItem exitmi;
73  protected Menu helpmn;
74  protected MenuItem onlinemi;
75  protected MenuItem keyassistmi;
76  protected QuickHelpJDialog keyassistdlg;
77  protected boolean invertx;
78  protected boolean inverty;
79  protected CheckboxMenuItem activemi;
80  protected String command;
81  protected List<IJCommand> filters;
82  protected ImagePlusLoader iploader;
83 
84  enum IJRequirement
85  {
86  BINARY, EIGHTBIT, IMAGEJ, STACK, THIRTYTWOBIT, RGB, VOLUME, INVERTX, INVERTY
87 
88  };
89 
90  public XmippMenuBar(XmippIJWindow xw)
91  {
92  filters = new ArrayList<IJCommand>();
93  this.xw = xw;
94  this.iploader = xw.getImagePlusLoader();
95  // menubar menus
96  filemn = new Menu("File");
97  imagemn = new Menu("Image");
98  advancedmn = new Menu("Advanced");
99  helpmn = new Menu("Help");
100 
101  add(filemn);
102  add(imagemn);
103  add(advancedmn);
104  add(helpmn);
105 
106  // menubar file menu
107 // savemi = new MenuItem("Save");
108 // savemi.setShortcut(new MenuShortcut(KeyEvent.VK_S));
109 // savemi.addActionListener(new ActionListener()
110 // {
111 //
112 // @Override
113 // public void actionPerformed(ActionEvent e)
114 // {
115 // try
116 // {
117 // if(XmippMenuBar.this.iploader.existsFile())
118 // XmippMenuBar.this.xw.saveData();
119 // else
120 // XmippMenuBar.this.saveAs();
121 // }
122 // catch (Exception ex)
123 // {
124 // ex.printStackTrace();
125 // XmippDialog.showInfo(null, ex.getMessage());
126 // }
127 //
128 // }
129 // });
130  saveasmi = new MenuItem("Save As...");
131  saveasmi.addActionListener(new ActionListener()
132  {
133 
134  @Override
135  public void actionPerformed(ActionEvent e)
136  {
137  saveAs();
138  }
139  });
140 
141 // openwith3dmi = new MenuItem("Open with 3D Viewer");
142 // openwith3dmi.setEnabled(xw.isVolume());
143 // openwith3dmi.setEnabled(Filename.isVolume(xw.getImageFilePath()));
144 // openwith3dmi.addActionListener(new ActionListener()
145 // {
146 //
147 // @Override
148 // public void actionPerformed(ActionEvent arg0)
149 // {
150 // ImagePlus imp = XmippMenuBar.this.iploader.getImagePlus();
151 // if (imp.getImageStackSize() == 1)
152 // XmippDialog.showInfo(null, "Only for Stack");
153 // else
154 // openImagePlusAs3D(imp);
155 //
156 // }
157 // });
158 // filemn.add(openwith3dmi);
159  MenuItem volviewermi = new MenuItem("Open with Volume Viewer/3D Slicer");
160  volviewermi.setActionCommand("Volume Viewer");
161  volviewermi.setEnabled(xw.isVolume());
162  volviewermi.addActionListener(new ActionListener()
163  {
164 
165  @Override
166  public void actionPerformed(ActionEvent e)
167  {
168  MenuItem mi = (MenuItem) e.getSource();
169  runCommand(mi.getActionCommand());
170 
171  }
172  });
173  filemn.add(volviewermi);
174 // addIJCheckMenuItem(filemn, "Open with Volume Viewer/3D Slicer", "Volume Viewer", IJRequirement.VOLUME);
175 // addIJCheckMenuItem(filemn, "Open with VolumeJ", "VolumeJ ", IJRequirement.VOLUME);
176  refreshmi = new MenuItem("Refresh");
177  refreshmi.setEnabled(iploader.allowsPoll());
178  refreshmi.setShortcut(new MenuShortcut(KeyEvent.VK_F5));
179  refreshmi.addActionListener(new ActionListener()
180  {
181 
182  @Override
183  public void actionPerformed(ActionEvent arg0)
184  {
185  XmippMenuBar.this.xw.loadData();
186 
187  }
188  });
189 
190  pollmi = new CheckboxMenuItem("Poll");
191  pollmi.setEnabled(iploader.allowsPoll());
192  pollmi.addItemListener(new ItemListener()
193  {
194 
195  @Override
196  public void itemStateChanged(ItemEvent e)
197  {
198  boolean poll = pollmi.getState();
199  if (poll)
200  poll();
201  else
202  polltimer.stop();
203  }
204  });
205 
206  ugmi = new CheckboxMenuItem("Use Geometry");
207  ugmi.setEnabled(iploader.hasGeometry());
208  ugmi.setState(iploader.getUseGeometry());
209  ugmi.addItemListener(new ItemListener()
210  {
211 
212  @Override
213  public void itemStateChanged(ItemEvent e)
214  {
215  boolean ug = ugmi.getState();
216  useGeometry(ug);
217 
218  }
219  });
220 
221 
222  wrapmi = new CheckboxMenuItem("Wrap");
223  wrapmi.setEnabled(iploader.hasGeometry());
224  wrapmi.setState(iploader.isWrap());
225  wrapmi.addItemListener(new ItemListener()
226  {
227 
228  @Override
229  public void itemStateChanged(ItemEvent e)
230  {
231  wrap(wrapmi.getState());
232 
233  }
234  });
235 
236 
237  exitmi = new MenuItem("Exit");
238  exitmi.setShortcut(new MenuShortcut(KeyEvent.VK_Q));
239  exitmi.addActionListener(new ActionListener() {
240 
241  @Override
242  public void actionPerformed(ActionEvent e) {
243 
244  close();
245  }
246  });
247 
248 
249 
250 // filemn.add(savemi);
251  filemn.add(saveasmi);
252 // addIJCheckMenuItem(filemn, "Duplicate", "Duplicate...", IJRequirement.IMAGEJ);
253  filemn.add(refreshmi);
254  filemn.add(pollmi);
255  filemn.add(ugmi);
256  filemn.add(wrapmi);
257  filemn.add(exitmi);
258 
259  // menubar image menu
260 // infomn = new Menu("Info");
261 // adjustmn = new Menu("Adjust");
262 // filtersmn = new Menu("Filters");
263 
264 // imagemn.add(infomn);
265 // imagemn.add(adjustmn);
266 // imagemn.add(transformmn);
267 // imagemn.add(filtersmn);
268 
269 
270  // image info menu
271 // addIJCheckMenuItem(infomn, "Show Info", "Show Info...");
272 // addIJCheckMenuItem(infomn, "Properties", "Properties...");
273 // addIJCheckMenuItem(infomn, "Histogram", "Histogram", IJRequirement.IMAGEJ);
274 // addIJCheckMenuItem(infomn, "Plot Profile", "Plot Profile", IJRequirement.IMAGEJ);
275 
276  // image adjust menu
277 
278 // addIJCheckMenuItem(adjustmn, "Crop", "Crop", IJRequirement.IMAGEJ);
279 // addIJCheckMenuItem(adjustmn, "Scale", "Scale...");
280 // addIJCheckMenuItem(adjustmn, "Untilt Stack", "Untilt Stack", IJRequirement.STACK);
281 
282 // addIJCheckMenuItem(adjustmn, "Reslice", "Reslice [/]...", IJRequirement.VOLUME);
283 
284  // image transform menu
285 
286 // addIJCheckMenuItem(transformmn, "Rotate 90 Degrees Left", "Rotate 90 Degrees Left");
287 // addIJCheckMenuItem(transformmn, "Rotate 90 Degrees Right", "Rotate 90 Degrees Right");
288 
289  // image filters menu
290  CheckboxMenuItem gbmi = addIJCheckMenuItem(imagemn, XmippImageJ.gaussianBlurFilter);
291  addIJCheckMenuItem(imagemn, XmippImageJ.bandPassFilter);
292 // addIJCheckMenuItem(imagemn, XmippImageJ.anisotropicDiffFilter, IJRequirement.EIGHTBIT);
293  CheckboxMenuItem ecmi = addIJCheckMenuItem(imagemn, XmippImageJ.enhanceContrastFilter);
294  addIJCheckMenuItem(imagemn, XmippImageJ.brightnessContrastFilter);
295  addIJCheckMenuItem(imagemn, XmippImageJ.invertLUTFilter);
296  addIJCheckMenuItem(imagemn, XmippImageJ.substractBackgroundFilter);
297  // menubar advanced menu
298  imagejmi = new MenuItem("ImageJ");
299  imagejmi.setShortcut(new MenuShortcut(KeyEvent.VK_I));
300  transformmn = new Menu("Transform");
301  thresholdingmn = new Menu("Thresholding");
302  binarymn = new Menu("Binary");
303  processmn = new Menu("Process");
304  drawmn = new Menu("Draw");
305  profilemn = new Menu("Profile");
306 
307  advancedmn.add(imagejmi);
308  advancedmn.add(thresholdingmn);
309  advancedmn.add(binarymn);
310  advancedmn.add(processmn);
311  advancedmn.add(drawmn);
312  advancedmn.add(profilemn);
313 // addIJCheckMenuItem(advancedmn, "Masks Tool Bar", "Masks Tool Bar", IJRequirement.IMAGEJ);// missing
314  // plugin
315  onlinemi = new MenuItem("Online Help");
316  onlinemi.addActionListener(new ActionListener()
317  {
318 
319 
320 
321  @Override
322  public void actionPerformed(ActionEvent arg0)
323  {
324  XmippWindowUtil.openURI("https://github.com/I2PC/scipion/wiki/ShowJ");
325  }
326  });
327  helpmn.add(onlinemi);
328  keyassistmi = new MenuItem("Tips");
329  keyassistmi.addActionListener(new ActionListener()
330  {
331 
332 
333 
334  @Override
335  public void actionPerformed(ActionEvent arg0)
336  {
337  try
338  {
339  if(keyassistdlg == null)
340  keyassistdlg = new QuickHelpJDialog(null, false, "Tips...", getKeyAssist());
341  keyassistdlg.setVisible(true);
342  }
343  catch(Exception e)
344  {
345  XmippDialog.showInfo(null, e.getMessage());
346  }
347  }
348  });
349  helpmn.add(keyassistmi);
350 
351  addIJMenuItem(transformmn, "Flip Horizontally", "Flip Horizontally", IJRequirement.INVERTX);
352  addIJMenuItem(transformmn, "Flip Vertically", "Flip Vertically", IJRequirement.INVERTY);
353 
354  // advanced threshold menu
355  addIJMenuItem(thresholdingmn, "Threshold", "Threshold...");
356  addIJMenuItem(thresholdingmn, "Otsu Threshold", "Otsu Thresholding", IJRequirement.EIGHTBIT);
357  addIJMenuItem(thresholdingmn, "Multi Otsu Threshold", "Multi OtsuThreshold");
358  addIJMenuItem(thresholdingmn, "Maximum Entropy Threshold", "Entropy Threshold", IJRequirement.EIGHTBIT);
359  addIJMenuItem(thresholdingmn, "Mixture Modeling Threshold", "Mixture Modeling", IJRequirement.EIGHTBIT);
360  addIJMenuItem(thresholdingmn, "Robust Automatic Threshold Selection", "RATS ");
361  //addIJMenuItem(thresholdingmn, "Simple Iterative Object Extraction", "SIOX Segmentation", IJRequirement.RGB);
362 
363  // advanced binary menu
364  addIJMenuItem(binarymn, "Voxel Counter", "Voxel Counter", IJRequirement.STACK);// stack required
365  addIJMenuItem(binarymn, "Erode", "Erode", IJRequirement.BINARY);
366  addIJMenuItem(binarymn, "Dilate", "Dilate", IJRequirement.BINARY);
367  addIJMenuItem(binarymn, "Open", "Open", IJRequirement.BINARY);
368  addIJMenuItem(binarymn, "Close", "Close", IJRequirement.BINARY);
369  addIJMenuItem(binarymn, "Float Morphology", "Float Morphology", IJRequirement.THIRTYTWOBIT);// missing plugin
370  addIJMenuItem(binarymn, "Outline", "Outline", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
371  addIJMenuItem(binarymn, "Fill Holes", "Fill Holes", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
372  addIJMenuItem(binarymn, "Skeletonize", "Skeletonize", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
373  addIJMenuItem(binarymn, "Distance Map", "Distance Map", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
374  addIJMenuItem(binarymn, "Ultimate Points", "Ultimate Points", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
375  addIJMenuItem(binarymn, "Watershed", "Watershed");
376  addIJMenuItem(binarymn, "Voronoi", "Voronoi", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
377 
378  // advanced process menu
379 
380 
381  addIJMenuItem(processmn, "Convolve", "Convolve...");
382  addIJMenuItem(processmn, "Median", "Median...");
383  addIJMenuItem(processmn, "FFT", "FFT", IJRequirement.IMAGEJ);// memory error
384  addIJMenuItem(processmn, "Straighten Curved Objects", "Straighten...", IJRequirement.IMAGEJ);
385 
386  // advanced drawn menu
387  addIJMenuItem(drawmn, "Dotted Line", "Dotted Line", IJRequirement.IMAGEJ);
388  addIJMenuItem(drawmn, "Radial Grid", "Radial Grid");
389  addIJMenuItem(drawmn, "Concenctric Circles", "Concentric Circles");
390 
391  // advanced profile menu
392  addIJMenuItem(profilemn, "Line Analyzer", "Plot Profile", IJRequirement.IMAGEJ);
393  addIJMenuItem(profilemn, "Oval Profile Plot", "Oval Profile", IJRequirement.IMAGEJ);
394 // addIJMenuItem(profilemn, "Contour Plotter", "ContourPlotter ");
395 
396  imagejmi.addActionListener(new ActionListener()
397  {
398 
399  @Override
400  public void actionPerformed(ActionEvent e)
401  {
402  XmippUtil.showImageJ(Tool.VIEWER);
403  }
404  });
405  addFilterAppliedListener();
406  ImagePlus imp = iploader.getImagePlus();
407  if(xw.getParams() != null && imp.getWidth() > 1024 && imp.getStackSize() == 1)
408  {
409  String value = System.getenv("SCIPION_MIC_NOGAUSS");
410 
411  if (value == null || !value.equals("1"))
412  {
413  gbmi.setState(true);
414  IJCommand ijcmd = new IJCommand(XmippImageJ.gaussianBlurFilter, "sigma =2");
415  IJ.run(imp, ijcmd.getCommand(), ijcmd.getOptions());
416  filters.add(ijcmd);
417  }
418 
419  value = System.getenv("SCIPION_MIC_NOENHANCE");
420  if (value == null || !value.equals("1"))
421  {
422  ecmi.setState(true);
423  IJCommand ijcmd = new IJCommand(XmippImageJ.enhanceContrastFilter, "saturated=0.4");
424  IJ.run(imp, ijcmd.getCommand(), ijcmd.getOptions());
425  filters.add(ijcmd);
426  }
427  }
428 
429  }
430 
431  protected void addFilterAppliedListener() {
432 
433  Recorder.record = true;
434  // detecting if a command is thrown by ImageJ
435  Executer.addCommandListener(new CommandListener() {
436  public String commandExecuting(String command) {
437 
438 
439  XmippMenuBar.this.command = command;
440  return command;
441 
442  }
443  });
444 
445  // detecting if a command is thrown by ImageJ
446 
447  ImagePlus.addImageListener(new ImageListener() {
448 
449  @Override
450  public void imageUpdated(ImagePlus imp) {
451  //activemi will contain last filter selected, if its the command runned we confirm selection
452  if(activemi != null && activemi.getActionCommand().equals(command))
453  {
454  activemi.setState(true);
455  String options = Recorder.getCommandOptions();
456  filters.add(new IJCommand(command, options));
457  activemi = null;
458  }
459 
460  }
461 
462  @Override
463  public void imageOpened(ImagePlus arg0) {
464 
465  }
466 
467  @Override
468  public void imageClosed(ImagePlus arg0) {
469  // TODO Auto-generated method stub
470 
471  }
472  });
473  }
474 
475 
476  protected void close()
477  {
478  Frame w = (Frame)xw;
479  w.setVisible(false);
480  w.dispose();
481  XmippApplication.removeInstance(false);
482  }
483 
484 
485  protected void useGeometry(boolean ug)
486  {
487  xw.getImagePlusLoader().setUseGeometry(ug);
488  xw.loadData();
489  }
490 
491  protected void saveAs()
492  {
493  XmippFileChooser fc = new XmippFileChooser();
494  int returnVal = fc.showOpenDialog(null);
495 
496  try
497  {
498  if (returnVal == XmippFileChooser.APPROVE_OPTION)
499  {
500  File file = fc.getSelectedFile();
501  XmippMenuBar.this.xw.saveDataAs(file.getAbsolutePath());
502  }
503  }
504  catch (Exception ex)
505  {
506  XmippDialog.showInfo(null, ex.getMessage());
507  }
508  }
509 
510 
511 
512  protected void wrap(boolean value)
513  {
514  xw.getImagePlusLoader().setWrap(value);
515  xw.loadData();
516  }
517 
518 
519 
520  public static void openImagePlusAs3D(ImagePlus ip) {
521  try {
522  int UNIVERSE_W = 400, UNIVERSE_H = 400;
523  // Checks if java3D is available or not.
524  Class.forName("javax.media.j3d.J3DBuffer");
525 
526  new StackConverter(ip).convertToRGB();
527 
528  Image3DUniverse universe = new Image3DUniverse(UNIVERSE_W,
529  UNIVERSE_H);
530 
531  // Adds the sphere image plus to universe.
532  Content c = universe.addSurfacePlot(ip, new Color3f(1f, 165f / 255,
533  82f / 255), "1", 50, new boolean[] { true, true, true }, 1);
534  c.displayAs(Content.SURFACE);
535  c.setColor(new Color3f(1f, 165f / 255, 82f / 255));
536 
537  universe.show(); // Shows...
538  } catch (final ClassNotFoundException e) {
539  IJ.error("Java 3D not found. Please, check your installation.");
540  }
541  }
542 
543  protected CheckboxMenuItem addIJCheckMenuItem(Menu mn, String command, IJRequirement... requirements)
544  {
545  return addIJCheckMenuItem(mn, command, command, requirements);
546 
547  }
548 
549  protected CheckboxMenuItem addIJCheckMenuItem(Menu mn, String name, String command, IJRequirement... requirements)
550  {
551  CheckboxMenuItem mi = new CheckboxMenuItem(name);
552  addCheckCommand(mi, command, requirements);
553  mn.add(mi);
554  return mi;
555  }
556 
557 
558  protected void poll()
559  {
560  if (timer == null)
561  polltimer = new PollTimer(xw);
562  polltimer.start();
563  }
564 
565  protected void addCheckCommand(CheckboxMenuItem mi, String command, final IJRequirement... requirements)
566  {
567  mi.setActionCommand(command);
568  for (IJRequirement requirement : requirements)
569  {
570  if (requirement == IJRequirement.STACK && !xw.isStack())
571  mi.setEnabled(false);
572  if (requirement == IJRequirement.VOLUME && !xw.isVolume())
573  mi.setEnabled(false);
574  }
575  mi.addItemListener(new ItemListener()
576  {
577 
578  @Override
579  public void itemStateChanged(ItemEvent e)
580  {
581  try
582  {
583  CheckboxMenuItem mi = (CheckboxMenuItem) e.getSource();
584  String command = mi.getActionCommand();
585  if(mi.getState())//checked
586  {
587  activemi = mi;
588  mi.setState(false);//confirm selected only after filter applied
589  runCommand(command, requirements);
590 
591  }
592  else
593  {
594  filters.remove(getFilter(command));
595  xw.loadData();
596  applyFilters();
597  }
598 
599  }
600  catch (Exception ex)
601  {
602  ex.printStackTrace();
603  }
604  }
605  });
606  }//function addCommand
607 
608  protected MenuItem addIJMenuItem(Menu mn, String name, String command, IJRequirement... requirements)
609  {
610  MenuItem mi = new MenuItem(name);
611  addCommand(mi, command, requirements);
612  mn.add(mi);
613  return mi;
614  }
615 
616 
617  protected void addCommand(MenuItem mi, String command, final IJRequirement... requirements)
618  {
619  mi.setActionCommand(command);
620  for (IJRequirement requirement : requirements)
621  {
622  if (requirement == IJRequirement.STACK && !xw.isStack())
623  mi.setEnabled(false);
624  if (requirement == IJRequirement.VOLUME && !xw.isVolume())
625  mi.setEnabled(false);
626  }
627  mi.addActionListener(new ActionListener()
628  {
629 
630  @Override
631  public void actionPerformed(java.awt.event.ActionEvent e) {
632 
633  try
634  {
635  MenuItem mi = (MenuItem) e.getSource();
636  String command = mi.getActionCommand();
637  runCommand(command, requirements);
638 
639  }
640  catch (Exception ex)
641  {
642  ex.printStackTrace();
643  }
644  }
645  });
646  }//function addCommand
647 
648  public void applyFilters()
649  {
650  ImagePlus imp = xw.getImagePlusLoader().getImagePlus();
651  for(IJCommand filter: filters)
652  IJ.run(imp, filter.getCommand(), filter.getOptions());
653  }
654 
655 
656  public IJCommand getFilter(String command)
657  {
658  for(IJCommand filter: filters)
659  {
660  if(filter.getCommand().equals(command))
661  return filter;
662  }
663  return null;
664  }
666  public void runCommand(String command, IJRequirement... requirements){
667  if (requirements != null)
668  for (IJRequirement requirement : requirements)
669  switch (requirement)
670  {
671  case IMAGEJ:
672  XmippUtil.showImageJ(Tool.VIEWER);
673  break;
674  case BINARY:
675  IJ.run("Make Binary");
676  XmippDialog.showInfo(null, "make binary applied");
677  break;
678  case EIGHTBIT:
679  IJ.run("8-bit");
680  XmippDialog.showInfo(null, "8-bit applied");
681  break;
682  case THIRTYTWOBIT:
683  IJ.run("32-bit");
684  XmippDialog.showInfo(null, "32-bit applied");
685  break;
686  case RGB:
687  IJ.run("RGB Color");
688  XmippDialog.showInfo(null, "RGB color applied");
689  break;
690  case INVERTX:
691  invertx = !invertx;
692  xw.getCanvas().setInvertX(invertx);
693  break;
694  case INVERTY:
695  inverty = !inverty;
696  xw.getCanvas().setInvertY(inverty);
697  break;
698 
699  }
700  ImagePlus imp = xw.getImagePlusLoader().getImagePlus();
701  IJ.run(imp, command, "");
702  }//function runCommand
703 
704  public Map<Object, Object> getKeyAssist()
705  {
706  Map<Object, Object> map = Collections.synchronizedMap(new LinkedHashMap<Object, Object>());
707  map.put("Shift + scroll up", "Zoom in");
708  map.put("Shift + scroll down", "Zoom out");
709  map.put("Right click + mouse move", "Moves image previously expanded");
710  return map;
711  }
712 
713 
714 }
xmipp.ij.commons.XmippMenuBar.openImagePlusAs3D
static void openImagePlusAs3D(ImagePlus ip)
Definition: XmippMenuBar.java:520
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xmipp.ij.commons.XmippMenuBar.addIJCheckMenuItem
CheckboxMenuItem addIJCheckMenuItem(Menu mn, String name, String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:549
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xmipp.ij.commons.XmippMenuBar.getKeyAssist
Map< Object, Object > getKeyAssist()
Definition: XmippMenuBar.java:704
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xmipp.ij.commons.XmippImageJ.bandPassFilter
static final String bandPassFilter
Definition: XmippImageJ.java:11
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xmipp.ij.commons.XmippImageJ.brightnessContrastFilter
static final String brightnessContrastFilter
Definition: XmippImageJ.java:15
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xmipp.ij.commons.XmippImageJ.substractBackgroundFilter
static final String substractBackgroundFilter
Definition: XmippImageJ.java:13
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xmipp.ij.commons.XmippImageJ.invertLUTFilter
static final String invertLUTFilter
Definition: XmippImageJ.java:16
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xmipp.ij.commons.XmippUtil.showImageJ
static XmippImageJ showImageJ(Tool tool)
Definition: XmippUtil.java:28
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xmipp.ij.commons.XmippIJWindow.saveDataAs
void saveDataAs(String file)
-
xmipp.ij.commons.XmippIJWindow.getCanvas
XmippImageCanvas getCanvas()
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.ij.commons.XmippMenuBar.addCheckCommand
void addCheckCommand(CheckboxMenuItem mi, String command, final IJRequirement... requirements)
Definition: XmippMenuBar.java:565
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xmipp.ij.commons.XmippMenuBar.addCommand
void addCommand(MenuItem mi, String command, final IJRequirement... requirements)
Definition: XmippMenuBar.java:617
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xmipp.ij.commons.XmippIJWindow.getImagePlusLoader
ImagePlusLoader getImagePlusLoader()
- - -
xmipp.ij.commons.XmippMenuBar.addIJCheckMenuItem
CheckboxMenuItem addIJCheckMenuItem(Menu mn, String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:543
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xmipp.ij.commons.XmippMenuBar.runCommand
void runCommand(String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:666
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xmipp.utils.XmippWindowUtil.openURI
static void openURI(String uri)
Definition: XmippWindowUtil.java:190
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xmipp.ij.commons.XmippApplication.removeInstance
static void removeInstance(boolean isijwindow)
Definition: XmippApplication.java:28
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xmipp.ij.commons.XmippMenuBar.getFilter
IJCommand getFilter(String command)
Definition: XmippMenuBar.java:656
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xmipp.ij.commons.XmippMenuBar.addIJMenuItem
MenuItem addIJMenuItem(Menu mn, String name, String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:608
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xmipp.ij.commons.XmippImageJ.gaussianBlurFilter
static final String gaussianBlurFilter
Definition: XmippImageJ.java:14
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xmipp.ij.commons.XmippMenuBar.XmippMenuBar
XmippMenuBar(XmippIJWindow xw)
Definition: XmippMenuBar.java:90
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static final String enhanceContrastFilter
Definition: XmippImageJ.java:17
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1 
2 
3 package xmipp.utils;
4 
5 import java.awt.event.ActionEvent;
6 import java.awt.event.ActionListener;
7 import java.util.HashMap;
8 import java.util.Hashtable;
9 import java.util.Map;
10 
11 import javax.swing.ButtonGroup;
12 import javax.swing.JCheckBoxMenuItem;
13 import javax.swing.JComponent;
14 import javax.swing.JMenu;
15 import javax.swing.JMenuItem;
16 import javax.swing.JRadioButtonMenuItem;
17 import javax.swing.KeyStroke;
18 
22 public abstract class XmippMenuCreator implements ActionListener {
23 
24  protected Map<String, JMenuItem> items;
29  protected Map<String, ButtonGroup> groups;
30  protected JComponent menu;
31 
33  public XmippMenuCreator(JComponent menu){
34  try {
35  this.menu = menu;
36  items = new Hashtable<String, JMenuItem>();
37  groups = new HashMap<String, ButtonGroup>();
38  createItems();
39  } catch (Exception e){
40  e.printStackTrace();
41  }
42  }
43 
44 
45 
56  public JMenuItem addItem(String key, String text, String... values){
57 
58  String name = key;
59  String parentname = null;
60  JMenuItem item = null;
61  JMenu parent = null;
62  boolean isMenu = false;
63 
64  try {
65  if (key.contains(".")) {
66  int pos = key.lastIndexOf(".");
67  name = key.substring(pos + 1);
68  parentname = key.substring(0, pos);
69  parent = (JMenu)getItem(parentname);
70  }
71 
72  // Create the right type of menu item
73  if (name.endsWith("cb"))
74  item = new JCheckBoxMenuItem();
75  else if (name.endsWith("rb")){
76  ButtonGroup group = groups.get(parentname);
77  if (group == null)
78  {
79  group = new ButtonGroup();
80  groups.put(parentname, group);
81  }
82  item = new JRadioButtonMenuItem();
83  group.add(item);
84 
85  }
86  else if (name.endsWith("mi"))
87  {
88  item = new JMenuItem();
89 
90  }
91  else {
92  item = new JMenu();
93  isMenu = true;
94  }
95  // Setup the item
96  item.setText(text);
97  item.setActionCommand(key);
98  item.addActionListener(this);
99  // Store item and add to menu
100  items.put(key, item);
101 
102  if (!isMenu) {
103  int n = values.length;
104  switch (n) {
105  case 2:
106  // The second argument could be the keystroke, be careful
107  item.setAccelerator(KeyStroke.getKeyStroke(values[1]));
108  case 1:
109  if (values[0] != null)
110  item.setIcon(XmippResource.getIcon(values[0]));
111  break;
112  case 0:
113  break; // ignore if no arguments
114  default:
115  throw new Exception(
116  "No more than 2 arguments to create menu item!!!");
117  }
118  }
119 
120  if (parent == null)
121  menu.add(item);
122  else
123  parent.add(item);
124  } catch (Exception e){
125  e.printStackTrace();
126  }
127  return item;
128  }
129 
130  public JMenuItem getItem(String key) {
131  return items.get(key);
132  }
133 
134  public boolean getItemEnabled(String key){
135  return getItem(key).isEnabled();
136  }
137 
138  public void setItemEnabled(String key, boolean value) {
139  getItem(key).setEnabled(value);
140  }
141 
142  public boolean getItemSelected(String key){
143  // Create the right type of menu item
144  if (key.endsWith("rb"))
145  return ((JRadioButtonMenuItem)getItem(key)).isSelected();
146  if (key.endsWith("cb"))
147  return ((JCheckBoxMenuItem)getItem(key)).isSelected();
148  return false;
149  }
150 
151  public void setItemSelected(String key, boolean value){
152  //DEBUG.printMessage("setItemSelected -> key:" + key);
153  // Create the right type of menu item
154  if (key.endsWith("rb"))
155  ((JRadioButtonMenuItem)getItem(key)).setSelected(value);
156  else if (key.endsWith("cb"))
157  ((JCheckBoxMenuItem)getItem(key)).setSelected(value);
158  }
159 
160  public void setItemVisible(String key, boolean value){
161  getItem(key).setVisible(value);
162  }
163 
164  @Override
165  public void actionPerformed(ActionEvent evt) {
166  handleActionPerformed(evt);
167  }
168 
170  abstract protected void handleActionPerformed(ActionEvent evt);
171 
175  abstract protected void createItems() throws Exception;
176 
178  public void initItems() { }
179 
180 
182  public final String FILE = "File";
183  public final String FILE_OPEN = "File.Open_mi";
184  public final String FILE_OPENWITH_IJ = "File.OpenWithIJ_mi";
185  public final String FILE_OPENMICROGRAPHS = "File.OpenMicrographs_mi";
186  public final String FILE_OPENWITH_CHIMERA = "File.OpenWithChimera_mi";
187  public final String FILE_INFO = "File.FileInfo_mi";
188  public final String FILE_SAVE = "File.Save_mi";
189  public final String FILE_SAVEAS = "File.SaveAs_mi";
190  public final String FILE_LOAD_SEL = "File.LoadSel_mi";
191  public final String FILE_SAVE_SEL = "File.SaveSel_mi";
192  public final String FILE_EXPORTIMAGES = "File.ExportImages_mi";
193  public final String FILE_REFRESH = "File.Refresh_mi";
194  public final String FILE_EXIT = "File.Exit_mi";
195  public final String FILE_LINK_CHIMERA = "File.LinkWithChimera_mi";
196  public final String DISPLAY = "Display";
197 
198 
199  public final String DISPLAY_SHOWLABELS = "Display.ShowLabel";
200  public final String DISPLAY_RENDERIMAGES = "Display.RenderImages_cb";
201 
202  public final String DISPLAY_RENDERIMAGE = "Display.RenderImage";
203 
204  public final String DISPLAY_INVERTY = "Display.InvertY_cb";
205  public final String DISPLAY_APPLYGEO = "Display.ApplyGeo_cb";
206  public final String DISPLAY_WRAP = "Display.Wrap_cb";
207  public final String DISPLAY_NORMALIZE = "Display.Normalize_cb";
208  public final String DISPLAY_COLUMNS = "Display.Columns_mi";
209  public final String DISPLAY_RESLICE = "Display.Reslice";
210  public final String DISPLAY_RESLICE_VIEWS[] = {
211  "Display.Reslice.ZNeg_rb",
212  "Display.Reslice.YNeg_rb",
213  "Display.Reslice.XNeg_rb",
214  "Display.Reslice.YPos_rb",
215  "Display.Reslice.XPos_rb"};
216 
217  public final String METADATA = "Metadata";
218 
219  public final String MD_CLASSES = "Metadata.Classes_mi";
220  public final String MD_EDIT_COLS = "Metadata.EditCols_mi";
221  public final String MD_ADD_OBJECT = "Metadata.AddObject_mi";
222  public final String MD_REMOVE_SELECTION = "Metadata.RemoveSelection_mi";
223  public final String MD_SAVE_SELECTION = "Metadata.SaveSelection_mi";
224  public final String MD_REMOVE_DISABLED = "Metadata.RemoveDisabled_mi";
225  public final String TOOLS = "Tools";
226  public final String TOOLS_AVGSTD = "Tools.AvgStd_mi";
227  public final String TOOLS_PCA = "Tools.Pca_mi";
228  public final String TOOLS_FSC = "Tools.Fsc_mi";
229  public final String TOOLS_PLOT = "Tools.Plot_mi";
230  public final String MD_FIND_REPLACE = "Tools.FindReplace_mi";
231 
232  public final String HELP = "Help";
233  public final String HELP_ONLINE = "Help.Online_mi";
234  public final String KEY_ASSIST = "Help.Key_mi";
235  //public final String HELP_ABOUT = "Help.About_mi";
236 
237 
238  public final static String ENABLED = "Enabled_mi";
239  public final static String DISABLED = "Disabled_mi";
240  public final static String REFRESH = "Refresh_mi";
241  public final static String OPEN = "Open_mi";
242  public final static String OPEN_ASTEXT = "OpenAsText_mi";
243  public final static String CTF_PROFILE = "CTFProfile_mi";
244  public final static String CTF_RECALCULATE = "CTFRecalculate_cb";
245  public final static String SELECT = "Select";
246  public final static String SELECT_ALL = "Select.All_mi";
247  public final static String SELECT_TOHERE = "Select.ToHere_mi";
248  public final static String SELECT_FROMHERE = "Select.FromHere_mi";
249  public final static String INVERT_SELECT = "Select.InvertSelection_mi";
250  public final static String SET_CLASS = "SetClass_mi";
251  public final static String OPEN_IMAGES = "OpenImages_mi";
252  public final static String SAVE_IMAGES = "SaveImages_mi";
253 
254 }
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xmipp.utils.XmippMenuCreator.setItemSelected
void setItemSelected(String key, boolean value)
Definition: XmippMenuCreator.java:151
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xmipp.utils.XmippMenuCreator.CTF_RECALCULATE
static final String CTF_RECALCULATE
Definition: XmippMenuCreator.java:244
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xmipp.utils.XmippMenuCreator.getItem
JMenuItem getItem(String key)
Definition: XmippMenuCreator.java:130
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xmipp.utils.XmippMenuCreator.getItemSelected
boolean getItemSelected(String key)
Definition: XmippMenuCreator.java:142
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xmipp.utils.XmippMenuCreator.SELECT_FROMHERE
static final String SELECT_FROMHERE
Definition: XmippMenuCreator.java:248
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xmipp.utils.XmippMenuCreator.actionPerformed
void actionPerformed(ActionEvent evt)
Definition: XmippMenuCreator.java:165
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xmipp.utils.XmippMenuCreator.groups
Map< String, ButtonGroup > groups
Definition: XmippMenuCreator.java:29
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xmipp.utils.XmippMenuCreator.addItem
JMenuItem addItem(String key, String text, String... values)
Definition: XmippMenuCreator.java:56
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xmipp.utils.XmippMenuCreator.getItemEnabled
boolean getItemEnabled(String key)
Definition: XmippMenuCreator.java:134
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xmipp.utils.XmippMenuCreator.items
Map< String, JMenuItem > items
Definition: XmippMenuCreator.java:24
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xmipp.utils.XmippResource.getIcon
static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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xmipp.utils.XmippMenuCreator.INVERT_SELECT
static final String INVERT_SELECT
Definition: XmippMenuCreator.java:249
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xmipp.utils.XmippMenuCreator.createItems
abstract void createItems()
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xmipp.utils.XmippMenuCreator.SELECT_TOHERE
static final String SELECT_TOHERE
Definition: XmippMenuCreator.java:247
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xmipp.utils.XmippMenuCreator.setItemVisible
void setItemVisible(String key, boolean value)
Definition: XmippMenuCreator.java:160
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xmipp.utils.XmippMenuCreator.setItemEnabled
void setItemEnabled(String key, boolean value)
Definition: XmippMenuCreator.java:138
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xmipp.utils.XmippMenuCreator.handleActionPerformed
abstract void handleActionPerformed(ActionEvent evt)
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 import java.awt.BorderLayout;
29 import java.awt.Color;
30 import java.awt.Dialog;
31 import java.awt.FlowLayout;
32 
33 import javax.swing.BorderFactory;
34 import javax.swing.JFrame;
35 import javax.swing.JPanel;
36 import javax.swing.JScrollPane;
37 import javax.swing.JTextArea;
38 
40 public class XmippMessageDialog extends XmippDialog {
41  private static final long serialVersionUID = 1L;
42  String message;
43  String iconPath;
44 
45  public XmippMessageDialog(JFrame parent, String title){
46  super(parent, title, true);
47  }
48 
49  public XmippMessageDialog(Dialog parent, String title){
50  super(parent, title, true);
51  }
52 
53  public XmippMessageDialog(JFrame parent, String title, String message,
54  String iconPath) {
55  super(parent, title, true);
56  init(removeColors(message), iconPath);
57  }
58 
59  public XmippMessageDialog(Dialog parent, String title, String message,
60  String iconPath) {
61  super(parent, title, true);
62  init(message, iconPath);
63  }
64 
66  protected void init(String message, String iconPath){
67  this.message = message;
68  this.iconPath = iconPath;
69  initComponents();
70  }
71 
72  @Override
73  protected void createContent(JPanel panel) {
74  panel.setLayout(new BorderLayout());
75  JPanel iconPanel = new JPanel();
76  iconPanel.add(XmippWindowUtil.getIconLabel(iconPath));
77  iconPanel.setBackground(Color.white);
78  panel.add(iconPanel, BorderLayout.LINE_START);
79  JTextArea text = new JTextArea(message, 5, 40);
80  text.setEditable(false);
81  text.setBackground(Color.white);
82  text.setBorder(BorderFactory.createEmptyBorder());
83  text.setLineWrap(true);
84  text.setWrapStyleWord(true);
85  // text
86  JScrollPane scrollPane = new JScrollPane(text);
87  scrollPane.setBorder(BorderFactory.createEmptyBorder());
88  scrollPane.setBackground(Color.white);
89  panel.add(scrollPane, BorderLayout.CENTER);
90  }
91 
92  @Override
93  protected void createButtons() {
94  super.createButtons();
95  panelBtn.setLayout(new FlowLayout());
96  }
97 }// class XmippMessageDialog
xmipp.utils.XmippWindowUtil.getIconLabel
static JLabel getIconLabel(String icon)
Definition: XmippWindowUtil.java:149
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xmipp.utils.XmippMessageDialog.XmippMessageDialog
XmippMessageDialog(Dialog parent, String title, String message, String iconPath)
Definition: XmippMessageDialog.java:59
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xmipp.utils.XmippDialog.removeColors
static String removeColors(String message)
Definition: XmippDialog.java:280
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xmipp.utils.XmippMessageDialog.init
void init(String message, String iconPath)
Definition: XmippMessageDialog.java:66
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XmippMessageDialog(JFrame parent, String title)
Definition: XmippMessageDialog.java:45
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XmippMessageDialog(JFrame parent, String title, String message, String iconPath)
Definition: XmippMessageDialog.java:53
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XmippMessageDialog(Dialog parent, String title)
Definition: XmippMessageDialog.java:49
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1 /***************************************************************************
2  * Authors: Airen Zaldivar (airen@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 
30 public class XmippMessage {
31 
32 
34  public static String getIllegalDeleteMsg(String item)
35  {
36  return String.format("There it must be at least one %s defined", item);
37  }
38 
39  public static String getAlreadyExistsGroupNameMsg(String name)
40  {
41  return String.format("Group %s already exists", name);
42  }
43 
44  public static String getEmptyFieldMsg(String field) {
45  return String.format("Must specify %s", field);
46  }
47 
48  public static String getAssociatedDataMsg(String field) {
49  return String.format("%s has associated data. Can not be removed");
50  }
51 
52  public static String getNoSuchFieldValueMsg(String field, Object value) {
53  return String.format("No such %s %s exists", field, value);
54  }
55 
56  public static String getOutOfBoundsMsg(Object o)
57  {
58  return String.format("%s out of bounds", o);
59  }
60 
61  public static String getNotImplementedYetMsg()
62  {
63  return "Not implemented yet";
64  }
65 
66  public static String getIllegalValueMsg(String field, Object value)
67  {
68  return String.format("Illegal value for %s: %s", field, value);
69  }
70 
71  public static String getPathNotExistsMsg(String path){
72  return String.format("Path '%s' doesn't exists.", path);
73  }
74 
75  public static String getIllegalStateForOperationMsg(String field, String value){
76  return String.format("Invalid operation for %s on state %s", field, value);
77  }
78 
79  public static String getIllegalValueMsgWithInfo(String field, Object value, String message)
80  {
81  return String.format("%s=%s\n%s", field, value, message);
82  }
83 
84  public static String getUnexpectedErrorMsg()
85  {
86  return "Unexpected error";
87  }
88 
89  public static String getInvalidDirectoryMsg(String outputdir) {
90  return String.format("Directory %s doesn't exists.", outputdir);
91  }
92 
93  public static String getFileTypeNotSupportedMsg(String path) {
94  return String.format("Extension not supported: %s", path); //To change body of generated methods, choose Tools | Templates.
95  }
96 
97 
98 
99 
100 }
xmipp.utils.XmippMessage.getFileTypeNotSupportedMsg
static String getFileTypeNotSupportedMsg(String path)
Definition: XmippMessage.java:93
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xmipp.utils.XmippMessage.getUnexpectedErrorMsg
static String getUnexpectedErrorMsg()
Definition: XmippMessage.java:84
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xmipp.utils.XmippMessage.getNotImplementedYetMsg
static String getNotImplementedYetMsg()
Definition: XmippMessage.java:61
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xmipp.utils.XmippMessage.getIllegalStateForOperationMsg
static String getIllegalStateForOperationMsg(String field, String value)
Definition: XmippMessage.java:75
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static String getIllegalValueMsgWithInfo(String field, Object value, String message)
Definition: XmippMessage.java:79
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static String getOutOfBoundsMsg(Object o)
Definition: XmippMessage.java:56
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static String getAssociatedDataMsg(String field)
Definition: XmippMessage.java:48
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xmipp.utils.XmippMessage.getPathNotExistsMsg
static String getPathNotExistsMsg(String path)
Definition: XmippMessage.java:71
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xmipp.utils.XmippMessage.getNoSuchFieldValueMsg
static String getNoSuchFieldValueMsg(String field, Object value)
Definition: XmippMessage.java:52
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xmipp.utils.XmippMessage.getIllegalValueMsg
static String getIllegalValueMsg(String field, Object value)
Definition: XmippMessage.java:66
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xmipp.utils.XmippMessage.getInvalidDirectoryMsg
static String getInvalidDirectoryMsg(String outputdir)
Definition: XmippMessage.java:89
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xmipp.utils.XmippMessage.getAlreadyExistsGroupNameMsg
static String getAlreadyExistsGroupNameMsg(String name)
Definition: XmippMessage.java:39
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xmipp.utils.XmippMessage.getEmptyFieldMsg
static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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xmipp.utils.XmippMessage.getIllegalDeleteMsg
static String getIllegalDeleteMsg(String item)
Definition: XmippMessage.java:34
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 import javax.swing.JPopupMenu;
29 
30 public abstract class XmippPopupMenuCreator extends XmippMenuCreator {
31 
32  public XmippPopupMenuCreator() {
33  super(new JPopupMenu());
34  }
35 
36  public JPopupMenu getPopupMenu(){
37  return (JPopupMenu)menu;
38  }
39 
40  public void addSeparator(){
41  getPopupMenu().addSeparator();
42  }
43 }
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
28 import java.awt.Dialog;
29 import java.awt.event.ActionEvent;
30 import javax.swing.JButton;
31 import javax.swing.JFrame;
32 
34 public class XmippQuestionDialog extends XmippMessageDialog {
35  private static final long serialVersionUID = 1L;
36 
37  protected JButton btnQuestionCancel; //Button cancel will be 'No' button
38  protected String btnQuestionCancelText = "Cancel";
39  protected boolean btnQuestionCancelDisplay = true;
40  protected boolean canceled = false;
41  private static final String TITLE = "QUESTION";
42  private static final String ICON = "question.gif";
43 
44  public static int YES_OPTION = 0;
45  public static int NO_OPTION = 1;
46  public static int CANCEL_OPTION = 2;
47  protected int option;
48 
49  public XmippQuestionDialog(JFrame parent, String message) {
50  super(parent, TITLE);
51  init(message, ICON);
52  }
53 
54  public XmippQuestionDialog(Dialog parent, String message) {
55  super(parent, TITLE);
56  init(message, ICON);
57  }
58 
59  public XmippQuestionDialog(JFrame parent, String message, boolean showCancel) {
60  super(parent, TITLE);
61  btnQuestionCancelDisplay = showCancel;
62  init(message, ICON);
63  }
64 
65  public XmippQuestionDialog(Dialog parent, String message, boolean showCancel) {
66  super(parent, TITLE);
67  btnQuestionCancelDisplay = showCancel;
68  init(message, ICON);
69  }
70 
71  @Override
72  public void handleActionPerformed(ActionEvent evt) {
73  JButton button = (JButton)evt.getSource();
74  if (btnQuestionCancel == button){
75  canceled = true;
76  close(false);
77  }
78 
79  }
80 
81  @Override
82  protected void createButtons() {
83  btnOkText = "Yes";
84  btnCancelText = "No";
85  super.createButtons();
86  if (btnQuestionCancelDisplay) {
87  btnQuestionCancel = XmippWindowUtil.getTextButton(btnQuestionCancelText, this);
88  panelBtn.add(btnQuestionCancel);
89  btnQuestionCancel.addActionListener(this);
90  }
91 
92  // Cancel close!
93  setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
94  }
95 
96  public boolean isCanceled(){
97  return canceled;
98  }
99 
100  public int getOption(){
101  if (result)
102  return YES_OPTION;
103  if (isCanceled())
104  return CANCEL_OPTION;
105  return NO_OPTION;
106  }
107 }//class XmippQuestionDialog
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XmippQuestionDialog(Dialog parent, String message, boolean showCancel)
Definition: XmippQuestionDialog.java:65
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void init(String message, String iconPath)
Definition: XmippMessageDialog.java:66
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void handleActionPerformed(ActionEvent evt)
Definition: XmippQuestionDialog.java:72
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void close(boolean result)
Definition: XmippDialog.java:174
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xmipp.utils.XmippWindowUtil.getTextButton
static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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XmippQuestionDialog(JFrame parent, String message, boolean showCancel)
Definition: XmippQuestionDialog.java:59
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XmippQuestionDialog(JFrame parent, String message)
Definition: XmippQuestionDialog.java:49
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XmippQuestionDialog(Dialog parent, String message)
Definition: XmippQuestionDialog.java:54
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1 /*
2  * To change this template, choose Tools | Templates
3  * and open the template in the editor.
4  */
5 package xmipp.utils;
6 
7 import java.awt.Image;
8 import java.io.File;
9 import java.io.IOException;
10 import java.util.Hashtable;
11 import java.util.Dictionary;
12 
13 import ij.ImagePlus;
14 import xmipp.jni.Filename;
15 
16 import javax.imageio.ImageIO;
17 import javax.swing.ImageIcon;
18 
23 public class XmippResource {
24 
25  public static int DEFAULT_PREVIEW_WIDTH = 80;
26  public static int DEFAULT_PREVIEW_HEIGHT = 80;
27 
28  //Path to resource folder
29  public static String PATH_ICONS;
30  //Icon names
31  public final static String MISSING = "missing.png";
32  public final static String MISSING2 = "missing2.png";
33  public final static String WAIT = "wait.gif";
34  public final static String WAIT_MENU = "wait_menu.gif";
35  public final static String NORMALIZE = "histogram.png";
36  public final static String APPLY_GEO = "rotate.png";
37  public final static String ADJUST_COLS = "resize.png";
38  public final static String GOTO = "goto.gif";
39  public final static String ZOOM = "zoom.png";
40  public final static String VIEW_MD = "md_view.gif";
41  public final static String VIEW_GALLERY = "table_view.gif";
42 
43  public static ImageIcon WAIT_ICON;
44  public static ImageIcon LOCK_ICON;
45  public static ImageIcon DELETE_ICON;
46  public static ImageIcon WAIT_MENU_ICON;
47  public static ImagePlus MISSING_ITEM;
48  public static ImageIcon VIEW_MD_ICON;
49  public static ImageIcon VIEW_GALLERY_ICON;
50  public static ImageIcon MISSING_ICON;
51 
52  private static Hashtable<String, ImageIcon> iconsPool;
53 
54 
55  static { //this block will be called just once, at class initialization
56  try {
57  PATH_ICONS = Filename.getXmippPath();//"/home/josem/xmipp_current/resources/";
58  }
59  catch (Exception e){
60  PATH_ICONS = ".";
61  }
62  DEBUG.printMessage(PATH_ICONS);
63  iconsPool = new Hashtable<String, ImageIcon>();
64 
65  WAIT_ICON = getIcon(WAIT);
66  LOCK_ICON = getIcon("locked.png");
67  DELETE_ICON = getIcon("delete_item.png");
68  WAIT_MENU_ICON = getIcon(WAIT_MENU);
69  VIEW_MD_ICON = getIcon(VIEW_MD);
70  VIEW_GALLERY_ICON = getIcon(VIEW_GALLERY);
71 
72  // For missing items.
73  MISSING_ICON = getIcon(MISSING2);
74  MISSING_ITEM = new ImagePlus("X", MISSING_ICON.getImage());
75  }
76 
77  // Create an icon using the xmipp resource path
78  public static ImageIcon getIcon(String name){
79  ImageIcon ii;
80  if (iconsPool.containsKey(name))
81  ii = iconsPool.get(name);
82  else {
83  String path = String.format("%s%sresources%s%s", PATH_ICONS, File.separator, File.separator, name);
84  ii = new ImageIcon(path);
85  iconsPool.put(name, ii);
86  }
87  return ii;
88  }
89 
90  public static String getPath(String resource)
91  {
92  try
93  {
94  return String.format("%s%sresources%s%s", Filename.getXmippPath(), File.separator, File.separator, resource);
95  }
96  catch (Exception e)
97  {
98  // TODO Auto-generated catch block
99  e.printStackTrace();
100  throw new IllegalArgumentException(e);
101  }
102  }
103 
104  public static Image getImage(String name)
105  {
106  try
107  {
108  return ImageIO.read(new File(getPath(name)));
109  }
110  catch (IOException e)
111  {
112  // TODO Auto-generated catch block
113  e.printStackTrace();
114  throw new IllegalArgumentException(e);
115  }
116  }
117 }
xmipp.utils.XmippResource.MISSING2
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Definition: XmippResource.java:32
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Definition: XmippResource.java:35
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Definition: XmippResource.java:43
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Definition: XmippResource.java:46
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Definition: XmippResource.java:41
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Definition: XmippResource.java:31
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Definition: XmippResource.java:45
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Definition: XmippResource.java:47
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Definition: XmippResource.java:90
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Definition: XmippResource.java:104
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Definition: DEBUG.java:18
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1 package xmipp.ij.commons;
2 
3 import ij.gui.StackWindow;
4 
5 import java.awt.Window;
6 import java.awt.event.WindowEvent;
7 
8 import xmipp.ij.commons.XmippMenuBar.IJRequirement;
9 import xmipp.utils.Params;
10 
11 public class XmippStackWindow extends StackWindow implements XmippIJWindow{
12 
13  private ImagePlusLoader ipl;
14  protected XmippMenuBar menu;
15  protected Params params;
16 
17  public XmippStackWindow(ImagePlusLoader ipl, String title, Params params)
18  {
19  super(ipl.getImagePlus(), new XmippImageCanvas(ipl.getImagePlus()));
20  this.ipl = ipl;
21  imp.setTitle(title);
22  menu = new XmippMenuBar(this);
23  setMenuBar(menu);
24  //getCanvas().adjustMagnification();
25  XmippApplication.addInstance(true);
26  this.params = params;
27 
28  }
29 
30  public XmippStackWindow(ImagePlusLoader ipl, Params params)
31  {
32  this(ipl, ipl.getName(), params);
33  }
34 
35 
36 
37 
38  @Override
39  public void loadData()
40  {
41  getCanvas().loadData(this);
42  }
43 
44  public void openMaskToolbar(){
45  menu.runCommand("Masks Tool Bar", new IJRequirement[]{IJRequirement.IMAGEJ});
46  }
47 
48  @Override
49  public void saveDataAs(String file) throws Exception
50  {
51 
52  XmippImageConverter.writeImagePlus(imp, file);
53  }
54 
55  @Override
56  public void saveData() throws Exception
57  {
58  saveDataAs(imp.getTitle());
59 
60  }
61 
62  public XmippImageCanvas getCanvas()
63  {
64  return ((XmippImageCanvas)super.getCanvas());
65  }
66 
67  @Override
68  public void windowClosing(WindowEvent e) {
69 
70  super.windowClosing(e);
71  XmippApplication.removeInstance(true);
72 
73  }
74 
75  @Override
76  public ImagePlusLoader getImagePlusLoader()
77  {
78  return ipl;
79  }
80 
81  @Override
82  public boolean isVolume()
83  {
84  return getImagePlusLoader().isVolume();
85  }
86 
87  @Override
88  public boolean isStack()
89  {
90  return true;
91  }
92 
93  public Params getParams()
94  {
95  return params;
96  }
97 
98 
99 }
xmipp.ij.commons.XmippStackWindow.XmippStackWindow
XmippStackWindow(ImagePlusLoader ipl, Params params)
Definition: XmippStackWindow.java:30
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xmipp.ij.commons.XmippImageConverter.writeImagePlus
static boolean writeImagePlus(ImagePlus imp, String filename)
Definition: XmippImageConverter.java:312
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xmipp.ij.commons.XmippMenuBar.runCommand
void runCommand(String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:666
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xmipp.ij.commons.XmippStackWindow.XmippStackWindow
XmippStackWindow(ImagePlusLoader ipl, String title, Params params)
Definition: XmippStackWindow.java:17
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xmipp.ij.commons.XmippApplication.removeInstance
static void removeInstance(boolean isijwindow)
Definition: XmippApplication.java:28
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xmipp.ij.commons.XmippApplication.addInstance
static void addInstance(boolean isijwindow)
Definition: XmippApplication.java:18
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XmippStringUtils.java
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 
26 package xmipp.utils;
27 
29 public class XmippStringUtils {
30 
32  public static String commonPrefix(String[] strings){
33  String prefix = "";
34 
35  int n = strings.length;
36  boolean common = true;
37 
38  int minLenght = Integer.MAX_VALUE;
39 
40  for (int i = 0; i < n; ++i)
41  minLenght = Math.min(minLenght, strings[i].length());
42 
43  for (int j = 0; j < minLenght && common; ++j){
44  char c = strings[0].charAt(j);
45  for (int i = 1; i < strings.length && common; ++i)
46  if (c != strings[i].charAt(j))
47  common = false;
48  prefix += c;
49  }
50 
51  return prefix;
52  }//function commonPrefix
53 
56  public static String commonPathPrefix(String [] strings){
57  String prefix = commonPrefix(strings);
58 
59  int pos = prefix.lastIndexOf('/');
60  if (pos > 0) {
61  ++pos; //If found /, also include in prefix
62  prefix = prefix.substring(0, pos);
63  }
64  else
65  prefix = "";
66 
67  return prefix;
68  }
69 
70  public static String getFileExtension(String filename) {
71 
72  try {
73  return filename.substring(filename.lastIndexOf("."));
74 
75  } catch (Exception e) {
76  return "";
77  }
78 
79 }
80 
81 }
xmipp.utils.XmippStringUtils.commonPrefix
static String commonPrefix(String[] strings)
Definition: XmippStringUtils.java:32
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xmipp.utils.XmippStringUtils.commonPathPrefix
static String commonPathPrefix(String [] strings)
Definition: XmippStringUtils.java:56
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xmipp.utils.XmippStringUtils.getFileExtension
static String getFileExtension(String filename)
Definition: XmippStringUtils.java:70
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XmippTest.java
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  *
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 package xmipp.test;
26 
27 import xmipp.jni.Filename;
28 import xmipp.jni.ImageGeneric;
29 
33 public class XmippTest {
34 
35  // Xmipp Tests dir
36  static String TESTS_PATH = Filename.getXmippPath("java/src/xmipp/test/");
37  static double EQUAL_ACCURACY = 0.001;
38 
40  public static String getTestFilename(String file) {
41  return TESTS_PATH + file;
42  }
43 
45  public static ImageGeneric getImageGeneric(String filename) throws Exception {
46  ImageGeneric image = new ImageGeneric(filename);
47  image.read(ImageGeneric.FIRST_SLICE);
48  return image;
49  }
50 
51 
52 }//class XmippTest
xmipp.jni.ImageGeneric.FIRST_SLICE
static final int FIRST_SLICE
Definition: ImageGeneric.java:9
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xmipp.test.XmippTest.getTestFilename
static String getTestFilename(String file)
Definition: XmippTest.java:40
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xmipp.jni.Filename.getXmippPath
static native String getXmippPath()
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.test.XmippTest.getImageGeneric
static ImageGeneric getImageGeneric(String filename)
Definition: XmippTest.java:45
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XmippUtil.java
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1 package xmipp.ij.commons;
2 
3 import ij.IJ;
4 import ij.ImagePlus;
5 import java.awt.Image;
6 import java.io.BufferedWriter;
7 import java.io.File;
8 import java.io.FileInputStream;
9 import java.io.FileOutputStream;
10 import java.io.FileWriter;
11 import java.io.IOException;
12 import java.io.InputStream;
13 import java.io.OutputStream;
14 import java.net.ServerSocket;
15 import java.util.logging.Level;
16 import java.util.logging.Logger;
17 import java.util.regex.Matcher;
18 import java.util.regex.Pattern;
19 import javax.swing.Icon;
20 import javax.swing.ImageIcon;
21 import xmipp.jni.ImageGeneric;
22 
23 
24 public class XmippUtil {
25 
26  private static XmippImageJ xij;
27 
28  public static XmippImageJ showImageJ(Tool tool) {
29  if (IJ.getInstance() == null) {
30  try {
31  xij = new XmippImageJ();
32 
33 //
34  File tempFile = File.createTempFile("macros", ".txt");
35  BufferedWriter writer = new BufferedWriter(new FileWriter(tempFile));
36  writer.write("macro \"Particle Picker Tool - C0a0L18f8L818f\" { }\nmacro \"Xmipp Micrograph Viewer Tool - C0a0L18f8L818f\" { }");
37  writer.close();
38  IJ.run("Install...", "install=" + tempFile.getAbsolutePath());
39  //Tool cannot be set if it is not a default one
40  } catch (Exception ex) {
41  Logger.getLogger(XmippUtil.class.getName()).log(Level.SEVERE, null, ex);
42  throw new IllegalArgumentException(ex);
43  }
44  } else if (!xij.isVisible())
45  xij.setVisible(true);
46  return xij;
47  }
48 
49  public static XmippImageJ getXmippImageJ() {
50  return xij;
51  }
52 
53 
54 
55  public static ImagePlus getImagePlus(String file) {
56  try {
57 
58  ImageGeneric ig = new ImageGeneric(file);
59  ig.read(ImageGeneric.FIRST_IMAGE);
60  ImagePlus imp = XmippImageConverter.convertToImagePlus(ig);
61  ig.destroy();
62 
63  return imp;
64  } catch (Exception e) {
65  e.printStackTrace();
66  throw new IllegalArgumentException(e.getMessage());
67  }
68  }
69 
70  public static Icon getImageIcon(Image imp, int width, int height)
71  {
72 
73  Image image = imp.getScaledInstance(width, height, Image.SCALE_SMOOTH);
74  Icon icon = new ImageIcon(image);
75 
76  return icon;
77  }
78 
79 
80 
81 
82 
83 
84  public static void copyFile(String source, String dest) throws IOException
85  {
86  copyFile(new File(source), new File(dest));
87  }
88 
89  public static void copyFile(File source, File dest)
90  throws IOException {
91  InputStream input = null;
92  OutputStream output = null;
93  try {
94  input = new FileInputStream(source);
95  output = new FileOutputStream(dest);
96  byte[] buf = new byte[1024];
97  int bytesRead;
98  while ((bytesRead = input.read(buf)) > 0) {
99  output.write(buf, 0, bytesRead);
100  }
101  } finally {
102  if(input != null)
103  input.close();
104  if(output != null)
105  output.close();
106  }
107  }
108 
109  public static boolean isInPath(String executable)
110  {
111  String[] paths = System.getenv("PATH").split(Pattern.quote(File.pathSeparator));
112  String exePath;
113  File file, exeFile;
114  for(String path: paths)
115  {
116  file = new File(path);
117  if(file.isDirectory())
118  {
119  exePath = path + File.separator + executable;
120  exeFile = new File(exePath);
121  if(exeFile.exists())
122  return true;
123  }
124  else if(file.getName().equals(executable))
125  return true;
126 
127  }
128  return false;
129  }
130 
131  public static String formatNumbers(String str)
132  {
133  Pattern p = Pattern.compile("(-?(\\d)+(\\.)?(\\d)*)");
134  Matcher m = p.matcher(str);
135  StringBuffer sb = new StringBuffer(str.length());
136  while(m.find())
137  {
138  String number = m.group(1);
139  m.appendReplacement(sb, String.format("%.2f", Double.parseDouble(number)));
140  }
141  m.appendTail(sb);
142  return sb.toString();
143  }
144 
145  public static int findFreePort()
146  throws IOException {
147  ServerSocket server = new ServerSocket(0);
148  int port = server.getLocalPort();
149  server.close();
150  return port;
151  }
152 
153 }
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Definition: XmippUtil.java:70
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static String formatNumbers(String str)
Definition: XmippUtil.java:131
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static void copyFile(File source, File dest)
Definition: XmippUtil.java:89
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static XmippImageJ getXmippImageJ()
Definition: XmippUtil.java:49
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static ImagePlus getImagePlus(String file)
Definition: XmippUtil.java:55
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static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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static XmippImageJ showImageJ(Tool tool)
Definition: XmippUtil.java:28
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void read(int slice)
Definition: ImageGeneric.java:126
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static void copyFile(String source, String dest)
Definition: XmippUtil.java:84
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static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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static boolean isInPath(String executable)
Definition: XmippUtil.java:109
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1 /***************************************************************************
2  * Authors: J.M. de la Rosa Trevin (jmdelarosa@cnb.csic.es)
3  * Airen Zaldivar Peraza (airenzp@cnb.csic.es)
4  *
5  * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
6  *
7  * This program is free software; you can redistribute it and/or modify
8  * it under the terms of the GNU General Public License as published by
9  * the Free Software Foundation; either version 2 of the License, or
10  * (at your option) any later version.
11  *
12  * This program is distributed in the hope that it will be useful,
13  * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * GNU General Public License for more details.
16  *
17  * You should have received a copy of the GNU General Public License
18  * along with this program; if not, write to the Free Software
19  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
20  * 02111-1307 USA
21  *
22  * All comments concerning this program package may be sent to the
23  * e-mail address 'xmipp@cnb.csic.es'
24  ***************************************************************************/
25 package xmipp.utils;
26 
27 import java.awt.Color;
28 import java.awt.Container;
29 import java.awt.Dimension;
30 import java.awt.GraphicsDevice;
31 import java.awt.GraphicsEnvironment;
32 import java.awt.GridBagConstraints;
33 import java.awt.Image;
34 import java.awt.Rectangle;
35 import java.awt.Window;
36 import java.awt.event.ActionListener;
37 import java.io.BufferedReader;
38 import java.io.File;
39 import java.io.IOException;
40 import java.io.InputStreamReader;
41 import java.io.PrintWriter;
42 import java.net.Socket;
43 import java.net.UnknownHostException;
44 import java.util.ArrayList;
45 import java.util.HashMap;
46 import java.util.List;
47 import java.util.Map;
48 
49 import javax.swing.Icon;
50 import javax.swing.JButton;
51 import javax.swing.JFrame;
52 import javax.swing.JLabel;
53 import javax.swing.JRootPane;
54 
55 public class XmippWindowUtil
56 {
57  public static final Color firebrick = Color.decode("#B22222");
58  public static final Color lightgrey = Color.decode("#EAEBEC");
59 
61  public static final Color LIGHT_BLUE = new Color(173, 216, 230);
62 
63 
64 
69  private static void setLocation(double positionx, double positiony, Container w, Rectangle bounds)
70  {
71  Rectangle abounds = w.getBounds();
72  int x = (int) (positionx * (bounds.width - abounds.width) + bounds.x);
73  int y = (int) (positiony * (bounds.height - abounds.height) + bounds.y);
74  w.setLocation(x, y);
75  }
76 
77  public static void setLocation(double positionx, double positiony, Window w)
78  {
79  setLocation(positionx, positiony, w, getScreenRectangle());
80  }
81 
82  public static Rectangle getScreenRectangle()
83  {
84  GraphicsDevice gd = GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice();
85  return gd.getDefaultConfiguration().getBounds();
86  }
87 
88  public static void setLocation(float positionx, float positiony, Container w, Container parent)
89  {
90  setLocation(positionx, positiony, w, parent.getBounds());
91  }
92 
94  public static void centerWindows(Window w)
95  {
96  setLocation(0.5f, 0.5f, w);
97  }
98 
100  public static void centerWindows(Container w, Container parent)
101  {
102  setLocation(0.5f, 0.5f, w, parent.getBounds());
103  }
104 
105  public static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
106  {
107  return getConstraints(constraints, x, y, 1, 1);
108  }
109 
110  public static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y, int columns)
111  {
112  return getConstraints(constraints, x, y, columns, 1);
113  }
114 
115 
116  public static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y, int columns, int rows, int fill)
117  {
118  constraints = getConstraints(constraints, x, y, columns, rows);
119  constraints.fill = fill;
120  return constraints;
121  }
122 
123 
124  public static JButton getIconButton(String icon, ActionListener listener){
125  JButton btn = new JButton();
126  btn.setIcon(XmippResource.getIcon(icon));
127  Dimension dim = btn.getPreferredSize();
128  dim.width = dim.height;
129  btn.setPreferredSize(dim);
130  btn.addActionListener(listener);
131  return btn;
132  }
133 
134  public static JButton getTextIconButton(String text, String icon, ActionListener listener){
135  JButton btn = new JButton(text, XmippResource.getIcon(icon));
136  btn.addActionListener(listener);
137  return btn;
138  }
139 
140  public static JButton getTextButton(String text, ActionListener listener)
141  {
142  JButton btn = new JButton(text);
143  //if(!isScipion)
144  // btn.setBackground(LIGHT_BLUE);
145  btn.addActionListener(listener);
146  return btn;
147  }
148 
149  public static JLabel getIconLabel(String icon)
150  {
151  JLabel label = new JLabel();
152  label.setIcon(XmippResource.getIcon(icon));
153  return label;
154  }
155 
156  public static JButton getScipionIconButton(String text) {
157  Icon icon = XmippResource.getIcon("fa-plus-circle.png");
158  JButton button = new JButton(text.replace("Create ", ""), icon);
159  button.setToolTipText(text);
160  button.setBackground(firebrick);
161  button.setForeground(Color.WHITE);
162  return button;
163  }
164 
165  public static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y, int columns, int rows)
166  {
167  constraints.gridx = x;
168  constraints.gridy = y;
169  constraints.gridwidth = columns;
170  constraints.gridheight = rows;
171  if (columns > 1 && rows > 1)
172  {
173  constraints.fill = GridBagConstraints.BOTH;
174  }
175  else if (columns > 1)
176  {
177  constraints.fill = GridBagConstraints.HORIZONTAL;
178  }
179  else if (rows > 1)
180  {
181  constraints.fill = GridBagConstraints.VERTICAL;
182  }
183  else
184  {
185  constraints.fill = GridBagConstraints.NONE;
186  }
187  return constraints;
188  }
189 
190  public static void openURI(String uri)
191  {
192 
193  if (!java.awt.Desktop.isDesktopSupported())
194  throw new IllegalArgumentException("Desktop is not supported (fatal)");
195 
196  if (uri == null)
197  throw new IllegalArgumentException("Usage: OpenURI [URI [URI ... ]]");
198 
199  java.awt.Desktop desktop = java.awt.Desktop.getDesktop();
200 
201  if (!desktop.isSupported(java.awt.Desktop.Action.BROWSE))
202  {
203 
204  throw new IllegalArgumentException("Desktop doesn't support the browse action (fatal)");
205  }
206  try
207  {
208 
209  java.net.URI myuri = new java.net.URI(uri);
210  desktop.browse(myuri);
211  }
212  catch (Exception e)
213  {
214  throw new IllegalArgumentException(e);
215  }
216  }
217 
219  public static void blockGUI(JFrame window, String status){
220 
221  blockGUI(window, status, false);
222  }
223 
231  public static void blockGUI(JFrame window, String status, boolean hideContent)
232  {
233  final InfiniteProgressPanel progressPanel = new InfiniteProgressPanel(window, status);
234  window.setGlassPane(progressPanel);
235  if (hideContent) {
236  window.getLayeredPane().setVisible(false);
237  }
238  progressPanel.start();
239  }
240 
242  public static void releaseGUI(JRootPane panel)
243  {
244  InfiniteProgressPanel progressPanel = (InfiniteProgressPanel) panel.getGlassPane();
245  progressPanel.stop();
246  progressPanel.setVisible(false);
247  panel.getLayeredPane().setVisible(true);
248  }
249 
250  public static void executeGUICommand(final String[] command, final JFrame frame, String msg)
251  {
252 
253 
254  XmippWindowUtil.blockGUI(frame, msg);
255  new Thread(new Runnable() {
256 
257  @Override
258  public void run() {
259 
260  try {
261 
262  String output = executeCommand(command, true);
263  XmippWindowUtil.releaseGUI(frame.getRootPane());
264 
265  if(output != null && !output.isEmpty())
266  System.out.println(output);
267 
268  } catch (Exception ex) {
269  throw new IllegalArgumentException(ex.getMessage());
270  }
271 
272  }
273  }).start();
274  }
275 
276  public static String executeCommand(String[] command, boolean wait) throws Exception {
277  //System.out.println(Arrays.toString(command));
278  Process p = Runtime.getRuntime().exec(command);
279  if(wait)
280  {
281  p.waitFor();
282  return readProcessOutput(p);
283  }
284  return null;
285  }
286 
287  public static String executeCommand(String command, boolean wait, String dir) throws Exception {
288  //System.out.println(command);
289  Process p = Runtime.getRuntime().exec(command, null, new File(dir));
290  if(wait)
291  {
292  p.waitFor();
293  return readProcessOutput(p);
294  }
295  return null;
296 }
297 
298  public static String executeCommand(String command, boolean wait) throws Exception {
299  DEBUG.printMessage(command);
300  Process p = Runtime.getRuntime().exec(new String[] { "bash", "-c", command });
301  if(wait)
302  {
303  p.waitFor();
304  return readProcessOutput(p);
305  }
306  return null;
307  }
308 
309  public static Map<String, String> env2Map(){
310 
311  Map<String, String> editableEnv = new HashMap<>();
312 
313  for (Map.Entry<String,String> var: System.getenv().entrySet()){
314  editableEnv.put(var.getKey(), var.getValue());
315  };
316  return editableEnv;
317  }
318  public static String executeCommand(String command, boolean wait , HashMap<String, String> envVars ) throws Exception {
319 
320  Map<String,String> curentEnv = env2Map();
321 
322  for (Map.Entry<String,String> newVar: envVars.entrySet()){
323  curentEnv.put(newVar.getKey(), newVar.getValue());
324  };
325 
326  List<String> env2Exec = new ArrayList<String>();
327  for (Map.Entry<String,String> var: curentEnv.entrySet()){
328  env2Exec.add(var.getKey() + "=" + var.getValue());
329  };
330 
331  DEBUG.printMessage(command);
332  Process p = Runtime.getRuntime().exec(command, env2Exec.toArray(new String[0]));
333  if(wait)
334  {
335  p.waitFor();
336  return readProcessOutput(p);
337  }
338  return null;
339 
340  }
341 
342  public static void runCommand(String command, Integer port) {
343  //System.out.println(command);
344  if(port == null)
345  {
346  XmippDialog.showError(null, XmippMessage.getEmptyFieldMsg("Scipion port"));
347  return;
348  }
349  String hostName = "";
350 
351  try {
352  Socket socket = new Socket(hostName, port);
353  PrintWriter out = new PrintWriter(socket.getOutputStream(), true);
354  BufferedReader in = new BufferedReader(new InputStreamReader(socket.getInputStream()));
355  DEBUG.printMessage("Sending to socket: " + command);
356  out.println(command);
357  in.readLine();
358  socket.close();
359 
360 
361  } catch (UnknownHostException e) {
362  System.err.println("Don't know about host " + hostName);
363  } catch (IOException e) {
364  System.err.println("Couldn't get I/O for the connection to " +
365  hostName);
366  }
367  }
368 
369  public static String readProcessOutput(Process p) throws IOException
370  {
371  StringBuffer output = new StringBuffer();
372  BufferedReader reader
373  = new BufferedReader(new InputStreamReader(p.getInputStream()));
374 
375 
376  String line = "";
377  while ((line = reader.readLine()) != null) {
378  output.append(line + "\n");
379  }
380  reader = new BufferedReader(new InputStreamReader(p.getErrorStream()));
381 
382  while ((line = reader.readLine()) != null) {
383  output.append(line + "\n");
384  }
385  return output.toString();
386 
387  }
388 
389  public static void setScipionImageIcon(Window w)
390  {
391  Image img = XmippResource.getIcon("scipion_logo.png").getImage();
392  w.setIconImage(img);
393  }
394 
395 }
xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y, int columns, int rows)
Definition: XmippWindowUtil.java:165
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xmipp.utils.XmippWindowUtil.blockGUI
static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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xmipp.utils.XmippWindowUtil.lightgrey
static final Color lightgrey
Definition: XmippWindowUtil.java:58
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xmipp.utils.XmippWindowUtil.readProcessOutput
static String readProcessOutput(Process p)
Definition: XmippWindowUtil.java:369
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xmipp.utils.XmippWindowUtil.setLocation
static void setLocation(double positionx, double positiony, Window w)
Definition: XmippWindowUtil.java:77
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xmipp.utils.XmippWindowUtil.getIconLabel
static JLabel getIconLabel(String icon)
Definition: XmippWindowUtil.java:149
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y, int columns)
Definition: XmippWindowUtil.java:110
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xmipp.utils.XmippWindowUtil.firebrick
static final Color firebrick
Definition: XmippWindowUtil.java:57
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xmipp.utils.XmippWindowUtil.blockGUI
static void blockGUI(JFrame window, String status, boolean hideContent)
Definition: XmippWindowUtil.java:231
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xmipp.utils.XmippWindowUtil.LIGHT_BLUE
static final Color LIGHT_BLUE
Definition: XmippWindowUtil.java:61
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xmipp.utils.XmippWindowUtil.centerWindows
static void centerWindows(Window w)
Definition: XmippWindowUtil.java:94
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xmipp.utils.XmippWindowUtil.executeGUICommand
static void executeGUICommand(final String[] command, final JFrame frame, String msg)
Definition: XmippWindowUtil.java:250
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xmipp.utils.XmippWindowUtil.executeCommand
static String executeCommand(String command, boolean wait)
Definition: XmippWindowUtil.java:298
-
xmipp.utils.XmippWindowUtil.executeCommand
static String executeCommand(String[] command, boolean wait)
Definition: XmippWindowUtil.java:276
-
xmipp.utils.XmippWindowUtil.env2Map
static Map< String, String > env2Map()
Definition: XmippWindowUtil.java:309
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xmipp.utils.XmippWindowUtil.releaseGUI
static void releaseGUI(JRootPane panel)
Definition: XmippWindowUtil.java:242
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y, int columns, int rows, int fill)
Definition: XmippWindowUtil.java:116
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xmipp.utils.XmippWindowUtil.getScipionIconButton
static JButton getScipionIconButton(String text)
Definition: XmippWindowUtil.java:156
-
xmipp.utils.XmippWindowUtil.setScipionImageIcon
static void setScipionImageIcon(Window w)
Definition: XmippWindowUtil.java:389
-
xmipp.utils.XmippResource.getIcon
static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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xmipp.utils.XmippWindowUtil.getTextButton
static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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xmipp.utils.XmippWindowUtil.runCommand
static void runCommand(String command, Integer port)
Definition: XmippWindowUtil.java:342
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xmipp.utils.XmippWindowUtil.centerWindows
static void centerWindows(Container w, Container parent)
Definition: XmippWindowUtil.java:100
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xmipp.utils.XmippWindowUtil.getTextIconButton
static JButton getTextIconButton(String text, String icon, ActionListener listener)
Definition: XmippWindowUtil.java:134
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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xmipp.utils.XmippWindowUtil.getScreenRectangle
static Rectangle getScreenRectangle()
Definition: XmippWindowUtil.java:82
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xmipp.utils.XmippWindowUtil.executeCommand
static String executeCommand(String command, boolean wait, HashMap< String, String > envVars)
Definition: XmippWindowUtil.java:318
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xmipp.utils.XmippWindowUtil.openURI
static void openURI(String uri)
Definition: XmippWindowUtil.java:190
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xmipp.utils.XmippWindowUtil.getIconButton
static JButton getIconButton(String icon, ActionListener listener)
Definition: XmippWindowUtil.java:124
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xmipp.utils.DEBUG.printMessage
static void printMessage(String message)
Definition: DEBUG.java:18
-
xmipp.utils.XmippMessage.getEmptyFieldMsg
static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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xmipp.utils.XmippWindowUtil.executeCommand
static String executeCommand(String command, boolean wait, String dir)
Definition: XmippWindowUtil.java:287
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xmipp.utils.XmippWindowUtil.setLocation
static void setLocation(float positionx, float positiony, Container w, Container parent)
Definition: XmippWindowUtil.java:88
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class  ZVI_Reader
 
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ZVI_Reader.java
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1 //
2 // ZVI_Reader.java
3 //
4 
5 import ij.*;
6 import ij.io.*;
7 import ij.plugin.*;
8 import java.io.*;
9 import java.util.*;
10 import ij.process.*;
11 
26 public class ZVI_Reader implements PlugIn {
27  boolean littleEndian = true;
28  private int theC, theZ, numC;
29 //+ (mb)
30  //+ new code
31  private Set C_Set = new HashSet(); // to hold C channel index collection
32 //- (mb)
33  private ImageProcessor ip1;
34  String fileName ;
35  // -- Constants --
36 
38  private static final byte[] ZVI_SIG = {
39  -48, -49, 17, -32, -95, -79, 26, -31
40  };
41 
43  private static final byte[] ZVI_MAGIC_BLOCK_1 = { // 41 00 10
44  65, 0, 16
45  };
46 
48  private static final byte[] ZVI_MAGIC_BLOCK_2 = { // 41 00 80
49  65, 0, -128
50  };
51 
53  private static final byte[] ZVI_MAGIC_BLOCK_3 = { // 20 00 10
54  32, 0, 16
55  };
56 
58  private static final int BUFFER_SIZE = 8192;
59 
61  private static final boolean DEBUG = false;
62 
63  // -- PlugIn API methods --
64 
66  public void run(String arg) {
67  OpenDialog od = new OpenDialog("Open ZVI...", arg);
68  String directory = od.getDirectory();
69  String fileName = od.getFileName();
70  if (fileName == null) return;
71 
72  IJ.showStatus("Opening: " + directory + fileName);
73  FileInfo[] fi = null;
74  try { fi = getHeaderInfo(directory, fileName); }
75  catch (Exception e) {
76  IJ.showStatus("");
77  IJ.showMessage("ZVI Reader", "" + e);
78  return;
79  }
80  if (fi == null) {
81  IJ.showStatus("");
82  IJ.showMessage("ZVI Reader", "Could not find header information.");
83  return;
84  }
85 
86  Opener opener = new Opener();
87  ImagePlus imp = opener.openTiffStack(fi); // is there a cleaner way?
88  if (imp == null) {
89  IJ.showStatus("");
90  IJ.showMessage("ZVI Reader", "Could not extract pixel data.");
91  return;
92  }
93  //setStack(fileName, imp.getStack());
94 
95  // addition by TjC
96  ImageStack istk = imp.getStack();
97 
98  int nSlice = istk .getSize();
99  int sWidth = istk.getWidth();
100  int sHeight = istk.getHeight();
101  String stackName="";
102 //+ (mb) new image stack construction.
103  //- original code removed
104  //- int sliceOffset = 1;
105  //- int sliceNumberPerChannel = nSlice/numC;
106  //-
107  //- //IJ.showMessage("nSlice = " +nSlice );
108  //- //IJ.showMessage("nSlice/ch = " +sliceNumberPerChannel);
109  //-
110  //- for (int i=1; i<=numC; i++)
111  //- {stackName= fileName + " Ch"+i;
112  //- ImageStack img = new ImageStack (sWidth,sHeight);
113  //- for(int j=0; j<sliceNumberPerChannel; j++)
114  //- {
115  //- //IJ.showMessage("j = " +j);
116  //- int theC = getChannel(fi[j*numC+i-1]);
117  //- IJ.showMessage("theC = "+ theC);
118  //-
119  //- ip1 = istk.getProcessor(j*numC+i);
120  //- img.addSlice(stackName, ip1);
121  //- }
122  //- new ImagePlus(stackName, img).show();
123  //- }
124  //-
125  //+ new code
126  // make ImageStack for each channel.
127  Hashtable img = new Hashtable();
128  Iterator it = C_Set.iterator();
129  while (it.hasNext()) {
130  Object theC = it.next();
131  img.put(theC, new ImageStack (sWidth,sHeight));
132  }
133  // iteratate thru all image slices and
134  // add slice to corresponding channel ImageStack.
135  for (int n=0; n< nSlice; n++) {
136  int theC = getChannel(fi[n]);
137  ip1 = istk.getProcessor(n+1);
138  ((ImageStack)img.get(new Integer(theC))).addSlice(null, ip1);
139  }
140  // name image stacks and show them.
141  it = C_Set.iterator();
142  while (it.hasNext()) {
143  Object theC = it.next();
144  stackName = fileName + " Ch"+ theC;
145  new ImagePlus(stackName, ((ImageStack)img.get(theC))).show();
146  }
147 //- (mb)
148 
149 //if (arg.equals("")) show();
150 
151 }
152 
153 
154  // -- Helper methods --
155 
157  private FileInfo[] getHeaderInfo(String directory, String fileName)
158  throws IOException
159  {
160  // Highly questionable decoding strategy:
161  //
162  // Note that all byte ordering is little endian, including 4-byte header
163  // fields. Other examples: 16-bit data is LSB MSB, and 3-channel data is
164  // BGR instead of RGB.
165  //
166  // 1) Find image header byte sequence:
167  // A) Find 41 00 10. (ZVI_MAGIC_BLOCK_1)
168  // B) Skip 19 bytes of stuff.
169  // C) Read 41 00 80. (ZVI_MAGIC_BLOCK_2)
170  // D) Read 11 bytes of 00.
171  // E) Read potential header information:
172  // - Z-slice (4 bytes)
173  // - channel (4 bytes)
174  // - timestep (4 bytes)
175  // F) Read 108 bytes of 00.
176  //
177  // 2) If byte sequence is not as expected at any point (e.g.,
178  // stuff that is supposed to be 00 isn't), start over at 1A.
179  //
180  // 3) Find 20 00 10. (ZVI_MAGIC_BLOCK_3)
181  //
182  // 4) Read more header information:
183  // - width (4 bytes)
184  // - height (4 bytes)
185  // - ? (4 bytes; always 1)
186  // - bytesPerPixel (4 bytes)
187  // - pixelType (this is what the AxioVision software calls it)
188  // - 1=24-bit (3 color components, 8-bit each)
189  // - 3=8-bit (1 color component, 8-bit)
190  // - 4=16-bit (1 color component, 16-bit)
191  // - 8=48-bit (3 color components, 16-bit each)
192  // - bitDepth (4 bytes--usually, but not always, bytesPerPixel * 8)
193  // - AK: seems that it is always 16
194  //
195  // 5) Read image data (width * height * bytesPerPixel)
196  //
197  // 6) Repeat the entire process until no more headers are identified.
198 
199  RandomAccessFile in = new RandomAccessFile(directory + fileName, "r");
200  byte[] sig = new byte[ZVI_SIG.length];
201  in.readFully(sig);
202  for (int i=0; i<sig.length; i++) {
203  if (sig[i] != ZVI_SIG[i]) return null;
204  }
205 //+ (mb)
206  //+ new code
207  Set Z_Set = new HashSet(); // to hold Z plan index collection.
208  Set T_Set = new HashSet(); // to hold T time index collection.
209 //- (mb)
210  long pos = 0;
211  Vector blockList = new Vector();
212  int numZ = 0, numT = 0;
213  numC=0;
214  while (true) {
215  // search for start of next image header
216  long header = findBlock(in, ZVI_MAGIC_BLOCK_1, pos);
217 
218  if (header < 0) {
219  // no more potential headers found; we're done
220  break;
221  }
222  pos = header + ZVI_MAGIC_BLOCK_1.length;
223 
224  if (DEBUG) System.err.println("Found potential image block: " + header);
225 
226  // these bytes don't matter
227  in.skipBytes(19);
228  pos += 19;
229 
230  // these bytes should match ZVI_MAGIC_BLOCK_2
231  byte[] b = new byte[ZVI_MAGIC_BLOCK_2.length];
232  in.readFully(b);
233  boolean ok = true;
234  for (int i=0; i<b.length; i++) {
235  if (b[i] != ZVI_MAGIC_BLOCK_2[i]) {
236  ok = false;
237  break;
238  }
239  pos++;
240  }
241  if (!ok) continue;
242 
243  // these bytes should be 00
244  b = new byte[11];
245  in.readFully(b);
246  for (int i=0; i<b.length; i++) {
247  if (b[i] != 0) {
248  ok = false;
249  break;
250  }
251  pos++;
252  }
253  if (!ok) continue;
254 
255  // read potential header information
256  int theZ = readInt(in);
257  int theC = readInt(in);
258  int theT = readInt(in);
259  pos += 12;
260 
261  // these bytes should be 00
262  b = new byte[108];
263  in.readFully(b);
264  for (int i=0; i<b.length; i++) {
265  if (b[i] != 0) {
266  ok = false;
267  break;
268  }
269  pos++;
270  }
271  if (!ok) continue;
272  // everything checks out; looks like an image header to me
273 
274 //+ (mb) decoding strategy modification
275  // Some zvi images have the following structure:
276  // ZVI_SIG Decoding:
277  // ZVI_MAGIC_BLOCK_1
278  // ZVI_MAGIC_BLOCK_2 <== Start of header information
279  // - Z-slice (4 bytes) -> theZ = 0
280  // - channel (4 bytes) -> theC = 0
281  // - timestep (4 bytes) -> theT = 0
282  // ZVI_MAGIC_BLOCK_2 <== Start of header information
283  // - Z-slice (4 bytes) -> theZ actual value
284  // - channel (4 bytes) -> theC actual value
285  // - timestep (4 bytes) -> theT actual value
286  // ZVI_MAGIC_BLOCK_3 <== End of header information
287  // ...
288  //
289  // Two consecutive Start of header information ZVI_MAGIC_BLOCK_2
290  // make test 3) of original decoding strategy fail. The first
291  // null values are taken as theZ, theC and theT values, the
292  // following actual values are ignored.
293  // Parsing the rest of the file appears to be ok.
294  //
295  // New decoding strategy looks for the last header information
296  // ZVI_MAGIC_BLOCK_2 / ZVI_MAGIC_BLOCK_3 to get proper image
297  // slice theZ, theC and theT values.
298 
299  //- original code removed
300  //- long magic3 = findBlock(in, ZVI_MAGIC_BLOCK_3, pos);
301  //- if (magic3 < 0) return null;
302  //- pos = magic3 + ZVI_MAGIC_BLOCK_3.length;
303  //-
304  //-
305  //+ new code
306  // these bytes don't matter
307  in.skipBytes(89);
308  pos += 89;
309 
310  byte[] magic3 = new byte[ZVI_MAGIC_BLOCK_3.length];
311  in.readFully(magic3);
312  for (int i=0; i<magic3.length; i++) {
313  if (magic3[i] != ZVI_MAGIC_BLOCK_3[i]) {
314  ok = false;
315  break;
316  }
317  }
318  if (!ok) continue;
319  pos += ZVI_MAGIC_BLOCK_3.length;
320 //- (mb)
321 
322  // read more header information
323  int w = readInt(in);
324  int h = readInt(in);
325  int alwaysOne = readInt(in); // don't know what this is for
326  int bytesPerPixel = readInt(in);
327  int pixelType = readInt(in); // not clear what this value signifies
328  int bitDepth = readInt(in); // doesn't always equal bytesPerPixel * 8
329  pos += 24;
330 
331  ZVIBlock zviBlock = new ZVIBlock(theZ, theC, theT,
332  w, h, alwaysOne, bytesPerPixel, pixelType, bitDepth, pos);
333  if (DEBUG) System.out.println(zviBlock);
334 //+ (mb)
335  //- original code removed
336  //- // perform some checks on the header info
337  //- if (theZ >= numZ) numZ = theZ + 1;
338  //- if (theC >= numC) numC = theC + 1;
339  //- if (theT >= numT) numT = theT + 1;
340  //+ new code
341  // populate Z, C and T index collections
342  Z_Set.add(new Integer(theZ));
343  C_Set.add(new Integer(theC));
344  T_Set.add(new Integer(theT));
345 //- (mb)
346  // save this image block's position
347  blockList.add(zviBlock);
348  pos += w * h * bytesPerPixel;
349  }
350 
351  if (blockList.isEmpty()) return null;
352 
353 //+ (mb)
354  //+ new code
355  // number of Z, C and T index
356  numZ = Z_Set.size();
357  numC = C_Set.size();
358  numT = T_Set.size();
359 //- (mb)
360 
361  if (numZ * numC * numT != blockList.size()) {
362  IJ.showMessage("ZVI Reader", "Warning: image counts do not match.");
363  }
364 
365  // convert ZVI blocks into single FileInfo object
366  FileInfo[] fi = new FileInfo[blockList.size()];
367  for (int i=0; i<fi.length; i++) {
368  ZVIBlock zviBlock = (ZVIBlock) blockList.elementAt(i);
369  int ft = -1;
370  if (zviBlock.numChannels == 1) {
371  if (zviBlock.bytesPerChannel == 1) ft = FileInfo.GRAY8;
372  else if (zviBlock.bytesPerChannel == 2) ft = FileInfo.GRAY16_UNSIGNED;
373  }
374  else if (zviBlock.numChannels == 3) {
375  if (zviBlock.bytesPerChannel == 1) ft = FileInfo.BGR;
376  else if (zviBlock.bytesPerChannel == 2) ft = FileInfo.RGB48;
377  }
378  if (ft < 0) {
379  IJ.showMessage("ZVI Reader",
380  "Warning: unknown file type for image plane #" + (i + 1));
381  ft = FileInfo.GRAY8; // better than nothing...
382  }
383  fi[i] = new FileInfo();
384  fi[i].fileFormat = FileInfo.RAW;
385  fi[i].fileName = fileName;
386  fi[i].directory = directory;
387  fi[i].nImages = 1;
388  fi[i].intelByteOrder = true;
389  fi[i].width = zviBlock.width;
390  fi[i].height = zviBlock.height;
391  fi[i].offset = (int) zviBlock.imagePos;
392  fi[i].fileType = ft;
393 //+ (mb)
394  //+ new code
395  // add Z, C and T index to file info.
396  fi[i].info = new String(zviBlock.theZ+"," +zviBlock.theC+"," +zviBlock.theT);
397 //- (mb)
398  }
399  return fi;
400  }
401 
406  private long findBlock(RandomAccessFile in, byte[] block, long start)
407  throws IOException
408  {
409  long filePos = start;
410  long fileSize = in.length();
411  byte[] buf = new byte[BUFFER_SIZE];
412  long spot = -1;
413  int step = 0;
414  boolean found = false;
415  in.seek(start);
416 
417  while (true) {
418  int len = (int) (fileSize - filePos);
419  if (len < 0) break;
420  if (len > buf.length) len = buf.length;
421  in.readFully(buf, 0, len);
422 
423  for (int i=0; i<len; i++) {
424  if (buf[i] == block[step]) {
425  if (step == 0) {
426  // could be a match; flag this spot
427  spot = filePos + i;
428  }
429  step++;
430  if (step == block.length) {
431  // found complete match; done searching
432  found = true;
433  break;
434  }
435  }
436  else {
437  // no match; reset step indicator
438  spot = -1;
439  step = 0;
440  }
441  }
442  if (found) break; // found a match; we're done
443  if (len < buf.length) break; // EOF reached; we're done
444 
445  filePos += len;
446  }
447 
448  // set file pointer to byte immediately following pattern
449  if (spot >= 0) in.seek(spot + block.length);
450 
451  return spot;
452  }
453 
455  private static int batoi(byte[] b) {
456  int len = b.length > 4 ? 4 : b.length;
457  int total = 0;
458  for (int i = 0; i < len; i++) {
459  int q = b[i] < 0 ? b[i] + 256 : b[i]; // convert to unsigned
460  int shift = 8 * i; // little endian
461  total += q << shift;
462  }
463  return total;
464  }
465 
467  private static int readInt(RandomAccessFile fin) throws IOException {
468  byte[] b = new byte[4];
469  fin.readFully(b);
470  return batoi(b);
471  }
472 
473 //+ (mb)
474  //+ new code
476  private static int getChannel(FileInfo theFi) {
477  StringTokenizer st = new StringTokenizer(theFi.info," ,");
478  int theZ = Integer.parseInt(st.nextToken()); // skip Z index
479  int theC = Integer.parseInt(st.nextToken());
480  // int theT = Integer.parseInt(st.nextToken());
481  return theC;
482  }
483 //- (mb)
484 
485 
486  // -- Helper classes --
487 
489  private class ZVIBlock {
490  private int theZ, theC, theT;
491  private int width, height;
492  private int alwaysOne;
493  private int bytesPerPixel;
494  private int pixelType;
495  private int bitDepth;
496  private long imagePos;
497 
498  private int numPixels;
499  private int imageSize;
500  private int numChannels;
501  private int bytesPerChannel;
502 
503  public ZVIBlock(int theZ, int theC, int theT, int width, int height,
504  int alwaysOne, int bytesPerPixel, int pixelType, int bitDepth,
505  long imagePos)
506  {
507  this.theZ = theZ;
508  this.theC = theC;
509  this.theT = theT;
510  this.width = width;
511  this.height = height;
512  this.alwaysOne = alwaysOne;
513  this.bytesPerPixel = bytesPerPixel;
514  this.pixelType = pixelType;
515  this.bitDepth = bitDepth;
516  this.imagePos = imagePos;
517 
518  numPixels = width * height;
519  imageSize = numPixels * bytesPerPixel;
520 
521  numChannels = 1;
522  // the second decision is redundant, but left there for further(?) pixel types
523  if ((pixelType == 1) | (pixelType == 8)) {
524  numChannels = 3;} // 1 and 8 are RGB 8-bit and 16-bit
525  else if ((pixelType == 3) | (pixelType == 4)) {
526  numChannels = 1;} // 3 and 4 are GRAY 8-bit and 16-bit
527 
528  if (bytesPerPixel % numChannels != 0) {
529  IJ.showMessage("ZVI Reader", "Warning: incompatible bytesPerPixel (" +
530  bytesPerPixel + ") and numChannels (" + numChannels +
531  "). Assuming grayscale data.");
532  numChannels = 1;
533  }
534  bytesPerChannel = bytesPerPixel / numChannels;
535 
536  // IJ.showMessage("ZVI Reader", "numChannels: " + numChannels + ", bytesPerPixel: " + bytesPerPixel + ", pixelType: " + pixelType + ", bitDepth: " + bitDepth + ", imagePos: " + imagePos);
537  }
538 
539  public String toString() {
540  return "Image header block:\n" +
541  " theZ = " + theZ + "\n" +
542  " theC = " + theC + "\n" +
543  " theT = " + theT + "\n" +
544  " width = " + width + "\n" +
545  " height = " + height + "\n" +
546  " alwaysOne = " + alwaysOne + "\n" +
547  " bytesPerPixel = " + bytesPerPixel + "\n" +
548  " pixelType = " + pixelType + "\n" +
549  " bitDepth = " + bitDepth;
550  }
551  }
552 
553 }
-
ZVI_Reader
Definition: ZVI_Reader.java:26
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ZVI_Reader.run
void run(String arg)
Definition: ZVI_Reader.java:66
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run(String arg)Averaging_Reducerinline
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shrink(ImageProcessor ip)Averaging_Reducerinline
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void run (String arg)
 
ImagePlus shrink (ImagePlus imp)
 
ImageProcessor shrink (ImageProcessor ip)
 
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Detailed Description

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Definition at line 8 of file Averaging_Reducer.java.

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void Averaging_Reducer.run (String arg)
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Definition at line 15 of file Averaging_Reducer.java.

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15  {
16  ImagePlus imp = IJ.getImage();
17  if (showDialog()) {
18  ImagePlus imp2 = shrink(imp);
19  imp2.show();
20  imp2.setSlice(imp2.getStackSize()/2);
21  imp2.getProcessor().resetMinAndMax();
22  }
23  }
Averaging_Reducer.shrink
ImagePlus shrink(ImagePlus imp)
Definition: Averaging_Reducer.java:25
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Definition at line 25 of file Averaging_Reducer.java.

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25  {
26  ImageStack stack1 = imp.getStack();
27  ImageStack stack2 = new ImageStack(imp.getWidth()/xshrink,imp.getHeight()/yshrink);
28  int n = stack1.getSize();
29  for (int i=1; i<=n; i++) {
30  IJ.showStatus(i+"/"+n);
31  IJ.showProgress(i, n);
32  ImageProcessor ip2 = shrink(stack1.getProcessor(i));
33  stack2.addSlice(null, ip2);
34  }
35  ImagePlus imp2 = new ImagePlus("Reduced "+imp.getShortTitle(), stack2);
36  imp2.setCalibration(imp.getCalibration());
37  Calibration cal2 = imp2.getCalibration();
38  if (cal2.scaled()) {
39  cal2.pixelWidth *= xshrink;
40  cal2.pixelHeight *= yshrink;
41  }
42  return imp2;
43  }
Averaging_Reducer.shrink
ImagePlus shrink(ImagePlus imp)
Definition: Averaging_Reducer.java:25
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Definition at line 45 of file Averaging_Reducer.java.

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45  {
46  if (ip instanceof FloatProcessor)
47  return shrinkFloat(ip);
48  samples = ip instanceof ColorProcessor?3:1;
49  int w = ip.getWidth()/xshrink;
50  int h = ip.getHeight()/yshrink;
51  ImageProcessor ip2 = ip.createProcessor(w, h);
52  for (int y=0; y<h; y++)
53  for (int x=0; x<w; x++)
54  ip2.putPixel(x, y, getAverage(ip, x, y));
55  return ip2;
56  }
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void run (String arg)
 
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Imports a Z series(image stack) from a Biorad MRC 600 confocal microscope. The width, height and number of images are extracted from the first 3 16-bit word in the 76 byte header. Use Image/Show Info to display the header information.

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See statements flagged // ghj 4/3/06 for modifications by "Greg Joss" gjoss.nosp@m.@bio.nosp@m..mq.e.nosp@m.du.a.nosp@m.u to open 16-bit little-endian (Intel) Biorad files from "Winnok De Vos (ir.)" winno.nosp@m.k.de.nosp@m.vos@u.nosp@m.gent.nosp@m..be some if (IJ.debugMode)IJ.log(statements were also added.

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Definition at line 22 of file Biorad_Reader.java.

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void Biorad_Reader.run (String arg)
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Definition at line 31 of file Biorad_Reader.java.

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31  {
32  OpenDialog od = new OpenDialog("Open Biorad...", arg);
33  directory = od.getDirectory();
34  fileName = od.getFileName();
35  if (fileName==null)
36  return;
37  IJ.showStatus("Opening: " + directory + fileName);
38  FileInfo fi = null;
39  try {fi = getHeaderInfo();}
40  catch (Exception e) {
41  IJ.showStatus("");
42  IJ.showMessage("BioradReader", ""+e);
43  return;
44  }
45  if (fi!=null) {
46 
47  if(fileName.toLowerCase().endsWith(".gz") && IJ.getVersion().compareTo("1.38s")<0) {
48  IJ.error("ImageJ 1.38s or later required to open gzipped Biorad PIC files");
49  return;
50  }
51 
52  FileOpener fo = new FileOpener(fi);
53  ImagePlus imp = fo.open(false);
54  if(IJ.debugMode)IJ.log("imp="+imp);
55  if (imp==null)
56  return;
57 
58  setStack(fileName, imp.getStack());
59  setFileInfo(fi);
60  if(IJ.debugMode) IJ.log("FileInfo="+fi);
61  try {
62  int pixelLength=1;
63  switch (fi.fileType) { // ghj 4/3/06
64  case FileInfo.GRAY8: pixelLength=1; break;
65  case FileInfo.GRAY16_UNSIGNED:pixelLength=2; break;
66  }
67  Calibration BioRadCal = getBioRadCalibration(fi.width, fi.height, fi.nImages, pixelLength); // ghj 4/3/0
68  setCalibration(BioRadCal);
69  } catch (Exception e) {
70  IJ.showStatus("");
71  String msg = e.getMessage();
72  if (e==null) msg = ""+e;
73  if (msg.indexOf("EOF")==-1)
74  IJ.showMessage("BioradReader", msg);
75  return;
76  }
77 
78  boolean hasLut = false;
79 
80  if (lutOffset!=-1) {
81  try {hasLut = getLut(fi);}
82  catch (Exception e) {
83  IJ.showStatus("");
84  IJ.showMessage("BioradReader",
85  "Can't read LUT from file because "+e);
86  hasLut = false;
87  }
88  }
89 
90  if (hasLut) {
91  ColorModel cm =
92  new IndexColorModel(8, 256, fi.reds, fi.greens, fi.blues);
93  getProcessor().setColorModel(cm);
94  getStack().setColorModel(cm);
95  }
96 
97  if (!notes.equals(""))
98  setProperty("Info", notes);
99  if(IJ.debugMode)IJ.log("arg=|"+arg+"|");
100  if (arg.equals("")) show();
101  }
102  if(IJ.debugMode)IJ.log("done");
103  }
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This is the complete list of members for Color_Transformer, including all inherited members.

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getAC1C2()Color_Transformerinline
getHSI()Color_Transformerinline
getHSL()Color_Transformerinline
getHSV()Color_Transformerinline
getI1I2I3()Color_Transformerinline
getLab()Color_Transformerinline
getLCHLab()Color_Transformerinline
getLCHLuv()Color_Transformerinline
getLSHLuv()Color_Transformerinline
getLuv()Color_Transformerinline
getXYZ()Color_Transformerinline
getYIQ()Color_Transformerinline
getYQ1Q2()Color_Transformerinline
getYUV()Color_Transformerinline
getYuv()Color_Transformerinline
getYxy()Color_Transformerinline
run(ImageProcessor ip)Color_Transformerinline
setup(String arg, ImagePlus imp)Color_Transformerinline
showDialog()Color_Transformerinline
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Color_Transformer Class Reference
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int setup (String arg, ImagePlus imp)
 
boolean showDialog ()
 
void run (ImageProcessor ip)
 
void getXYZ ()
 
void getYxy ()
 
void getYUV ()
 
void getYIQ ()
 
void getAC1C2 ()
 
void getLuv ()
 
void getLab ()
 
void getI1I2I3 ()
 
void getYuv ()
 
void getYQ1Q2 ()
 
void getHSI ()
 
void getHSL ()
 
void getHSV ()
 
void getLCHLuv ()
 
void getLSHLuv ()
 
void getLCHLab ()
 
-

Detailed Description

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Color_Transformer.java Converts an RGB colour image into a colour space represented by a stack

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Author
Maria E. Barilla-Perez
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-Birmingham University, United Kingdom
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-baril.nosp@m.lame.nosp@m.@yaho.nosp@m.o.co.nosp@m..uk and perez.nosp@m.m@ee.nosp@m.e.bha.nosp@m.m.ac.nosp@m..uk
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Version
1.0
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WAHeeschen modifications(2013-Feb-14): The conversion to L*a*b* was missing a step. The XYZ space calculation generates an output that is nominally based on values of 100, but the L*a*b* algorithm assumes that the XYZ values have been normalized by a white reference. The white reference is dependent on the color temperature (D50, D65, etc.). I decided to use the D65 white reference from the ImageJ plugin called Color_Space_Converter: Xref=95.0429 Yref=100.0 Zref=108.8900 I updated both of the converters that generate an L*a*b* value: getLAB() and getLCHLab() I added comments related to these edits that include my initials: WAH A couple of references: http://www.brucelindbloom.com/ http://www.easyrgb.com/ The results match those obtained with Color_Space_Converter for D65 white point. Results are similar to FIJI output.

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Definition at line 32 of file Color_Transformer.java.

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Member Function Documentation

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◆ getAC1C2()

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void Color_Transformer.getAC1C2 ()
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Definition at line 320 of file Color_Transformer.java.

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320  {
321  //@ARTICLE{FaugerasO79:art,
322  // author = {O. Faugeras},
323  // title = {Digital color image processing within the framework of a human visual model},
324  // journal = {IEEE Transactions on Acoustics, Speech, and Signal Processing},
325  // year = {1979},
326  // volume = {27},
327  // pages = {380- 393},
328  // number = {4},
329  // month = {August},
330  //}
331  for(int q=0; q<size; q++){
332  float L, M, S;
333  float A, C1, C2;
334  L = 0.3634f * rf[q] + 0.6102f * gf[q] + 0.0264f * bf[q];
335  M = 0.1246f * rf[q] + 0.8138f * gf[q] + 0.0616f * bf[q];
336  S = 0.0009f * rf[q] + 0.0602f * gf[q] + 0.9389f * bf[q];
337 
338  L = new Double(Math.log(L)).floatValue();
339  M = new Double(Math.log(M)).floatValue();
340  S = new Double(Math.log(S)).floatValue();
341 
342  A = 13.8312f * L + 8.3394f * M + 0.4294f * S;
343  C1 = 64.0000f * L - 64.000f * M + 0.0000f * S;
344  C2 = 10.0000f * L + 0.0000f * M - 10.000f * S;
345 
346  c1[q] = A;
347  c2[q] = C1;
348  c3[q] = C2;
349  }
350  }
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◆ getHSI()

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void Color_Transformer.getHSI ()
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Definition at line 542 of file Color_Transformer.java.

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542  {
543  // @BOOK{MalacaraD01:book,
544  // title = {Color Vision and Colorimetry, Theory and Applications},
545  // publisher = {SPIE International Society for Optical Engineering},
546  // year = {2001},
547  // author = {D. Malacara},
548  // address = {Bellingham, Washington USA},
549  //}
550  for(int q=0; q<size; q++){
551  float var_Min = Math.min(rf[q], gf[q]); //Min. value of RGB
552  var_Min = Math.min(var_Min, bf[q]);
553  float var_Max = Math.max(rf[q], gf[q]); //Max. value of RGB
554  var_Max = Math.max(var_Max, bf[q]);
555  float del_Max = var_Max - var_Min; //Delta RGB value
556 
557  c3[q] = (rf[q] + gf[q] + bf[q])/3f;
558 
559  if ( del_Max == 0f ){ //This is a gray, no chroma...
560  c1[q] = 0f; //HSL results = 0 � 1
561  c2[q] = 0f;
562  }
563  else{ //Chromatic data...
564  c2[q] = 1 - (var_Min / c3[q]);
565 
566  float del_R = ( ( ( var_Max - rf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
567  float del_G = ( ( ( var_Max - gf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
568  float del_B = ( ( ( var_Max - bf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
569 
570  if ( rf[q] == var_Max ) c1[q] = del_B - del_G;
571  else if ( gf[q] == var_Max ) c1[q] = ( 1f / 3f ) + del_R - del_B;
572  else if ( bf[q] == var_Max ) c1[q] = ( 2f / 3f ) + del_G - del_R;
573 
574  if ( c1[q] < 0 ) c1[q] += 1;
575  if ( c1[q] > 1 ) c1[q] -= 1;
576  }
577  }
578  }
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◆ getHSL()

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void Color_Transformer.getHSL ()
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Definition at line 580 of file Color_Transformer.java.

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580  {
581  // http://www.easyrgb.com/math.html
582  for(int q=0; q<size; q++){
583  float H=0, S=0, L=0;
584  float var_Min = Math.min(rf[q], gf[q]); //Min. value of RGB
585  var_Min = Math.min(var_Min, bf[q]);
586  float var_Max = Math.max(rf[q], gf[q]); //Max. value of RGB
587  var_Max = Math.max(var_Max, bf[q]);
588  float del_Max = var_Max - var_Min; //Delta RGB value
589 
590  L = (var_Max + var_Min)/2;
591 
592  if ( del_Max == 0f){ //This is a gray, no chroma...
593  H = 0f; //HSL results = 0 � 1
594  S = 0f;
595  }
596  else{ //Chromatic data...
597  if ( L < 0.5f ) S = del_Max / ( var_Max + var_Min );
598  else S = del_Max / ( 2f - var_Max - var_Min );
599 
600  float del_R = ( ( ( var_Max - rf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
601  float del_G = ( ( ( var_Max - gf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
602  float del_B = ( ( ( var_Max - bf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
603 
604  if ( rf[q] == var_Max ) H = del_B - del_G;
605  else if ( gf[q] == var_Max ) H = ( 1f / 3f ) + del_R - del_B;
606  else if ( bf[q] == var_Max ) H = ( 2f / 3f ) + del_G - del_R;
607 
608  if ( H < 0f ) H += 1f;
609  if ( H > 1f ) H -= 1f;
610  }
611  c1[q] = H;
612  c2[q] = S;
613  c3[q] = L;
614  }
615  }
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◆ getHSV()

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void Color_Transformer.getHSV ()
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Definition at line 617 of file Color_Transformer.java.

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617  { // HSV_Stack Plugin (HSV colour space is also known as HSB where B means brightness)
618  // http://www.easyrgb.com/math.html
619  for(int q=0; q<size; q++){ // http://www.easyrgb.com/
620  float H=0, S=0, V=0;
621  float var_Min = Math.min(rf[q], gf[q]); //Min. value of RGB
622  var_Min = Math.min(var_Min, bf[q]);
623  float var_Max = Math.max(rf[q], gf[q]); //Max. value of RGB
624  var_Max = Math.max(var_Max, bf[q]);
625  float del_Max = var_Max - var_Min; //Delta RGB value
626 
627  V = var_Max*1f;
628  if ( del_Max == 0 ){ //This is a gray, no chroma...
629  H = 0f; //HSV results = 0 � 1
630  S = 0f;
631  }
632  else{ //Chromatic data...
633  S = del_Max / var_Max;
634  float del_R = ( ( ( var_Max - rf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
635  float del_G = ( ( ( var_Max - gf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
636  float del_B = ( ( ( var_Max - bf[q] ) / 6f ) + ( del_Max / 2f ) ) / del_Max;
637 
638  if ( rf[q] == var_Max ) H = del_B - del_G;
639  else if ( gf[q] == var_Max ) H = ( 1f / 3f ) + del_R - del_B;
640  else if ( bf[q] == var_Max ) H = ( 2f / 3f ) + del_G - del_R;
641 
642  if ( H < 0 ) H += 1;
643  if ( H > 1 ) H -= 1;
644  }
645  c1[q] = H;
646  c2[q] = S;
647  c3[q] = V;
648  }
649 
650  }
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Definition at line 472 of file Color_Transformer.java.

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472  {
473  // @ARTICLE{Ohta80:art,
474  // author = {Y. Ohta and T. Kanade and T. Sakai},
475  // title = {Color Information for Region Segmentation},
476  // journal = {Computer Graphics and Image Processing},
477  // year = {1980},
478  // volume = {13},
479  // pages = {222 - 241},
480  // number = {3},
481  // month = {July},
482  //}
483  for(int q=0; q<size; q++){
484  float I1 = (rf[q] + gf[q] + bf[q])/3f;
485  float I2 = (rf[q] - bf[q])/2f;
486  float I3 = (2f * gf[q] - rf[q] - bf[q])/4f;
487  c1[q] = I1;
488  c2[q] = I2;
489  c3[q] = I3;
490  }
491  }
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◆ getLab()

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Definition at line 412 of file Color_Transformer.java.

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412  {
413  // http://www.easyrgb.com/math.html AND
414  // @INBOOK{RonnierLuoM98colour:chapterbook,
415  // chapter = {Colour science},
416  // pages = {27-65},
417  // title = {The Colour Image Processing Handbook},
418  // publisher = {Springer},
419  // year = {1998},
420  // editor = {R. E.N. Horne},
421  // author = {Ronnier Luo},
422  //}
423  for(int q=0; q<size; q++){
424  float l, a, b;
425  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055f)/1.055f)*2.4f))).floatValue():rf[q]/12.92f;
426  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055f)/1.055f)*2.4f))).floatValue():gf[q]/12.92f;
427  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055f)/1.055f)*2.4f))).floatValue():bf[q]/12.92f;
428 
429  rf[q] = rf[q] * 100f;
430  gf[q] = gf[q] * 100f;
431  bf[q] = bf[q] * 100f;
432 
433  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
434  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
435  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
436 
437  // XYZ to Lab
438  float fX, fY, fZ;
439  float La, aa, bb;
440  //WAH normalize to L*a*b* color space using D65 white reference
441  // from Color_Space_Converter code: public double[] D65 = {95.0429, 100.0, 108.8900};
442 
443  X = X / 95.0429f;
444  Y = Y / 100.0f;
445  Z = Z / 108.89f;
446 
447  if ( X > 0.008856f )
448  fX = (new Double(Math.exp(Math.log(X)/3f))).floatValue();
449  else
450  fX = ((7.787f * X) + (16f/116f));
451 
452  if ( Y > 0.008856f )
453  fY = (new Double(Math.exp(Math.log(Y)/3f))).floatValue();
454  else
455  fY = ((7.787f * Y) + (16f/116f));
456 
457  if ( Z > 0.008856f )
458  fZ = (new Double(Math.exp(Math.log(Z)/3f))).floatValue();
459  else
460  fZ = ((7.787f * Z) + (16f/116f));
461 
462  l = ( 116f * fY ) - 16f;
463  a = 500f * ( fX - fY );
464  b = 200f * ( fY - fZ );
465 
466  c1[q] = l;
467  c2[q] = a;
468  c3[q] = b;
469  }
470  }
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Definition at line 790 of file Color_Transformer.java.

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790  {
791  // @BOOK{MalacaraD01:book,
792  // title = {Color Vision and Colorimetry, Theory and Applications},
793  // publisher = {SPIE International Society for Optical Engineering},
794  // year = {2001},
795  // author = {D. Malacara},
796  // address = {Bellingham, Washington USA},
797  //}
798  for(int q=0; q<size; q++){
799  float L=0f, C=0f, H=0f;
800  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055f)/1.055f)*2.4f))).floatValue():rf[q]/12.92f;
801  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055f)/1.055f)*2.4f))).floatValue():gf[q]/12.92f;
802  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055f)/1.055f)*2.4f))).floatValue():bf[q]/12.92f;
803 
804  rf[q] = rf[q] * 100f;
805  gf[q] = gf[q] * 100f;
806  bf[q] = bf[q] * 100f;
807 
808  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
809  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
810  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
811 
812  float fX, fY, fZ;
813  // XYZ to Lab
814  //WAH normalize to L*a*b* color space using D65 white reference
815  // from Color_Space_Converter code: public double[] D65 = {95.0429, 100.0, 108.8900};
816 
817  X = X / 95.0429f;
818  Y = Y / 100.0f;
819  Z = Z / 108.89f;
820 
821  if ( X > 0.008856f )
822  fX = (new Double(Math.exp(Math.log(X)/3f))).floatValue();
823  else
824  fX = ((7.787f * X) + (16f/116f));
825 
826  if ( Y > 0.008856f )
827  fY = (new Double(Math.exp(Math.log(Y)/3f))).floatValue();
828  else
829  fY = ((7.787f * Y) + (16f/116f));
830 
831  if ( Z > 0.008856f )
832  fZ = (new Double(Math.exp(Math.log(Z)/3f))).floatValue();
833  else
834  fZ = ((7.787f * Z) + (16f/116f));
835 
836  float l = ( 116f * fY ) - 16f;
837  float a = 500f * ( fX - fY );
838  float b = 200f * ( fY - fZ );
839 
840  L = l;
841  C = new Double(Math.sqrt((a*a)+(b*b))).floatValue();
842 
843  if ( a == 0f ){ //This is a gray, no chroma...
844  H = 0f; //LCH results = 0 � 1
845  }
846  else{
847  if (a>=0f && b>=0f) H = new Double(Math.atan(b/a)).floatValue();
848  else if (a>=0f && b<0f) H = new Double(Math.atan(b/a) + Math.PI).floatValue();
849  else if (a<0f && b<0f) H = new Double(Math.atan(b/a) + Math.PI).floatValue();
850  else if (a<0f && b>=0f) H = new Double(Math.atan(b/a) + (2*Math.PI)).floatValue();
851  }
852  c1[q] = L;
853  c2[q] = C;
854  c3[q] = H;
855  }
856  }
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un' corresponding to Yn

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vn' corresponding to Yn

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Definition at line 652 of file Color_Transformer.java.

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652  {
653  // @BOOK{MalacaraD01:book,
654  // title = {Color Vision and Colorimetry, Theory and Applications},
655  // publisher = {SPIE International Society for Optical Engineering},
656  // year = {2001},
657  // author = {D. Malacara},
658  // address = {Bellingham, Washington USA},
659  //}
661  //X = 95.047, Y = 100.0, Z = 108.883;
662  float yn = 1f;
663 
665  // un' = 4X/(X + 15Y + 3Z)
666  float unp = 0.19784f;
667 
669  // vn = 9Y/(X + 15Y + 3Z)
670  float vnp = 0.4683f;
671 
672  for(int q=0; q<size; q++){
673  float L=0f, C=0f, H=0f;
674  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
675  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
676  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
677 
678  rf[q] = rf[q] * 100f;
679  gf[q] = gf[q] * 100f;
680  bf[q] = bf[q] * 100f;
681 
682  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
683  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
684  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
685 
686  // As yn = 1.0, we will just consider Y value as yyn
687  //yyn = (Y/yn);
688  float f_yyn = Y / 100f;
689 
690  if (f_yyn > 0.008856f) {
691  f_yyn=new Double(Math.exp(Math.log(f_yyn)/3f)).floatValue();
692  } else {
693  f_yyn = ((7.787f * f_yyn) + (16f/116f));
694  }
695 
696  float up = (X == 0f && Y == 0f && Z == 0f)? 0f : (4f*X / ((X + 15f*Y + 3f*Z)));
697  float vp = (X == 0f && Y == 0f && Z == 0f)? 0f : (9f*Y / ((X + 15f*Y + 3f*Z)));
698 
699  float l = (116f *f_yyn)-16f;
700  float u = 13f * l * (up - unp);
701  float v = 13f * l * (vp - vnp);
702 
703  L = l;
704  C = new Double(Math.sqrt((u*u)+(v*v))).floatValue();
705 
706  if ( u == 0 ){ //This is a gray, no chroma...
707  H = 0f; //LCH results = 0 � 1
708  }
709  else{
710  if (u>=0f && v>=0f) H = new Double(Math.atan(v/u)).floatValue();
711  else if (u>=0f && v<0f) H = new Double(Math.atan(v/u) + Math.PI).floatValue();
712  else if (u<0f && v<0f) H = new Double(Math.atan(v/u) + Math.PI).floatValue();
713  else if (u<0f && v>=0f) H = new Double(Math.atan(v/u) + (2*Math.PI)).floatValue();
714  }
715  c1[q] = L;
716  c2[q] = C;
717  c3[q] = H;
718  }
719  }
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◆ getLSHLuv()

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void Color_Transformer.getLSHLuv ()
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-
-

Illuminant = D65

-

un' corresponding to Yn

-

vn' corresponding to Yn

- -

Definition at line 721 of file Color_Transformer.java.

-
721  {
722  // @BOOK{MalacaraD01:book,
723  // title = {Color Vision and Colorimetry, Theory and Applications},
724  // publisher = {SPIE International Society for Optical Engineering},
725  // year = {2001},
726  // author = {D. Malacara},
727  // address = {Bellingham, Washington USA},
728  //}
730  //X = 95.047, Y = 100.0, Z = 108.883;
731  float yn = 1f;
732 
734  // un' = 4X/(X + 15Y + 3Z)
735  float unp = 0.19784f;
736 
738  // vn = 9Y/(X + 15Y + 3Z)
739  float vnp = 0.4683f;
740 
741  for(int q=0; q<size; q++){
742  float L=0f, S=0f, H=0f;
743  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
744  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
745  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
746 
747  rf[q] = rf[q] * 100f;
748  gf[q] = gf[q] * 100f;
749  bf[q] = bf[q] * 100f;
750 
751  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
752  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
753  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
754 
755  // As yn = 1.0, we will just consider Y value as yyn
756  //yyn = (Y/yn);
757  float f_yyn = Y / 100f;
758 
759  if (f_yyn > 0.008856f) {
760  f_yyn=new Double(Math.exp(Math.log(f_yyn)/3f)).floatValue();
761  } else {
762  f_yyn = ((7.787f * f_yyn) + (16f/116f));
763  }
764 
765  float up = (X == 0f && Y == 0f && Z == 0f)? 0f : (4f*X / ((X + 15f*Y + 3f*Z)));
766  float vp = (X == 0f && Y == 0f && Z == 0f)? 0f : (9f*Y / ((X + 15f*Y + 3f*Z)));
767 
768  float l = (116f *f_yyn)-16f;
769  float u = 13f * l * (up - unp);
770  float v = 13f * l * (vp - vnp);
771 
772  L = l;
773  S = (new Double(13*Math.sqrt(((u-up)*(u-up))+((v-vp)*(v-vp))))).floatValue();
774 
775  if ( u == 0 ){ //This is a gray, no chroma...
776  H = 0f; //LCH results = 0 � 1
777  }
778  else{
779  if (u>=0f && v>=0f) H = new Double(Math.atan(v/u)).floatValue();
780  else if (u>=0f && v<0f) H = new Double(Math.atan(v/u) + Math.PI).floatValue();
781  else if (u<0f && v<0f) H = new Double(Math.atan(v/u) + Math.PI).floatValue();
782  else if (u<0f && v>=0f) H = new Double(Math.atan(v/u) + (2*Math.PI)).floatValue();
783  }
784  c1[q] = L;
785  c2[q] = S;
786  c3[q] = H;
787  }
788  }
-
-
- -

◆ getLuv()

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void Color_Transformer.getLuv ()
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-
-

Illuminant = D65

-

un' corresponding to Yn

-

vn' corresponding to Yn

- -

Definition at line 352 of file Color_Transformer.java.

-
352  {
353  // http://www.easyrgb.com/math.html AND
354  // @INBOOK{RonnierLuoM98colour:chapterbook,
355  // chapter = {Colour science},
356  // pages = {27-65},
357  // title = {The Colour Image Processing Handbook},
358  // publisher = {Springer},
359  // year = {1998},
360  // editor = {R. E.N. Horne},
361  // author = {Ronnier Luo},
362  //}
363 
365  //X = 95.047, Y = 100.0, Z = 108.883;
366  float yn = 1f;
367 
369  // un' = 4X/(X + 15Y + 3Z)
370  float unp = 0.19784f;
371 
373  // vn = 9Y/(X + 15Y + 3Z)
374  float vnp = 0.4683f;
375 
376  for(int q=0; q<size; q++){
377  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
378  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
379  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
380 
381  rf[q] = rf[q] * 100f;
382  gf[q] = gf[q] * 100f;
383  bf[q] = bf[q] * 100f;
384 
385  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
386  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
387  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
388 
389  // As yn = 1.0, we will just consider Y value as yyn
390  //yyn = (Y/yn);
391  float f_yyn = Y / 100f;
392 
393  if (f_yyn > 0.008856f) {
394  f_yyn=new Double(Math.exp(Math.log(f_yyn)/3f)).floatValue();
395  } else {
396  f_yyn = ((7.787f * f_yyn) + (16f/116f));
397  }
398 
399  float up = (X == 0f && Y == 0f && Z == 0f)? 0f : (4f*X / ((X + 15f*Y + 3f*Z)));
400  float vp = (X == 0f && Y == 0f && Z == 0f)? 0f : (9f*Y / ((X + 15f*Y + 3f*Z)));
401 
402  float l = (116f *f_yyn)-16f;
403  float u = 13f * l * (up - unp);
404  float v = 13f * l * (vp - vnp);
405 
406  c1[q] = l;
407  c2[q] = u;
408  c3[q] = v;
409  }
410  }
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◆ getXYZ()

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void Color_Transformer.getXYZ ()
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-
- -

Definition at line 224 of file Color_Transformer.java.

-
224  {
225  // http://www.easyrgb.com/math.html
226  for(int q=0; q<size; q++){
227  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
228  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
229  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
230 
231  rf[q] = rf[q] * 100f;
232  gf[q] = gf[q] * 100f;
233  bf[q] = bf[q] * 100f;
234 //WAH - these are the D65 values per BruceLindbloom, so I decided to stick with D65
235  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
236  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
237  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
238 
239  c1[q] = X;
240  c2[q] = Y;
241  c3[q] = Z;
242  }
243  }
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◆ getYIQ()

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void Color_Transformer.getYIQ ()
- 		-inline
-
- -

Definition at line 299 of file Color_Transformer.java.

-
299  {
300  //@ARTICLE{ChengHD00:art,
301  // author = {H.D. Cheng and X.H. Jiang and Y. Sun and J.L. Wang},
302  // title = {Color Image Segmentation: Advances and Prospects},
303  // journal = {Pattern Recognition},
304  // year = {2000},
305  // volume = {34},
306  // pages = {2259-2281},
307  // month = {September},
308  //}
309  for(int q=0; q<size; q++){
310  float Y = 0.299f * rf[q] + 0.587f * gf[q] + 0.114f * bf[q];
311  float I = 0.596f * rf[q] - 0.274f * gf[q] - 0.322f * bf[q];
312  float Q = 0.211f * rf[q] - 0.253f * gf[q] - 0.312f * bf[q];
313 
314  c1[q] = Y;
315  c2[q] = I;
316  c3[q] = Q;
317  }
318  }
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◆ getYQ1Q2()

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void Color_Transformer.getYQ1Q2 ()
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Definition at line 521 of file Color_Transformer.java.

-
521  {
522  // @ARTICLE{LittmanE97colour:art,
523  // author = {E. Littmann and H. Ritter},
524  // title = {Adaptive Color Segmentation - A comparison of Neural and Statistical Methods},
525  // journal = {IEEE Transactions on neural networks},
526  // year = {1997},
527  // volume = {8},
528  // pages = {175-185},
529  // number = {1},
530  // month = {January},
531  //}
532  for(int q=0; q<size; q++){
533  float Y = (rf[q] + gf[q] + bf[q])/3f;
534  float Q1 = ((rf[q] + gf[q]) != 0f)?rf[q]/(rf[q] + gf[q]):0f;
535  float Q2 = ((rf[q] + bf[q]) != 0f)?rf[q]/(rf[q] + bf[q]):0f;
536  c1[q] = Y;
537  c2[q] = Q1;
538  c3[q] = Q2;
539  }
540  }
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◆ getYUV()

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void Color_Transformer.getYUV ()
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Definition at line 278 of file Color_Transformer.java.

-
278  {
279  //@ARTICLE{ChengHD00:art,
280  // author = {H.D. Cheng and X.H. Jiang and Y. Sun and J.L. Wang},
281  // title = {Color Image Segmentation: Advances and Prospects},
282  // journal = {Pattern Recognition},
283  // year = {2000},
284  // volume = {34},
285  // pages = {2259-2281},
286  // month = {September},
287  //}
288  for(int q=0; q<size; q++){
289  float Y = 0.299f * rf[q] + 0.587f * gf[q] + 0.114f * bf[q];
290  float U = -0.147f * rf[q] - 0.289f * gf[q] + 0.437f * bf[q];
291  float V = 0.615f * rf[q] - 0.515f * gf[q] - 0.100f * bf[q];
292 
293  c1[q] = Y;
294  c2[q] = U;
295  c3[q] = V;
296  }
297  }
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◆ getYuv()

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void Color_Transformer.getYuv ()
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Definition at line 493 of file Color_Transformer.java.

-
493  {
494  // @ARTICLE{LittmanE97colour:art,
495  // author = {E. Littmann and H. Ritter},
496  // title = {Adaptive Color Segmentation - A comparison of Neural and Statistical Methods},
497  // journal = {IEEE Transactions on neural networks},
498  // year = {1997},
499  // volume = {8},
500  // pages = {175-185},
501  // number = {1},
502  // month = {January},
503  //}
504  for(int q=0; q<size; q++){
505  float u, v;
506  float Y = (rf[q] + gf[q] + bf[q])/3f;
507  if(Y != 0f){
508  u = 3f*(rf[q] - bf[q])/2f*Y;
509  v = (new Double(Math.sqrt(3.0)).floatValue())*(2f * gf[q] - rf[q] - bf[q])/2f*Y;
510  }
511  else{
512  u = 0f;
513  v = 0f;
514  }
515  c1[q] = Y;
516  c2[q] = u;
517  c3[q] = v;
518  }
519  }
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◆ getYxy()

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void Color_Transformer.getYxy ()
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Definition at line 245 of file Color_Transformer.java.

-
245  {
246  // @ARTICLE{TrussellHJ95colour:art,
247  // author = {H. J. Trussell and E. Saber and M. Vrhel},
248  // title = {Color image processing [basics and special issue overview]},
249  // journal = {IEEE Signal Processing Magazine},
250  // year = {2005},
251  // volume = {22},
252  // pages = {14 - 22},
253  // number = {1},
254  // month = {January},
255  //}
256  for(int q=0; q<size; q++){
257  rf[q] = (rf[q] > 0.04045f)?(new Double(Math.exp(Math.log((rf[q]+0.055)/1.055)*2.4))).floatValue():rf[q]/12.92f;
258  gf[q] = (gf[q] > 0.04045f)?(new Double(Math.exp(Math.log((gf[q]+0.055)/1.055)*2.4))).floatValue():gf[q]/12.92f;
259  bf[q] = (bf[q] > 0.04045f)?(new Double(Math.exp(Math.log((bf[q]+0.055)/1.055)*2.4))).floatValue():bf[q]/12.92f;
260 
261  rf[q] = rf[q] * 100f;
262  gf[q] = gf[q] * 100f;
263  bf[q] = bf[q] * 100f;
264 
265  float X = 0.4124f * rf[q] + 0.3576f * gf[q] + 0.1805f * bf[q];
266  float Y = 0.2126f * rf[q] + 0.7152f * gf[q] + 0.0722f * bf[q];
267  float Z = 0.0193f * rf[q] + 0.1192f * gf[q] + 0.9505f * bf[q];
268 
269  float xx = (X == 0f && Y == 0f && Z == 0f)? 0f : (X / ((X + Y + Z)));
270  float yy = (X == 0f && Y == 0f && Z == 0f)? 0f : (Y / ((X + Y + Z)));
271 
272  c1[q] = Y;
273  c2[q] = xx;
274  c3[q] = yy;
275  }
276  }
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◆ run()

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void Color_Transformer.run (ImageProcessor ip)
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Definition at line 78 of file Color_Transformer.java.

-
78  {
79  if (!showDialog())
80  return;
81  int offset, i;
82  width = ip.getWidth();
83  height = ip.getHeight();
84  size = width*height;
85  c1 = new float[size];
86  c2 = new float[size];
87  c3 = new float[size];
88  rf = new float[size];
89  gf = new float[size];
90  bf = new float[size];
91  for (int row = 0; row < height; row++){
92  offset = row*width;
93  for (int col = 0; col < width; col++) {
94  i = offset + col;
95  int c = ip.getPixel(col, row);
96  rf[i] = ((c&0xff0000)>>16)/255f; //R 0..1
97  gf[i] = ((c&0x00ff00)>>8)/255f; //G 0..1
98  bf[i] = (c&0x0000ff)/255f; //B 0..1
99  }
100  }
101 
102  if(colourspace.equals("XYZ")){
103  n1 = "X";
104  n2 = "Y";
105  n3 = "Z";
106  getXYZ();
107  }
108  if(colourspace.equals("Yxy")){
109  n1 = "Y";
110  n2 = "x";
111  n3 = "y";
112  getYxy();
113  }
114  if(colourspace.equals("YUV")){
115  n1 = "Y";
116  n2 = "U";
117  n3 = "V";
118  getYUV();
119  }
120  if(colourspace.equals("YIQ")){
121  n1 = "Y";
122  n2 = "I";
123  n3 = "Q";
124  getYIQ();
125  }
126  if(colourspace.equals("AC1C2")){
127  n1 = "A";
128  n2 = "C1";
129  n3 = "C2";
130  getAC1C2();
131  }
132  if(colourspace.equals("Luv")){
133  n1 = "L";
134  n2 = "u";
135  n3 = "v";
136  getLuv();
137  }
138  if(colourspace.equals("Lab")){
139  n1 = "L";
140  n2 = "a";
141  n3 = "b";
142  getLab();
143  }
144  if(colourspace.equals("I1I2I3")){
145  n1 = "I1";
146  n2 = "I2";
147  n3 = "I3";
148  getI1I2I3();
149  }
150  if(colourspace.equals("Yuv")){
151  n1 = "Y";
152  n2 = "u";
153  n3 = "v";
154  getYuv();
155  }
156  if(colourspace.equals("YQ1Q2")){
157  n1 = "Y";
158  n2 = "Q1";
159  n3 = "Q2";
160  getYQ1Q2();
161  }
162  if(colourspace.equals("HSI")){
163  n1 = "I";
164  n2 = "H";
165  n3 = "S";
166  getHSI();
167  }
168  if(colourspace.equals("HSV")){
169  n1 = "V";
170  n2 = "H";
171  n3 = "S";
172  getHSV();
173  }
174  if(colourspace.equals("HSL")){
175  n1 = "L";
176  n2 = "H";
177  n3 = "S";
178  getHSL();
179  }
180  if(colourspace.equals("LCHLuv")){
181  n1 = "L";
182  n2 = "H";
183  n3 = "C";
184  getLCHLuv();
185  }
186  if(colourspace.equals("LSHLuv")){
187  n1 = "L";
188  n2 = "H";
189  n3 = "S";
190  getLSHLuv();
191  }
192  if(colourspace.equals("LSHLab")){
193  n1 = "L";
194  n2 = "H";
195  n3 = "S";
196  getLCHLab();
197  }
198 
199  title = imp.getTitle();
200  sstack=new ImageStack(width,height); // Create new float stack for output
201 
202  ImagePlus imc1=NewImage.createFloatImage(n1,width,height,1,NewImage.FILL_BLACK);
203  ImageProcessor ipc1=imc1.getProcessor();
204  ipc1.setPixels(c1);
205  sstack.addSlice(n1,ipc1);
206 
207  ImagePlus imc2=NewImage.createFloatImage(n2,width,height,1,NewImage.FILL_BLACK);
208  ImageProcessor ipc2=imc2.getProcessor();
209  ipc2.setPixels(c2);
210  sstack.addSlice(n2,ipc2);
211 
212  ImagePlus imc3=NewImage.createFloatImage(n3,width,height,1,NewImage.FILL_BLACK);
213  ImageProcessor ipc3=imc3.getProcessor();
214  ipc3.setPixels(c3);
215  sstack.addSlice(n3,ipc3);
216 
217  ImagePlus imluv=new ImagePlus(colourspace,sstack);
218  imluv.show();
219  IJ.resetMinAndMax();
220 
221  }
Color_Transformer.getXYZ
void getXYZ()
Definition: Color_Transformer.java:224
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Color_Transformer.getLab
void getLab()
Definition: Color_Transformer.java:412
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Color_Transformer.getLCHLuv
void getLCHLuv()
Definition: Color_Transformer.java:652
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Color_Transformer.getLSHLuv
void getLSHLuv()
Definition: Color_Transformer.java:721
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Color_Transformer.getAC1C2
void getAC1C2()
Definition: Color_Transformer.java:320
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Color_Transformer.getYxy
void getYxy()
Definition: Color_Transformer.java:245
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Color_Transformer.getLCHLab
void getLCHLab()
Definition: Color_Transformer.java:790
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Color_Transformer.getYuv
void getYuv()
Definition: Color_Transformer.java:493
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Color_Transformer.getYIQ
void getYIQ()
Definition: Color_Transformer.java:299
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Color_Transformer.getHSV
void getHSV()
Definition: Color_Transformer.java:617
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Color_Transformer.showDialog
boolean showDialog()
Definition: Color_Transformer.java:52
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Color_Transformer.getI1I2I3
void getI1I2I3()
Definition: Color_Transformer.java:472
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Color_Transformer.getYUV
void getYUV()
Definition: Color_Transformer.java:278
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Color_Transformer.getYQ1Q2
void getYQ1Q2()
Definition: Color_Transformer.java:521
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Color_Transformer.getHSL
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Definition: Color_Transformer.java:580
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Color_Transformer.getHSI
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Definition: Color_Transformer.java:542
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Definition: Color_Transformer.java:352
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Definition at line 45 of file Color_Transformer.java.

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45  {
46  this.imp = imp;
47  if (arg.equals("about"))
48  {showAbout(); return DONE;}
49  return DOES_ALL;
50  }
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Definition at line 52 of file Color_Transformer.java.

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52  {
53  String[] colourspaces = {"XYZ",
54  "Yxy",
55  "YUV",
56  "YIQ",
57  "Luv",
58  "Lab",
59  "AC1C2",
60  "I1I2I3",
61  "Yuv",
62  "YQ1Q2",
63  "HSI",
64  "HSV",
65  "HSL",
66  "LCHLuv",
67  "LSHLuv",
68  "LSHLab"};
69  GenericDialog gd = new GenericDialog("Colour Transform");
70  gd.addChoice("Colour space:", colourspaces, colourspaces[0]);
71  gd.showDialog();
72  if (gd.wasCanceled())
73  return false;
74  colourspace = colourspaces[gd.getNextChoiceIndex()];
75  return true;
76  }
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- - diff --git a/html/classColor__Transformer__coll__graph.dot b/html/classColor__Transformer__coll__graph.dot deleted file mode 100644 index 8b7c6b09..00000000 --- a/html/classColor__Transformer__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Color_Transformer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="Color_Transformer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="PlugInFilter",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classColor__Transformer__coll__graph.md5 b/html/classColor__Transformer__coll__graph.md5 deleted file mode 100644 index 2f676962..00000000 --- a/html/classColor__Transformer__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -074042f8136056aa06ed25177ec60692 \ No newline at end of file diff --git a/html/classColor__Transformer__inherit__graph.dot b/html/classColor__Transformer__inherit__graph.dot deleted file mode 100644 index 33035dc6..00000000 --- a/html/classColor__Transformer__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Color_Transformer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="Color_Transformer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugInFilter",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classColor__Transformer__inherit__graph.md5 b/html/classColor__Transformer__inherit__graph.md5 deleted file mode 100644 index ed918d19..00000000 --- a/html/classColor__Transformer__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -d93a5b882083b9f1e2a37a64e1e1d4a7 \ No newline at end of file diff --git a/html/classDM3__Reader-members.html b/html/classDM3__Reader-members.html deleted file mode 100644 index 9b50effb..00000000 --- a/html/classDM3__Reader-members.html +++ /dev/null @@ -1,81 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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load(String directory, String fileName)DM3_Readerinline
run(String arg)DM3_Readerinline
useGatanMinMaxDM3_Reader
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DM3_Reader Class Reference
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-Public Member Functions

void run (String arg)
 
ImagePlus load (String directory, String fileName)
 
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boolean useGatanMinMax = true
 
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Detailed Description

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Definition at line 133 of file DM3_Reader.java.

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Member Function Documentation

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◆ load()

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ImagePlus DM3_Reader.load (String directory,
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Definition at line 234 of file DM3_Reader.java.

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234  {
235 
236  if ((fileName == null) || (fileName == "")) return null;
237 
238  if (!directory.endsWith(File.separator)) directory += File.separator;
239 
240  IJ.showStatus("Loading DM3 File: " + directory + fileName);
241 
242  // Clear the lists of tags in which additional info will be stored
243  tagHash.clear();
244  storedTags.clear();
245  // Try calling the parse routine
246  try{ parseDM3(directory, fileName);}
247  catch (Exception e) {
248  IJ.showStatus("parseDM3() error");
249  IJ.showMessage("DM3_Reader", ""+e);
250  return null;
251  }
252 
253  // Make a blank file information object
254  fi = new FileInfo();
255 
256  // Go and fetch the DM3 specific file Information
257  try {fi=getDM3FileInfo(directory, fileName);}
258  // This is in case of trouble parsing the tag table
259  catch (Exception e) {
260  IJ.showStatus("");
261  IJ.showMessage("DM3_Reader", "gDM3:"+e);
262  return null;
263  }
264 
265  // Write out Calculated Offset if reqd
266  if(debugLevel>1) IJ.write("Calculated offset = "+fi.offset);
267  if(debugLevel>1) IJ.write("Chosen image = "+chosenImage);
268 
269  // Open the image!
270  FileOpener fo = new FileOpener(fi);
271  ImagePlus imp = fo.open(false);
272  //if(debugLevel>5) if(imp==null) IJ.write("Image load failed!");
273 
274  // Write out the contents of the storedTags list
275  // and set the value of notes
276  StringBuffer notesBuffer=new StringBuffer();
277  for (int i = 0; i<storedTags.size();i++){
278  // Can decide whether I want to do this
279  //IJ.log((String) storedTags.elementAt(i));
280  notesBuffer.append( (String) storedTags.elementAt(i) + "\n");
281  }
282  notes=notesBuffer.toString();
283  if (!notes.equals("")) imp.setProperty("Info", notes);
284 
285  // Set (spatial) calibration
286  // nb pass the current calibration in case that contains useful info
287  // already (such as a brightness calibration)
288  try {
289  imp.setCalibration(getDM3CalibrationInfo(imp.getCalibration()));
290  }
291  catch (Exception e) {
292  IJ.showStatus("No Calibration info in "+fileName);
293  }
294  // If this is a diffraction (ie reciprocal space) image then set the
295  // FHT property so that ImageJ displays inverse scale
296  String imagingMode = (String) tagHash.get(IMGLIST+chosenImage+".ImageTags.Microscope Info.Imaging Mode");
297  if (imagingMode!=null && imagingMode.toUpperCase().equals("DIFFRACTION")){
298  imp.setProperty("FHT", "Dummy FHT");
299  }
300 
301 
302  // Set the min and max brightness for display purposes
303  // from DM3 header info if required - ImageJ can do this
304  // but is less robust
305  if(useGatanMinMax) {
306  // now searches through all tags
307  // after bug report by <Charles.P.Daghlian@Dartmouth.EDU>
308  double hiVal=0.0, loVal=0.0;
309  // Iterate over components of the taglist
310  // looking for the image brightness tag
311  // all this because I don't know how to partially match a hash key
312  for (Enumeration e = tagHash.keys() ; e.hasMoreElements() ;) {
313  String thisElementString = (String) e.nextElement();
314 
315  if( (thisElementString).endsWith("ImageDisplayInfo.HighLimit"))
316  hiVal = ((Float) tagHash.get(thisElementString)).doubleValue();
317  if( (thisElementString).endsWith("ImageDisplayInfo.LowLimit"))
318  loVal = ((Float) tagHash.get(thisElementString)).doubleValue();
319  }
320 
321  // If we found at least one, then set the min max brightness
322  if (hiVal!=0.0 || loVal!=0.0) {
323  // min,max are set through the image processor, so get it
324  ImageProcessor ip = imp.getProcessor();
325  // set them - nb setMinMax expects raw pixel values
326  // if a brightness calibration is in force then getRawValue()
327  // does the appropriate conversion
328  ip.setMinAndMax(imp.getCalibration().getRawValue(loVal),imp.getCalibration().getRawValue(hiVal));
329  }
330  }
331 
332  return imp;
333  }
DM3_Reader.useGatanMinMax
boolean useGatanMinMax
Definition: DM3_Reader.java:138
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Definition at line 192 of file DM3_Reader.java.

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192  {
193  String directory = "";
194  String fileName = arg;
195  //if (debugLevel>5);
196 
197  if (debugLevel>5) IJ.write("IN:dir = "+directory+", file="+fileName);
198  if ((arg==null) || (arg==""))
199  { // Choose a file since none specified
200  OpenDialog od = new OpenDialog("Load DM3 File...", arg);
201  fileName = od.getFileName();
202  if (fileName==null)
203  return;
204  directory = od.getDirectory();
205  if (debugLevel>5) IJ.write("IF:dir = "+directory+", file="+fileName);
206  }
207  else
208  { // we were sent a filename to open
209  File dest = new File(arg);
210  directory = dest.getParent();
211  fileName = dest.getName();
212  if (debugLevel>5) IJ.write("ELSE:dir = "+directory+", file="+fileName);
213  }
214 
215  // Load in the image
216  ImagePlus imp = load(directory, fileName);
217  if (imp==null) return;
218 
219  // Attach the Image Processor
220  setProcessor(fileName, imp.getProcessor());
221  // Copy the scale info over
222  copyScale(imp);
223  // Copy the Show Info field over
224  setProperty("Info",imp.getProperty("Info"));
225  // and the FHT property (to handle diffraction mode images)
226  if(imp.getProperty("FHT")!=null) setProperty("FHT", imp.getProperty("FHT"));
227 
228  // Show the image if it was selected by the file
229  // chooser, don't if an argument was passed ie
230  // some other ImageJ process called the plugin
231  if (arg.equals("")) show();
232  }
DM3_Reader.load
ImagePlus load(String directory, String fileName)
Definition: DM3_Reader.java:234
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Member Data Documentation

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◆ useGatanMinMax

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boolean DM3_Reader.useGatanMinMax = true
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Definition at line 138 of file DM3_Reader.java.

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void run (String arg)
 
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Detailed Description

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This plugin tests the updated PlotWindow class

Author
Hajime Hirase
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Version
1.0
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Definition at line 10 of file Example_Plot.java.

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Member Function Documentation

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◆ run()

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void Example_Plot.run (String arg)
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Definition at line 12 of file Example_Plot.java.

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12  {
13  if (IJ.versionLessThan("1.27t"))
14  return;
15 
16  float[] x = {0.1f, 0.25f, 0.35f, 0.5f, 0.61f,0.7f,0.85f,0.89f,0.95f}; // x-coordinates
17  float[] y = {2f,5.6f,7.4f,9f,9.4f,8.7f,6.3f,4.5f,1f}; // x-coordinates
18  float[] e = {.8f,.6f,.5f,.4f,.3f,.5f,.6f,.7f,.8f}; // error bars
19 
20  PlotWindow plot = new PlotWindow("Example Plot","x-axis","y-axis",x,y);
21  plot.setLimits(0, 1, 0, 10);
22  plot.addErrorBars(e);
23 
24  // add a second curve
25  float x2[] = {.4f,.5f,.6f,.7f,.8f};
26  float y2[] = {4,3,3,4,5};
27  plot.setColor(Color.red);
28  plot.addPoints(x2,y2,PlotWindow.X);
29  plot.addPoints(x2,y2,PlotWindow.LINE);
30 
31  plot.setColor(Color.blue);
32  plot.draw();
33  }
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dialogItemChanged(GenericDialog gd, AWTEvent e)Fast_Filtersinline
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setup(String arg, ImagePlus imp)Fast_Filtersinline
showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr)Fast_Filtersinline
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int setup (String arg, ImagePlus imp)
 
int showDialog (ImagePlus imp, String command, PlugInFilterRunner pfr)
 
boolean dialogItemChanged (GenericDialog gd, AWTEvent e)
 
void run (ImageProcessor ip)
 
void setNPasses (int nPasses)
 
-

Detailed Description

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A collection of fast filters (mean, min, max, median, background, ...) working on a rectangular n*m or square n*n kernel. Unidirectional filtering can be done with a kernel size of n*0 or 0*n pixels. Apart form the speed, the kernel type is the main difference to the built-in ImageJ Process>Filters, which are working on a circular kernel, see Process>Filters>Show Circular Masks.

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"Filter Types":

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  • Mean: Average over n*m pixels, where out-of-image pixels are replaced by nearest border pixel. For large kerner sizes (radii), this gives high weight to the border pixels.
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  • Border-limited mean: Average over n*m pixels; in contrast to most ImageJ filters, out-of-image pixels are not replaced by border pixels but rather the area for averaging is reduced at the border.
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  • Median: For unidirectional filters (i.e., with one of the radii = 0) the pixel is replaced by the median of the pixels within a distance of 8x or y-)radius. For bidirectional filters (i.e., if both x and y radii are >0), a fast and rough approximation to the median in a rectangular surrounding is used: First a median filter is applied in x direction, then in y direction. In contrast to most ImageJ filters, out-of-image pixels are not replaced by border pixels but rather the area for median determination is reduced at the border.
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  • Minimum: Minimum over n*m pixels
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  • Maximum: Maximum over n*m pixels
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  • Eliminate maxima: Runs "minimum" and "maximum" filters in succession. Eliminates maxima smaller than the kernel.
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  • Eliminate minima: Runs "maximum" and "minimum" filters in succession. Eliminates minima smaller than the kernel.
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  • Background from minima: eliminates maxima (see above) and smoothens the result (border-limited mean)
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  • Background from maxima: eliminates minima (see above) and smoothens the result (border-limited mean)
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  • Background from median: runs a median (median approximation for bidirectional filtering, see above), then smoothens the result (border-limited mean)
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"x Radius" and "y Radius" determine the kernel size of the filters (in pixels, irrespective of any spatial calibration of the image). For each target (output) pixel, the simple operations (mean, min, max) are performed over a neighborhood given by a rectangle of width = 2*xRadius+1 and height = 2*yRadius+1. x Radius = 0 or y Radius=0 results in no filter operation in that direction.

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Check "Link x & y" if a square kernel (x Radius = y Radius) is desired.

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"Preprocessing" is an operation applied before all others. It can be "none", "smooth" or "median". For unidirectinal filtering (y radius = 0 or x radius = 0), preprocessing is also unidirectional: the kernel size for unidirectional preprocessing is 5x1 or 1x5 pixels. For bidirectional filters (i.e., if both x and y radii are >0), for preprocessing averaging or the (approximated) median runs over a 3x3 pixel kernel. Preprocessing helps to eliminate outliers for the "minimum", "maximum" and related filters.

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"Subtract Filtered" does not output the result of the filter operation above, but rather the original (input) image minus the result of the filter operation, plus an offset. With "mean" filters, "Subtract Filtered" results in a high-pass filter; with "median" it highlights outliers. With the "minimum" and "maximum" filters, "Subtract Filtered" is a kind of edge detection, and with the other filters it provides various types of background subtraction. Especially the "Background from minima" and "Background from maxima" filters are suitable for background subtraction in images with particles: Make sure that xRadius and yRadius are large enough to eliminate any particles (use preview without "Subtract Filtered", then apply the filter with "Subtract Filtered").

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"Offset" is added to the data when subtracting a filtered image from the original one. The offset is needed except for 32-bit float images to keep the result in the range of the image type, e.g. 0-255 for 8-bit grayscale and 8-bit/channel RGB. Use a low value (e.g., 10) for subtracting "background from minima", high values (e.g. 245) for subtracting "background from maxima".

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Notes for users:

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  • All operations are performed on raw pixel values, not taking any grayscale calibration into account.
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  • This plugin provides a 'top hat' filter with "Eliminate Maxima" or "Eliminate Minima", and the "Subtract Filtered" option enabled. When using "Background from maxima", set a suitable offset, i.e., 255 for 8-bit and RGB, and the maximum of the image data range for 16-bit images (65535, or, e.g., 4096 if your data are limited to 12 bits).
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  • The top-hat filter is also handy as a fast alternative to filtering 16-bit images with the ImageJ built-in "Subtract Background" command with the traditional algorithm (rolling ball, not sliding paraboloid) and produces similar results (especially for large pixel value ranges), but the "Background from minima" and "Background from maxima" filters usually produce better results (smoother background).
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Implementation notes:

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  • The plugin handles stack slices in parallel as long as there is enough free memory. This is faster than parallel processing of lines in each image because it also parallelizes the conversion to float.
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  • Creation and destruction of a thread needs about 0.1 msec on a typical year-2011 computer (Intel core i5, Sun Java 1.6.0). This could significantly hamper the performance when processing many slices and creating new threads for each slice (90% of CPU time for thread creation/destruction at 50x50-pixel images!). Thus, small images (<0.1 MPixels) are processed in only one thread.
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Performance on Intel i5 2.4 GHz, 1067 MHz DDR3, Java 1.6.0_24 for Mac, 4000*4000 pixel float image (data: 'add noise' on blank image), radius 5*5: mean: 0.27 s maximum: 0.31 s pseudo median: 1.45 s

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Code by Michael Schmid 2008-11-21 released 2010-04-16 Parallel threads for multi-CPU machines, proper handling of NaN pixels

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Definition at line 107 of file Fast_Filters.java.

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Member Function Documentation

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◆ dialogItemChanged()

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boolean Fast_Filters.dialogItemChanged (GenericDialog gd,
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Definition at line 199 of file Fast_Filters.java.

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199  {
200  Vector numFields = gd.getNumericFields();
201  TextField xNumField = (TextField)numFields.get(0);
202  TextField yNumField = (TextField)numFields.get(1);
203  Checkbox linkCheckbox = (Checkbox)gd.getCheckboxes().get(0);
204  linkXY = gd.getNextBoolean();
205  if (linkXY && !xNumField.getText().equals(yNumField.getText())) {
206  if (e.getSource() == xNumField || e.getSource() == linkCheckbox)
207  yNumField.setText(xNumField.getText());
208  else if (e.getSource() == yNumField)
209  xNumField.setText(yNumField.getText());
210  }
211  type = gd.getNextChoiceIndex();
212  xRadius = (int)gd.getNextNumber();
213  yRadius = (int)gd.getNextNumber();
214  preProcess = gd.getNextChoiceIndex();
215  subtract = gd.getNextBoolean();
216  offset[impType] = gd.getNextNumber();
217  return (!gd.invalidNumber() && xRadius>=0 && yRadius>=0 && xRadius<1000000 && yRadius<1000000);
218  }
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◆ run()

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void Fast_Filters.run (ImageProcessor ip)
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Definition at line 222 of file Fast_Filters.java.

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222  {
223  int width = ip.getWidth();
224  int height = ip.getHeight();
225  Rectangle roiRect = ip.getRoi();
226  int[] taskList = taskLists[type];
227  int nTasks = taskList.length;
228  int extraX = xRadius*(nTasks-1); //out-of-roi margin that has to be processed for next steps
229  int extraY = yRadius*nTasks;
230  if (preProcess > 0) {
231  extraX += xRadius;
232  if (xRadius>0 && yRadius>0) {
233  filterFloat(ip, preProcess, 1, true, extraX, extraY+1, maxThreads);
234  filterFloat(ip, preProcess, 1, false, extraX, extraY, maxThreads);
235  extraY++;
236  } else if (xRadius>0) {
237  filterFloat(ip, preProcess, 2, true, extraX, extraY, maxThreads);
238  } else if (yRadius>0) {
239  filterFloat(ip, preProcess, 2, false, extraX, extraY, maxThreads);
240  }
241  }
242  for (int iTask=0; iTask<nTasks; iTask++) {
243  if (xRadius>0)
244  filterFloat(ip, taskList[iTask], xRadius, true, xRadius*(nTasks-iTask-1), yRadius*(nTasks-iTask), maxThreads);
245  if (yRadius>0)
246  filterFloat(ip, taskList[iTask], yRadius, false, xRadius*(nTasks-iTask-1), yRadius*(nTasks-iTask-1), maxThreads);
247  if (Thread.currentThread().isInterrupted()) return; // interruption for new parameters during preview?
248  }
249  if (subtract) {
250  float[] pixels = (float[])ip.getPixels();
251  float[] snapPixels = (float[])ip.getSnapshotPixels();
252  float fOffset = (float)offset[impType];
253  for (int y=roiRect.y; y<roiRect.y+roiRect.height; y++)
254  for (int x=roiRect.x, p=x+y*width; x<roiRect.x+roiRect.width; x++,p++)
255  pixels[p] = snapPixels[p] - pixels[p] + fOffset;
256  if (Thread.currentThread().isInterrupted()) return;
257  }
258  if (roiRect.height!=height || roiRect.width!=width)
259  resetOutOfRoi(ip, extraX, extraY); // reset out-of-Rectangle pixels above and below roi
260  showProgress(1.0);
261  return;
262  }
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◆ setNPasses()

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void Fast_Filters.setNPasses (int nPasses)
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This method is called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar

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Definition at line 297 of file Fast_Filters.java.

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297  {
298  if (xRadius>0 && yRadius>0) nPasses *= 2;
299  this.nPasses = nPasses * taskLists[type].length;
300  pass = 0;
301  }
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◆ setup()

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int Fast_Filters.setup (String arg,
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This method is called by ImageJ for initialization.

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argUnused here. For plugins in a .jar file this argument string can be specified in the plugins.config file of the .jar archive.
impThe ImagePlus containing the image (or stack) to process.
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Returns
The method returns flags (i.e., a bit mask) specifying the capabilities (supported formats, etc.) and needs of the filter. See PlugInFilter.java and ExtendedPlugInFilter in the ImageJ sources for details.
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Definition at line 158 of file Fast_Filters.java.

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158  {
159  if (IJ.versionLessThan("1.38x")) // generates an error message for older versions
160  return DONE;
161  return flags;
162  }
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◆ showDialog()

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int Fast_Filters.showDialog (ImagePlus imp,
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Definition at line 165 of file Fast_Filters.java.

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165  {
166  impType = imp.getType();
167  int digits = (impType == ImagePlus.GRAY32) ? 2 : 0;
168  GenericDialog gd = new GenericDialog(command+"...");
169  gd.addChoice("Filter Type", TYPES, TYPES[type]);
170  gd.addNumericField("x Radius", xRadius, 0);
171  gd.addNumericField("y Radius", yRadius, 0);
172  gd.addCheckbox("Link x & y", linkXY);
173  gd.addChoice("Preprocessing", PREPROCESSES, PREPROCESSES[preProcess]);
174  gd.addCheckbox("Subtract Filtered", subtract);
175  gd.addNumericField("Offset (subtract only)", offset[impType], digits);
176  gd.addPreviewCheckbox(pfr); // passing pfr makes the filter ready for preview
177  gd.addDialogListener(this); // the DialogItemChanged method will be called on user input
178  gd.showDialog(); // display the dialog; preview runs in the background now
179  if (gd.wasCanceled()) return DONE;
180  IJ.register(this.getClass()); // protect static class variables (filter parameters) from garbage collection
181  Runtime.getRuntime().availableProcessors();
182  flags = IJ.setupDialog(imp, flags); // ask whether to process all slices of stack (if a stack)
183  // parallel processing of stacks is faster than prallel filtering of lines of one image.
184  if ((flags&DOES_STACKS)!=0) {
185  long bytesPerPixelNeeded = impType==ImagePlus.GRAY32 ? 4 : 8; // for conversion to float and snapshot
186  long bytesParallelNeeded = imp.getWidth()*imp.getHeight()*bytesPerPixelNeeded*Prefs.getThreads();
187  long freeMemory = Runtime.getRuntime().freeMemory();
188  if (freeMemory > bytesParallelNeeded*11/10) { //enough memory for stack parallelization?
189  flags |= PARALLELIZE_STACKS;
190  maxThreads = Math.max((int)Math.ceil(1.1*maxThreads/imp.getStackSize()), 1); //fewer threads for each image
191  }
192  //IJ.log("needed/free="+(bytesParallelNeeded/(1024L*1024L))+"/"+(freeMemory/(1024L*1024L))+"M");
193  //IJ.log("StackParall="+((flags&PARALLELIZE_STACKS)!=0)+" maxThreads="+maxThreads);
194  }
195  return flags;
196  }
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Fit_Polynomial Member List
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This is the complete list of members for Fit_Polynomial, including all inherited members.

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dialogItemChanged(GenericDialog gd, AWTEvent e)Fit_Polynomialinline
invertSymmetricMatrix(double[][] matrix)Fit_Polynomialinlinestatic
run(ImageProcessor ip)Fit_Polynomialinline
setNPasses(int nPasses)Fit_Polynomialinline
setup(String arg, ImagePlus imp)Fit_Polynomialinline
showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr)Fit_Polynomialinline
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Fit_Polynomial Class Reference
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-Public Member Functions

int setup (String arg, ImagePlus imp)
 
int showDialog (ImagePlus imp, String command, PlugInFilterRunner pfr)
 
boolean dialogItemChanged (GenericDialog gd, AWTEvent e)
 
void run (ImageProcessor ip)
 
void setNPasses (int nPasses)
 
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-Static Public Member Functions

static boolean invertSymmetricMatrix (double[][] matrix)
 
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Detailed Description

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This plugin-filter fits a polynomial of variable order to an image. The selection (if any) determines the image area the polynomial is fitted to. Output can be the polynomial fit or the image with the fit subtracted. Output area is always the whole image, irrespective of the selection.

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The order of the polynomial can be selected separarely for x, y and mixed terms. E.g. with orders 2, 3, and 2 for x, y, and xy, respectively, the polynomial will be a + b*x + c*x^2 + d*y + e*y^2 + f*y^3 + g*xy (note that the lowest-order mixed term, xy, has order 2)

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"Output Fit (Don't Subtract)" determines whether the output should be the polynomial function. If unchecked, the polynomial is subtracted from the image.

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"Shift Values to Display Range" uses the mean value of the current display range, (max+min)/2, as zero for the subtracted output image. If unchecked, zero output corresponds to 128 for 8-bit and RGB, 32768 for 16-bit and 0 for float images. This option has no effect if "Output Fit (Don't Subtract)" is checked.

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For 8-bit and 16-bit images with no or linear calibration, the image will be calibrated by shifting the zero value appropriately.

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Restrictions:

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  • Undo will revert only the image contents, not the calibration.
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  • In some cases (some non-rectangular rois and/or very high order of the polynomials), the fit may fail although mathematically possible or produce no "Fit failed" message although there are not enough points for the given order of the polynomial.
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Hints for usage:

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  • To exclude particles or other foreground objects from the fit, select a threshold to include the background only, then run Edit>Selection>Create Selection to restrict the fit to the selection (i.e., to the background).
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  • For subtracting the background of 8-bit, 16-bit and RGB images, saturation of the output can be avoided by setting "Brightness&Contrast" to such values that desired background level is in the middle of the displayed range, and selecting "Shift Values -to Display Range". Example: For an 8-bit image with background values around 30 and no significant area of foreground objects in the selection, set a display range of 0-60 before running the filter, and check "Shift Values to Display Range".
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This plugin-filter requires ImageJ 1.38u, which provides provisions for preview.

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Version 2007-Jul-13 Michael Schmid

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Definition at line 65 of file Fit_Polynomial.java.

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Member Function Documentation

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◆ dialogItemChanged()

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boolean Fit_Polynomial.dialogItemChanged (GenericDialog gd,
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Definition at line 135 of file Fit_Polynomial.java.

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135  {
136  Vector numericFields = gd.getNumericFields();
137  xOrder = (int)gd.getNextNumber();
138  yOrder = (int)gd.getNextNumber();
139  xyOrder = (int)gd.getNextNumber();
140  if (xOrder < 0 || yOrder < 0 || xyOrder < 0 || xOrder>50 || yOrder>50 || xyOrder>10)
141  return false;
142  outputFit = gd.getNextBoolean();
143  shiftToDisplay = gd.getNextBoolean();
144  if (e!=null && !(e.getSource() instanceof Checkbox))
145  matrixCalculated = false;
146  setOffset();
147  return true;
148  }
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◆ invertSymmetricMatrix()

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static boolean Fit_Polynomial.invertSymmetricMatrix (double matrix[][])
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Invert a symmetric n*n matrix. Returns false on error (singular matrix). Needs a reasonably well-conditioned matrix

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Definition at line 324 of file Fit_Polynomial.java.

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324  {
325  int n = matrix.length;
326  if (matrix[0].length != n) {
327  IJ.error("invertSymmetricMatrix - not a square matrix");
328  return false;
329  }
330  boolean[] processed = new boolean[n];
331  double[] qq = new double[n];
332  double[] pp = new double[n];
333  double pivot0 = 1e-50; //absolute value of the first (largest) pivot
334  //IJ.log("---invert matrix---"); printMatrix(matrix);
335  for (int i=0; i<n; i++) { //loop: process all matrix lines&columns
336  double max = pivot0 * 1e-14; //pivot must be bigger than this
337  int iPivot = -1;
338  for (int j=0; j<n; j++) //find pivot
339  if (!processed[j]) {
340  double abs = matrix[j][j];
341  abs = abs<0 ? -abs : abs;//abs = Math.abs(matrix[j][j]); but faster
342  if (abs > max) {
343  max = abs;
344  iPivot = j;
345  }
346  }
347  if (iPivot < 0)
348  return false; //no pivot large enough, looks singular
349  if (i==0)
350  pivot0 = max;
351  processed[iPivot] = true;
352  pp[iPivot] = 1.;
353  double q = 1./matrix[iPivot][iPivot];
354  qq[iPivot] = q;
355  matrix[iPivot][iPivot] = 0.;
356  for (int j=0; j<iPivot; j++) {
357  pp[j] = matrix[j][iPivot];
358  qq[j] = matrix[j][iPivot]*q*(processed[j]?1:-1);
359  matrix[j][iPivot] = 0.;
360  }
361  for (int j=iPivot+1; j<n; j++) {
362  pp[j] = matrix[iPivot][j]*(processed[j]?-1:1);
363  qq[j] = -matrix[iPivot][j]*q;
364  matrix[iPivot][j] = 0.;
365  }
366  for (int j=0; j<n; j++)
367  for (int k=j; k<n; k++)
368  matrix[j][k] += pp[j]*qq[k];
369  //printMatrix(matrix);
370  } //for i
371  //IJ.log("asymmetric:");printMatrix(matrix);
372  for (int i=1; i<n; i++) //fill bottom left to make symmetric again
373  for (int j=0; j<i; j++)
374  matrix[i][j] = matrix[j][i];
375  //IJ.log("result:");printMatrix(matrix);
376  return true;
377  }
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◆ run()

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void Fit_Polynomial.run (ImageProcessor ip)
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This method is invoked for each slice and color channel during execution.

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Definition at line 188 of file Fit_Polynomial.java.

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188  {
189  Rectangle roi = ip.getRoi();
190  int width = ip.getWidth();
191  int height = ip.getHeight();
192  float[] pixels = (float[])ip.getPixels();
193  byte[] mask = ip.getMaskArray();
194  Thread thread = Thread.currentThread();
195  synchronized(this) {
196  if (!matrixCalculated) {
197  matrixCalculated = true;
198  calculateMatrixEtc(ip);
199  if (matrix == null)
200  IJ.error("Fit failed, use lower order.");
201  }
202  }
203  if (matrix==null || thread.isInterrupted()) return;
204  double[] vector = new double[baseSize]; //calculate fit
205  long lastTime = System.currentTimeMillis();
206  for (int y=roi.y, powerY=y*endPower; y<roi.y+roi.height; y++, powerY+=endPower) {
207  long time = System.currentTimeMillis();
208  if (time-lastTime > 100) {
209  lastTime = time;
210  if (thread.isInterrupted()) return;
211  showProgress((y-roi.y)/(double)(roi.height));
212  }
213  for (int x=roi.x, p=width*y+x, m=(y-roi.y)*roi.width, powerX=x*endPower; x<roi.x+roi.width; x++, p++, m++, powerX+=endPower)
214  if (mask == null || mask[m] != 0)
215  for (int iBase=0; iBase<baseSize; iBase++)
216  vector[iBase] += pixels[p]*
217  powerOfX[powerX+xPower[iBase]]*powerOfY[powerY+yPower[iBase]];
218  //for iBase
219  //if inside mask
220  //for x
221  } //for y
222  pass++;
223  double[] coeff = new double[baseSize];
224  for (int i=0; i<baseSize; i++)
225  for (int j=0; j<baseSize; j++)
226  coeff[i] += matrix[i][j]*vector[j];
227  //IJ.log("coeff:");printVector(coeff);
228  // // apply fit
229  for (int y=0, p=0, powerY=0; y<height; y++, powerY+=endPower) {
230  long time = System.currentTimeMillis();
231  if (time-lastTime > 100) {
232  lastTime = time;
233  if (thread.isInterrupted()) return;
234  showProgress(y/(double)(height));
235  }
236  for (int x=0, powerX=0; x<width; x++, p++, powerX+=endPower) {
237  double background = 0.;
238  for (int iBase=0; iBase<baseSize; iBase++)
239  background += coeff[iBase]*powerOfX[powerX+xPower[iBase]]*powerOfY[powerY+yPower[iBase]];
240  if (outputFit)
241  pixels[p] = (float)background;
242  else
243  pixels[p] += offset - (float)background;
244  } //for x
245  } //for y
246  pass++;
247  }
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void Fit_Polynomial.setNPasses (int nPasses)
- 		-inline
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This method is called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar

- -

Definition at line 380 of file Fit_Polynomial.java.

-
380  {
381  this.nPasses = 2*nPasses; //one pass for fitting, one for subtracting
382  if (!matrixCalculated) this.nPasses += MAKE_MATRIX_PASSES; //+time for making the matrix
383  pass = 0;
384  }
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ImagePlus imp 
)
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Definition at line 105 of file Fit_Polynomial.java.

-
105  {
106  if (arg.equals("final") && !outputFit) {
107  setCalibration(); //at the very end: calibration (non-float images)
108  return DONE;
109  } else {
110  if (IJ.versionLessThan("1.38u")) // generates an error message for older versions
111  return DONE;
112  this.imp = imp;
113  return flags;
114  }
115  }
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String command,
PlugInFilterRunner pfr 
)
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-

Ask the user for the parameters

- -

Definition at line 119 of file Fit_Polynomial.java.

-
119  {
120  GenericDialog gd = new GenericDialog(command);
121  gd.addSlider("x Direction: Order", 0., 10., xOrder);
122  gd.addSlider("y Direction: Order", 0., 10., yOrder);
123  gd.addSlider("mixed xy: Order", 0., 10., xyOrder);
124  gd.addCheckbox("Output Fit (Don't Subtract)", outputFit);
125  gd.addCheckbox("Shift Values to Display Range", shiftToDisplay);
126  gd.addPreviewCheckbox(pfr);
127  gd.addDialogListener(this);
128  gd.addHelp("http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:fit_polynomial:start");
129  gd.showDialog(); //input by the user (or macro) happens here
130  if (gd.wasCanceled()) return DONE;
131  IJ.register(this.getClass()); //protect static class variables (filter parameters) from garbage collection
132  return IJ.setupDialog(imp, flags); //ask whether to process all slices of stack (if a stack)
133  }
-
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The documentation for this class was generated from the following file: -
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- - diff --git a/html/classFit__Polynomial__coll__graph.dot b/html/classFit__Polynomial__coll__graph.dot deleted file mode 100644 index b1e14bb8..00000000 --- a/html/classFit__Polynomial__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "Fit_Polynomial" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="Fit_Polynomial",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="ExtendedPlugInFilter",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="DialogListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classFit__Polynomial__coll__graph.md5 b/html/classFit__Polynomial__coll__graph.md5 deleted file mode 100644 index d262d1ac..00000000 --- a/html/classFit__Polynomial__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -a022ce2a61cdd292cf216c4c57fd5ed9 \ No newline at end of file diff --git a/html/classFit__Polynomial__inherit__graph.dot b/html/classFit__Polynomial__inherit__graph.dot deleted file mode 100644 index afa56c99..00000000 --- a/html/classFit__Polynomial__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "Fit_Polynomial" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="Fit_Polynomial",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="ExtendedPlugInFilter",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="DialogListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classFit__Polynomial__inherit__graph.md5 b/html/classFit__Polynomial__inherit__graph.md5 deleted file mode 100644 index 11bea2e5..00000000 --- a/html/classFit__Polynomial__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -42a0981f157a3ef62de5fdc1cf6bcbef \ No newline at end of file diff --git a/html/classFloyd__Steinberg__Dithering-members.html b/html/classFloyd__Steinberg__Dithering-members.html deleted file mode 100644 index 8cebc596..00000000 --- a/html/classFloyd__Steinberg__Dithering-members.html +++ /dev/null @@ -1,79 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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run(String arg)Floyd_Steinberg_Ditheringinline
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-Public Member Functions

void run (String arg)
 
-

Detailed Description

-

Converts the current image to binary (0 and 255) using the Floyd Steinberg dithering algorithm. http://en.wikipedia.org/wiki/Floyd-Steinberg_dithering

- -

Definition at line 9 of file Floyd_Steinberg_Dithering.java.

-

Member Function Documentation

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◆ run()

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void Floyd_Steinberg_Dithering.run (String arg)
- 		-inline
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- -

Definition at line 11 of file Floyd_Steinberg_Dithering.java.

-
11  {
12  ImagePlus imp = IJ.getImage();
13  Undo.setup(Undo.TRANSFORM, imp);
14  ImageProcessor ip = imp.getProcessor();
15  int width = imp.getWidth();
16  int height = imp.getHeight();
17  ip = ip.convertToByte(true);
18  int[][] pixel = ip.getIntArray();
19  int oldpixel, newpixel, error;
20  boolean nbottom, nleft, nright;
21  for (int y=0; y<height; y++) {
22  nbottom=y<height-1;
23  for (int x=0; x<width; x++) {
24  nleft=x>0; nright=x<width-1;
25  oldpixel = pixel[x][y];
26  newpixel = oldpixel<128?0:255;
27  pixel[x][y] = newpixel;
28  error = oldpixel-newpixel;
29  if (nright) pixel[x+1][y] += 7*error/16;
30  if (nleft&nbottom) pixel[x-1][y+1] += 3*error/16;
31  if (nbottom) pixel[x][y+1] += 5*error/16;
32  if (nright&&nbottom) pixel[x+1][y+1] += error/16;
33  }
34  }
35  ip.setIntArray(pixel);
36  imp.setProcessor(null, ip);
37  }
-
-
-
The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classFloyd__Steinberg__Dithering__coll__graph.dot b/html/classFloyd__Steinberg__Dithering__coll__graph.dot deleted file mode 100644 index 2f25cd98..00000000 --- a/html/classFloyd__Steinberg__Dithering__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Floyd_Steinberg_Dithering" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="Floyd_Steinberg_Dithering",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classFloyd__Steinberg__Dithering__coll__graph.md5 b/html/classFloyd__Steinberg__Dithering__coll__graph.md5 deleted file mode 100644 index 083a64a6..00000000 --- a/html/classFloyd__Steinberg__Dithering__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -1af78776729c2299c3aa240ac07dbe18 \ No newline at end of file diff --git a/html/classFloyd__Steinberg__Dithering__inherit__graph.dot b/html/classFloyd__Steinberg__Dithering__inherit__graph.dot deleted file mode 100644 index 759da52b..00000000 --- a/html/classFloyd__Steinberg__Dithering__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Floyd_Steinberg_Dithering" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="Floyd_Steinberg_Dithering",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classFloyd__Steinberg__Dithering__inherit__graph.md5 b/html/classFloyd__Steinberg__Dithering__inherit__graph.md5 deleted file mode 100644 index 06c8507b..00000000 --- a/html/classFloyd__Steinberg__Dithering__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -5cd978f22282ae03045f504247128066 \ No newline at end of file diff --git a/html/classGrid__-members.html b/html/classGrid__-members.html deleted file mode 100644 index 2e934994..00000000 --- a/html/classGrid__-members.html +++ /dev/null @@ -1,80 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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dialogItemChanged(GenericDialog gd, AWTEvent e)Grid_inline
run(String arg)Grid_inline
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void run (String arg)
 
boolean dialogItemChanged (GenericDialog gd, AWTEvent e)
 
-

Detailed Description

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Definition at line 10 of file Grid_.java.

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Member Function Documentation

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◆ dialogItemChanged()

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boolean Grid_.dialogItemChanged (GenericDialog gd,
AWTEvent e 
)
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Definition at line 131 of file Grid_.java.

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131  {
132  int width = imp.getWidth();
133  int height = imp.getHeight();
134  type = gd.getNextChoice();
135  areaPerPoint = gd.getNextNumber();
136  color = gd.getNextChoice();
137  randomOffset = gd.getNextBoolean();
138 
139  double minArea= (width*height)/50000.0;
140  if (type.equals(types[CROSSES])&&minArea<144.0)
141  minArea = 144.0;
142  else if (minArea<16)
143  minArea = 16.0;
144  if (areaPerPoint/(pixelWidth*pixelHeight)<minArea) {
145  String err = "\"Area per Point\" too small";
146  if (gd.wasOKed())
147  IJ.error("Grid", err);
148  else
149  IJ.showStatus(err);
150  return true;
151  }
152  double tileSize = Math.sqrt(areaPerPoint);
153  tileWidth = tileSize/pixelWidth;
154  tileHeight = tileSize/pixelHeight;
155  if (randomOffset) {
156  xstart = (int)(random.nextDouble()*tileWidth);
157  ystart = (int)(random.nextDouble()*tileHeight);
158  } else {
159  xstart = (int)(tileWidth/2.0+0.5);
160  ystart = (int)(tileHeight/2.0+0.5);
161  }
162  linesV = (int)((width-xstart)/tileWidth)+1;
163  linesH = (int)((height-ystart)/tileHeight)+1;
164  if (gd.invalidNumber())
165  return true;
166  if (type.equals(types[LINES]))
167  drawLines();
168  else if (type.equals(types[HLINES]))
169  drawHorizontalLines();
170  else if (type.equals(types[CROSSES]))
171  drawCrosses();
172  else if (type.equals(types[POINTS]))
173  drawPoints();
174  else
175  showGrid(null);
176  return true;
177  }
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Definition at line 26 of file Grid_.java.

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26  {
27  if (IJ.versionLessThan("1.43u")) return;
28  imp = IJ.getImage();
29  showDialog();
30  }
-
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The documentation for this class was generated from the following file:
    -
  • xmippViz/external/imagej/plugins/Analyze/Grid_.java
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- - diff --git a/html/classGrid____coll__graph.dot b/html/classGrid____coll__graph.dot deleted file mode 100644 index d27a120d..00000000 --- a/html/classGrid____coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "Grid_" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="Grid_",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="DialogListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classGrid____coll__graph.md5 b/html/classGrid____coll__graph.md5 deleted file mode 100644 index 6d1a3cda..00000000 --- a/html/classGrid____coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -01aa827a4a03448e3d20e7d19c55830c \ No newline at end of file diff --git a/html/classGrid____inherit__graph.dot b/html/classGrid____inherit__graph.dot deleted file mode 100644 index a488694c..00000000 --- a/html/classGrid____inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "Grid_" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="Grid_",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="DialogListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classGrid____inherit__graph.md5 b/html/classGrid____inherit__graph.md5 deleted file mode 100644 index 3a1b2ad3..00000000 --- a/html/classGrid____inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -4e5d27fc032b6fe43c4a4d1086803512 \ No newline at end of file diff --git a/html/classHandleExtraFileTypes-members.html b/html/classHandleExtraFileTypes-members.html deleted file mode 100644 index 5ebb892d..00000000 --- a/html/classHandleExtraFileTypes-members.html +++ /dev/null @@ -1,80 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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run(String path)HandleExtraFileTypesinline
run(String path)HandleExtraFileTypesinline
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-Public Member Functions

void run (String path)
 
void run (String path)
 
-

Detailed Description

-

Plugin to handle file types which are not implemented directly in ImageJ through io.Opener.

-

Description of the Class

-
Author
cedric 26 juin 2006
- -

Definition at line 24 of file HandleExtraFileTypes.java.

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void HandleExtraFileTypes.run (String path)
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Called from io/Opener.java.

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Definition at line 29 of file HandleExtraFileTypes.java.

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29  {
30  if (path.equals("")) return;
31  File theFile = new File(path);
32  String directory = theFile.getParent();
33  String fileName = theFile.getName();
34  if (directory == null) directory = "";
35 
36  // Try and recognise file type and load the file if recognised
37  ImagePlus imp = openImage(directory, fileName, path);
38  if (imp==null) {
39  IJ.showStatus("");
40  return; // failed to load file or plugin has opened and displayed it
41  }
42  ImageStack stack = imp.getStack();
43  // get the title from the stack (falling back to the fileName)
44  String title=imp.getTitle().equals("")?fileName:imp.getTitle();
45  // set the stack of this HandleExtraFileTypes object
46  // to that attached to the ImagePlus object returned by openImage()
47  setStack(title, stack);
48  // copy over the calibration info since it doesn't come with the ImageProcessor
49  setCalibration(imp.getCalibration());
50  // also copy the Show Info field over if it exists
51  if (imp.getProperty("Info") != null)
52  setProperty("Info", imp.getProperty("Info"));
53  // copy the FileInfo
54  setFileInfo(imp.getOriginalFileInfo());
55  // copy dimensions
56  if (IJ.getVersion().compareTo("1.38s")>=0)
57  setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
58  if (IJ.getVersion().compareTo("1.41o")>=0)
59  setOpenAsHyperStack(imp.getOpenAsHyperStack());
60  }
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void HandleExtraFileTypes.run (String path)
- 		-inline
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Main processing method for the HandleExtraFileTypes object

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Parameters
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pathDescription of the Parameter
-
-
- -

Definition at line 53 of file HandleExtraFileTypes.java.

-
53  {
54  if (IJ.versionLessThan("1.30u")) {
55  return;
56  }
57  if (path.equals("")) {
58  return;
59  }
60  File theFile = new File(path);
61  String directory = theFile.getParent();
62  String fileName = theFile.getName();
63  if (directory == null) {
64  directory = "";
65  }
66 
67  // Try and recognise file type and load the file if recognised
68  ImagePlus imp = openImage(directory, fileName);
69  if (imp == null) {
70  // failed to load file or plugin has opened and displayed it
71  IJ.showStatus("");
72  return;
73  // failed to load file or plugin has opened and displayed it
74  }
75  ImageStack stack = imp.getStack();
76  // Set the stack of this HandleExtraFileTypes object
77  // to that attached to the ImagePlus object returned by openImage()
78  setStack(fileName, stack);
79  // Copy over the calibration info since it doesn't come with the ImageProcessor
80  setCalibration(imp.getCalibration());
81  // Also copy the Show Info field over if it exists
82  if (imp.getProperty("Info") != null) {
83  setProperty("Info", imp.getProperty("Info"));
84  }
85  // Copy over the FileInfo
86  setFileInfo(imp.getOriginalFileInfo());
87  }
-
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run(String arg)IPLab_Readerinline
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-Public Member Functions

void run (String arg)
 
-

Detailed Description

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This plugin opens images in the IPLab/Windows (.IPL) format.

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Definition at line 8 of file IPLab_Reader.java.

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Member Function Documentation

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◆ run()

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void IPLab_Reader.run (String arg)
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Definition at line 16 of file IPLab_Reader.java.

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16  {
17  OpenDialog od = new OpenDialog("Open IPLab...", arg);
18  String directory = od.getDirectory();
19  String name = od.getFileName();
20  if (name==null)
21  return;
22  IJ.showStatus("Opening: " + directory + name);
23  open(directory, name, arg);
24  }
-
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- - diff --git a/html/classIPLab__Reader__coll__graph.dot b/html/classIPLab__Reader__coll__graph.dot deleted file mode 100644 index 51a37756..00000000 --- a/html/classIPLab__Reader__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "IPLab_Reader" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="IPLab_Reader",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classIPLab__Reader__coll__graph.md5 b/html/classIPLab__Reader__coll__graph.md5 deleted file mode 100644 index d42f50c4..00000000 --- a/html/classIPLab__Reader__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -c735c6575ac8c700ab34d04104b56630 \ No newline at end of file diff --git a/html/classIPLab__Reader__inherit__graph.dot b/html/classIPLab__Reader__inherit__graph.dot deleted file mode 100644 index 5f0bb726..00000000 --- a/html/classIPLab__Reader__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "IPLab_Reader" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="IPLab_Reader",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classIPLab__Reader__inherit__graph.md5 b/html/classIPLab__Reader__inherit__graph.md5 deleted file mode 100644 index 54fa2644..00000000 --- a/html/classIPLab__Reader__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -1c3cd7fbe1839295155e60ab70898988 \ No newline at end of file diff --git a/html/classIP__Demo-members.html b/html/classIP__Demo-members.html deleted file mode 100644 index 850fe989..00000000 --- a/html/classIP__Demo-members.html +++ /dev/null @@ -1,81 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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actionPerformed(ActionEvent e)IP_Demoinline
IP_Demo()IP_Demoinline
processWindowEvent(WindowEvent e)IP_Demoinline
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class  Runner
 
- - - - - - - -

-Public Member Functions

 IP_Demo ()
 
void actionPerformed (ActionEvent e)
 
void processWindowEvent (WindowEvent e)
 
-

Detailed Description

-

Image Processing Demo. Demonstrates how to create a custom user interface, how to use ImageJ's ImageProcessor class, and how to run commands in a separate thread.

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Definition at line 13 of file IP_Demo.java.

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◆ IP_Demo()

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Definition at line 18 of file IP_Demo.java.

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18  {
19  super("IP Demo");
20  if (instance!=null) {
21  instance.toFront();
22  return;
23  }
24  instance = this;
25  addKeyListener(IJ.getInstance());
26 
27  setLayout(new FlowLayout());
28  panel = new Panel();
29  panel.setLayout(new GridLayout(4, 4, 5, 5));
30  addButton("Reset");
31  addButton("Flip");
32  addButton("Invert");
33  addButton("Rotate");
34  addButton("Lighten");
35  addButton("Darken");
36  addButton("Zoom In");
37  addButton("Zoom Out");
38  addButton("Smooth");
39  addButton("Sharpen");
40  addButton("Find Edges");
41  addButton("Threshold");
42  addButton("Add Noise");
43  addButton("Reduce Noise");
44  addButton("Macro1");
45  addButton("Macro2");
46  add(panel);
47 
48  pack();
49  GUI.center(this);
50  setVisible(true);
51  }
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◆ actionPerformed()

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Definition at line 60 of file IP_Demo.java.

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60  {
61  ImagePlus imp = WindowManager.getCurrentImage();
62  if (imp==null) {
63  IJ.beep();
64  IJ.showStatus("No image");
65  previousID = 0;
66  return;
67  }
68  if (!imp.lock())
69  {previousID = 0; return;}
70  int id = imp.getID();
71  if (id!=previousID)
72  imp.getProcessor().snapshot();
73  previousID = id;
74  String label = e.getActionCommand();
75  if (label==null)
76  return;
77  new Runner(label, imp);
78  }
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Definition at line 80 of file IP_Demo.java.

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80  {
81  super.processWindowEvent(e);
82  if (e.getID()==WindowEvent.WINDOW_CLOSING) {
83  instance = null;
84  }
85  }
-
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- - diff --git a/html/classIP__Demo__coll__graph.dot b/html/classIP__Demo__coll__graph.dot deleted file mode 100644 index e772fbe2..00000000 --- a/html/classIP__Demo__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "IP_Demo" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="IP_Demo",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="PlugInFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classIP__Demo__coll__graph.md5 b/html/classIP__Demo__coll__graph.md5 deleted file mode 100644 index a0b5b881..00000000 --- a/html/classIP__Demo__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -fa1a5f0a5ea477e83c4703548a8b27d9 \ No newline at end of file diff --git a/html/classIP__Demo__inherit__graph.dot b/html/classIP__Demo__inherit__graph.dot deleted file mode 100644 index 34e40293..00000000 --- a/html/classIP__Demo__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "IP_Demo" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="IP_Demo",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugInFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classIP__Demo__inherit__graph.md5 b/html/classIP__Demo__inherit__graph.md5 deleted file mode 100644 index 97075e3c..00000000 --- a/html/classIP__Demo__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -0e22c6fc4f1b2cdd36a3fa171e5dd9f3 \ No newline at end of file diff --git a/html/classImage__Inverter-members.html b/html/classImage__Inverter-members.html deleted file mode 100644 index e030fa8b..00000000 --- a/html/classImage__Inverter-members.html +++ /dev/null @@ -1,80 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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run(ImageProcessor ip)Image_Inverterinline
setup(String arg, ImagePlus imp)Image_Inverterinline
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-Public Member Functions

int setup (String arg, ImagePlus imp)
 
void run (ImageProcessor ip)
 
-

Detailed Description

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This sample ImageJ plugin filter inverts images.

-

A few things to note: 1) Filter plugins must implement the PlugInFilter interface. 2) User plugins do not use the package statement; 3) Plugins residing in the "plugins" folder, and with at least one underscore in their name, are automatically installed in the PlugIns menu. 4) Plugins can be installed in other menus by packaging them as JAR files. 5) The class name ("Image_Inverter") and file name ("Image_Inverter.java") must be the same. 6) This filter works with selections, including non-rectangular selections. 7) It will be called repeatedly to process all the slices in a stack. 8) It supports Undo for single images. 9) "~" is the bitwise complement operator. 10) It is slower than the built in Edit>Invert command, which works directly with the pixel array, because of the two time-consuming method calls in the inner loop.

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Definition at line 27 of file Image_Inverter.java.

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void Image_Inverter.run (ImageProcessor ip)
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Definition at line 33 of file Image_Inverter.java.

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33  {
34  Rectangle r = ip.getRoi();
35  for (int y=r.y; y<(r.y+r.height); y++)
36  for (int x=r.x; x<(r.x+r.width); x++)
37  ip.set(x, y, ~ip.get(x,y));
38  }
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Definition at line 29 of file Image_Inverter.java.

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29  {
30  return DOES_ALL+DOES_STACKS+SUPPORTS_MASKING;
31  }
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The documentation for this class was generated from the following file: -
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- - diff --git a/html/classImage__Inverter__coll__graph.dot b/html/classImage__Inverter__coll__graph.dot deleted file mode 100644 index 0e1f4a7b..00000000 --- a/html/classImage__Inverter__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Image_Inverter" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="Image_Inverter",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="PlugInFilter",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classImage__Inverter__coll__graph.md5 b/html/classImage__Inverter__coll__graph.md5 deleted file mode 100644 index aaaae85d..00000000 --- a/html/classImage__Inverter__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -63568ee7b973a55d4681e334ae3e8cdc \ No newline at end of file diff --git a/html/classImage__Inverter__inherit__graph.dot b/html/classImage__Inverter__inherit__graph.dot deleted file mode 100644 index 8f8304a9..00000000 --- a/html/classImage__Inverter__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Image_Inverter" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="Image_Inverter",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugInFilter",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classImage__Inverter__inherit__graph.md5 b/html/classImage__Inverter__inherit__graph.md5 deleted file mode 100644 index 843913dc..00000000 --- a/html/classImage__Inverter__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -a81b88a034698132821f25daeebfcb63 \ No newline at end of file diff --git a/html/classKalman__Stack__Filter-members.html b/html/classKalman__Stack__Filter-members.html deleted file mode 100644 index 4c182dc5..00000000 --- a/html/classKalman__Stack__Filter-members.html +++ /dev/null @@ -1,83 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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filter(ImageStack stack, double percentvar, double gain)Kalman_Stack_Filterinline
filterRGB(ImageStack stack, double percentvar, double gain)Kalman_Stack_Filterinline
fromDouble(double[] array, int bitDepth)Kalman_Stack_Filterinline
run(String arg)Kalman_Stack_Filterinline
toDouble(Object array, int bitDepth)Kalman_Stack_Filterinline
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void run (String arg)
 
void filter (ImageStack stack, double percentvar, double gain)
 
ImageStack filterRGB (ImageStack stack, double percentvar, double gain)
 
Object fromDouble (double[] array, int bitDepth)
 
double [] toDouble (Object array, int bitDepth)
 
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Definition at line 28 of file Kalman_Stack_Filter.java.

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Member Function Documentation

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◆ filter()

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void Kalman_Stack_Filter.filter (ImageStack stack,
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double gain 
)
- 		-inline
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- -

Definition at line 59 of file Kalman_Stack_Filter.java.

-
59  {
60  ImageProcessor ip = stack.getProcessor(1);
61  int bitDepth = 0;
62  if (ip instanceof ByteProcessor)
63  bitDepth = 8;
64  else if (ip instanceof ShortProcessor)
65  bitDepth = 16;
66  else if (ip instanceof FloatProcessor)
67  bitDepth = 32;
68  else
69  throw new IllegalArgumentException("RGB stacks not supported");
70 
71  int width = stack.getWidth();
72  int height = stack.getHeight();
73  int dimension = width*height;
74  int stacksize = stack.getSize();
75  double[] stackslice = new double[dimension];
76  double[] filteredslice = new double[dimension];
77  double[] noisevar = new double[dimension];
78  double[] average = new double[dimension];
79  double[] predicted = new double[dimension];
80  double[] predictedvar = new double[dimension];
81  double[] observed = new double[dimension];
82  double[] Kalman = new double[dimension];
83  double[] corrected = new double[dimension];
84  double[] correctedvar = new double[dimension];
85 
86  for (int i=0; i<dimension; ++i)
87  noisevar[i] = percentvar;
88  predicted = toDouble(stack.getPixels(1), bitDepth);
89  predictedvar = noisevar;
90 
91  for(int i=1; i<stacksize; ++i) {
92  IJ.showProgress(i, stacksize);
93  stackslice = toDouble(stack.getPixels(i+1), bitDepth);
94  observed = toDouble(stackslice, 64);
95  for(int k=0;k<Kalman.length;++k)
96  Kalman[k] = predictedvar[k]/(predictedvar[k]+noisevar[k]);
97  for(int k=0;k<corrected.length;++k)
98  corrected[k] = gain*predicted[k]+(1.0-gain)*observed[k]+Kalman[k]*(observed[k] - predicted[k]);
99  for(int k=0;k<correctedvar.length;++k)
100  correctedvar[k] = predictedvar[k]*(1.0 - Kalman[k]);
101  predictedvar = correctedvar;
102  predicted = corrected;
103  stack.setPixels(fromDouble(corrected, bitDepth), i+1);
104  }
105  }
Kalman_Stack_Filter.toDouble
double [] toDouble(Object array, int bitDepth)
Definition: Kalman_Stack_Filter.java:139
-
Kalman_Stack_Filter.fromDouble
Object fromDouble(double[] array, int bitDepth)
Definition: Kalman_Stack_Filter.java:118
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◆ filterRGB()

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ImageStack Kalman_Stack_Filter.filterRGB (ImageStack stack,
double percentvar,
double gain 
)
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Definition at line 107 of file Kalman_Stack_Filter.java.

-
107  {
108  RGBStackSplitter splitter = new RGBStackSplitter();
109  splitter.split(stack, false);
110  filter(splitter.red, percentvar, gain);
111  filter(splitter.green, percentvar, gain);
112  filter(splitter.blue, percentvar, gain);
113  RGBStackMerge merge = new RGBStackMerge();
114  ImageProcessor ip = splitter.red.getProcessor(1);
115  return merge.mergeStacks(ip.getWidth(), ip.getHeight(), splitter.red.getSize(), splitter.red, splitter.green, splitter.blue, false);
116  }
Kalman_Stack_Filter.filter
void filter(ImageStack stack, double percentvar, double gain)
Definition: Kalman_Stack_Filter.java:59
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int bitDepth 
)
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Definition at line 118 of file Kalman_Stack_Filter.java.

-
118  {
119  switch (bitDepth) {
120  case 8:
121  byte[] bytes = new byte[array.length];
122  for(int i=0; i<array.length; i++)
123  bytes[i] = (byte)array[i];
124  return bytes;
125  case 16:
126  short[] shorts = new short[array.length];
127  for(int i=0; i<array.length; i++)
128  shorts[i] = (short)array[i];
129  return shorts;
130  case 32:
131  float[] floats = new float[array.length];
132  for(int i=0; i<array.length; i++)
133  floats[i] = (float)array[i];
134  return floats;
135  }
136  return null;
137  }
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void Kalman_Stack_Filter.run (String arg)
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Definition at line 32 of file Kalman_Stack_Filter.java.

-
32  {
33  ImagePlus imp = IJ.getImage();
34  if (imp.getStackSize()==1)
35  {IJ.error("Stack required"); return;}
36  String ErrorMessage = new String("One of your values was not properly formatted.\nThe default values will be used.");
37  GenericDialog d = new GenericDialog("Kalman Stack Filter");
38  d.addNumericField("Acquisition_noise variance estimate:", percentvar, 2);
39  d.addNumericField("Bias to be placed on the prediction:", gain, 2);
40  d.showDialog();
41  if(d.wasCanceled()) return;
42  double percentvar = d.getNextNumber();
43  gain = d.getNextNumber();
44  if(d.invalidNumber())
45  {IJ.error("Invalid input Number"); return;}
46  if(percentvar>1.0||gain>1.0||percentvar<0.0||gain<0.0){
47  IJ.error(ErrorMessage);
48  percentvar = 0.05;
49  gain = 0.8;
50  }
51  ImageStack stack = imp.getStack();
52  if (imp.getBitDepth()==24)
53  stack = filterRGB(stack, percentvar, gain);
54  else
55  filter(stack, percentvar, gain);
56  imp.setStack(null, stack);
57  }
Kalman_Stack_Filter.filter
void filter(ImageStack stack, double percentvar, double gain)
Definition: Kalman_Stack_Filter.java:59
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Kalman_Stack_Filter.filterRGB
ImageStack filterRGB(ImageStack stack, double percentvar, double gain)
Definition: Kalman_Stack_Filter.java:107
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◆ toDouble()

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double [] Kalman_Stack_Filter.toDouble (Object array,
int bitDepth 
)
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Definition at line 139 of file Kalman_Stack_Filter.java.

-
139  {
140  double[] doubles = null;
141  switch (bitDepth) {
142  case 8:
143  byte[] bytes = (byte[])array;
144  doubles = new double[bytes.length];
145  for(int i=0; i<doubles.length; i++)
146  doubles[i] = (bytes[i]&0xff);
147  break;
148  case 16:
149  short[] shorts = (short[])array;
150  doubles = new double[shorts.length];
151  for(int i=0; i<doubles.length; i++)
152  doubles[i] = (shorts[i]&0xffff);
153  break;
154  case 32:
155  float[] floats = (float[])array;
156  doubles = new double[floats.length];
157  for(int i=0; i<doubles.length; i++)
158  doubles[i] = floats[i];
159  break;
160  case 64:
161  double[] doubles0 = (double[])array;
162  doubles = new double[doubles0.length];
163  for(int i=0; i<doubles.length; i++)
164  doubles[i] = doubles0[i];
165  break;
166  }
167  return doubles;
168  }
-
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-
The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classKalman__Stack__Filter__coll__graph.dot b/html/classKalman__Stack__Filter__coll__graph.dot deleted file mode 100644 index 861d0d79..00000000 --- a/html/classKalman__Stack__Filter__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Kalman_Stack_Filter" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="Kalman_Stack_Filter",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classKalman__Stack__Filter__coll__graph.md5 b/html/classKalman__Stack__Filter__coll__graph.md5 deleted file mode 100644 index c9a6e6c3..00000000 --- a/html/classKalman__Stack__Filter__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ad2afcb45ee8b7f42a7e4d2caf80b08a \ No newline at end of file diff --git a/html/classKalman__Stack__Filter__inherit__graph.dot b/html/classKalman__Stack__Filter__inherit__graph.dot deleted file mode 100644 index aa27fb22..00000000 --- a/html/classKalman__Stack__Filter__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Kalman_Stack_Filter" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="Kalman_Stack_Filter",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classKalman__Stack__Filter__inherit__graph.md5 b/html/classKalman__Stack__Filter__inherit__graph.md5 deleted file mode 100644 index 00b193f6..00000000 --- a/html/classKalman__Stack__Filter__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -17ac71e0f2ecbd2f75ce86e1b5a3321a \ No newline at end of file diff --git a/html/classRed__And__Blue-members.html b/html/classRed__And__Blue-members.html deleted file mode 100644 index b2928496..00000000 --- a/html/classRed__And__Blue-members.html +++ /dev/null @@ -1,79 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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-Public Member Functions

void run (String arg)
 
-

Detailed Description

-

This a prototype ImageJ plugin.

- -

Definition at line 8 of file Red_And_Blue.java.

-

Member Function Documentation

- -

◆ run()

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void Red_And_Blue.run (String arg)
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Definition at line 10 of file Red_And_Blue.java.

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10  {
11  long start = System.currentTimeMillis();
12  int w = 400, h = 400;
13  ImageProcessor ip = new ColorProcessor(w, h);
14  int[] pixels = (int[])ip.getPixels();
15  int i = 0;
16  for (int y = 0; y < h; y++) {
17  int red = (y * 255) / (h - 1);
18  for (int x = 0; x < w; x++) {
19  int blue = (x * 255) / (w - 1);
20  pixels[i++] = (255 << 24) | (red << 16) | blue;
21  }
22  }
23  new ImagePlus("Red and Blue", ip).show();
24  IJ.showStatus(""+(System.currentTimeMillis()-start));
25  }
-
-
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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classRed__And__Blue__coll__graph.dot b/html/classRed__And__Blue__coll__graph.dot deleted file mode 100644 index e6c5dfa2..00000000 --- a/html/classRed__And__Blue__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Red_And_Blue" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="Red_And_Blue",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classRed__And__Blue__coll__graph.md5 b/html/classRed__And__Blue__coll__graph.md5 deleted file mode 100644 index ff2bf039..00000000 --- a/html/classRed__And__Blue__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -f289348611c1f530a3af7dd8a711351e \ No newline at end of file diff --git a/html/classRed__And__Blue__inherit__graph.dot b/html/classRed__And__Blue__inherit__graph.dot deleted file mode 100644 index 78c94a6c..00000000 --- a/html/classRed__And__Blue__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Red_And_Blue" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="Red_And_Blue",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classRed__And__Blue__inherit__graph.md5 b/html/classRed__And__Blue__inherit__graph.md5 deleted file mode 100644 index 2441f767..00000000 --- a/html/classRed__And__Blue__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -5cdeaea86e8fbf9af1f18f675c13104c \ No newline at end of file diff --git a/html/classTransparent__Image__Overlay-members.html b/html/classTransparent__Image__Overlay-members.html deleted file mode 100644 index 0c97ae08..00000000 --- a/html/classTransparent__Image__Overlay-members.html +++ /dev/null @@ -1,79 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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- - diff --git a/html/classTransparent__Image__Overlay.html b/html/classTransparent__Image__Overlay.html deleted file mode 100644 index 74f506d0..00000000 --- a/html/classTransparent__Image__Overlay.html +++ /dev/null @@ -1,133 +0,0 @@ - - - - - - - -Xmipp: Transparent_Image_Overlay Class Reference - - - - - - - - - -
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-Public Member Functions

void run (String arg)
 
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Detailed Description

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-

Definition at line 8 of file Transparent_Image_Overlay.java.

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Member Function Documentation

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◆ run()

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void Transparent_Image_Overlay.run (String arg)
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Definition at line 10 of file Transparent_Image_Overlay.java.

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10  {
11  if (IJ.versionLessThan("1.46p"))
12  return;
13  ImagePlus imp = IJ.openImage("http://imagej.nih.gov/ij/images/cardio.dcm.zip");
14  ImageProcessor ip = imp.getProcessor();
15  ip = ip.crop();
16  ip.setRoi(142, 132, 654, 616);
17  int width = ip.getWidth()/2;
18  int height = ip.getHeight()/2;
19  ip = ip.resize(width, height, true);
20  ip.setColor(Color.red);
21  ip.setFont(new Font("SansSerif",Font.PLAIN,28));
22  ip.drawString("Transparent\nImage\nOverlay", 0, 40);
23  ImageRoi imageRoi = new ImageRoi(100, 25, ip);
24  imageRoi.setZeroTransparent(true);
25  ImagePlus boats = IJ.openImage("http://imagej.nih.gov/ij/images/boats.gif");
26  Overlay overlay = new Overlay(imageRoi);
27  boats.setOverlay(overlay);
28  boats.setRoi(imageRoi);
29  boats.show();
30  for (int a=0; a<=360; a++) {
31  imageRoi.setAngle(a);
32  boats.draw();
33  IJ.wait(20);
34  }
35  }
-
-
-
The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classTransparent__Image__Overlay__coll__graph.dot b/html/classTransparent__Image__Overlay__coll__graph.dot deleted file mode 100644 index 90d858e6..00000000 --- a/html/classTransparent__Image__Overlay__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Transparent_Image_Overlay" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="Transparent_Image_Overlay",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classTransparent__Image__Overlay__coll__graph.md5 b/html/classTransparent__Image__Overlay__coll__graph.md5 deleted file mode 100644 index 85c022f5..00000000 --- a/html/classTransparent__Image__Overlay__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -023c636784e8e27effba82ba92b5e11e \ No newline at end of file diff --git a/html/classTransparent__Image__Overlay__inherit__graph.dot b/html/classTransparent__Image__Overlay__inherit__graph.dot deleted file mode 100644 index 5db3e202..00000000 --- a/html/classTransparent__Image__Overlay__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "Transparent_Image_Overlay" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="Transparent_Image_Overlay",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classTransparent__Image__Overlay__inherit__graph.md5 b/html/classTransparent__Image__Overlay__inherit__graph.md5 deleted file mode 100644 index 57c4d560..00000000 --- a/html/classTransparent__Image__Overlay__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -c2f52cb7524a57255d7c1f5696f0be47 \ No newline at end of file diff --git a/html/classZVI__Reader-members.html b/html/classZVI__Reader-members.html deleted file mode 100644 index 52314969..00000000 --- a/html/classZVI__Reader-members.html +++ /dev/null @@ -1,79 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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-Public Member Functions

void run (String arg)
 
-

Detailed Description

-

Imports a Z series (image stack) from a Zeiss ZVI file. This plugin was created through trial and error (i.e., reverse engineering several example ZVI files), and most likely does not work with some types of ZVI.

-
Author
Curtis Rueden ctrueden at wisc.edu
-

Modified by Michel Boudinot (mb) 24 Aug 2006. michel.boudinot at inaf.cnrs-gif.fr

    -
  • improved decoding strategy, more robust against zvi file structure diversity.
    • -
  • new approach to compute the number of channels.
    • -
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    • -
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Definition at line 26 of file ZVI_Reader.java.

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Member Function Documentation

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◆ run()

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void ZVI_Reader.run (String arg)
- 		-inline
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Executes the plugin.

- -

Definition at line 66 of file ZVI_Reader.java.

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66  {
67  OpenDialog od = new OpenDialog("Open ZVI...", arg);
68  String directory = od.getDirectory();
69  String fileName = od.getFileName();
70  if (fileName == null) return;
71 
72  IJ.showStatus("Opening: " + directory + fileName);
73  FileInfo[] fi = null;
74  try { fi = getHeaderInfo(directory, fileName); }
75  catch (Exception e) {
76  IJ.showStatus("");
77  IJ.showMessage("ZVI Reader", "" + e);
78  return;
79  }
80  if (fi == null) {
81  IJ.showStatus("");
82  IJ.showMessage("ZVI Reader", "Could not find header information.");
83  return;
84  }
85 
86  Opener opener = new Opener();
87  ImagePlus imp = opener.openTiffStack(fi); // is there a cleaner way?
88  if (imp == null) {
89  IJ.showStatus("");
90  IJ.showMessage("ZVI Reader", "Could not extract pixel data.");
91  return;
92  }
93  //setStack(fileName, imp.getStack());
94 
95  // addition by TjC
96  ImageStack istk = imp.getStack();
97 
98  int nSlice = istk .getSize();
99  int sWidth = istk.getWidth();
100  int sHeight = istk.getHeight();
101  String stackName="";
102 //+ (mb) new image stack construction.
103  //- original code removed
104  //- int sliceOffset = 1;
105  //- int sliceNumberPerChannel = nSlice/numC;
106  //-
107  //- //IJ.showMessage("nSlice = " +nSlice );
108  //- //IJ.showMessage("nSlice/ch = " +sliceNumberPerChannel);
109  //-
110  //- for (int i=1; i<=numC; i++)
111  //- {stackName= fileName + " Ch"+i;
112  //- ImageStack img = new ImageStack (sWidth,sHeight);
113  //- for(int j=0; j<sliceNumberPerChannel; j++)
114  //- {
115  //- //IJ.showMessage("j = " +j);
116  //- int theC = getChannel(fi[j*numC+i-1]);
117  //- IJ.showMessage("theC = "+ theC);
118  //-
119  //- ip1 = istk.getProcessor(j*numC+i);
120  //- img.addSlice(stackName, ip1);
121  //- }
122  //- new ImagePlus(stackName, img).show();
123  //- }
124  //-
125  //+ new code
126  // make ImageStack for each channel.
127  Hashtable img = new Hashtable();
128  Iterator it = C_Set.iterator();
129  while (it.hasNext()) {
130  Object theC = it.next();
131  img.put(theC, new ImageStack (sWidth,sHeight));
132  }
133  // iteratate thru all image slices and
134  // add slice to corresponding channel ImageStack.
135  for (int n=0; n< nSlice; n++) {
136  int theC = getChannel(fi[n]);
137  ip1 = istk.getProcessor(n+1);
138  ((ImageStack)img.get(new Integer(theC))).addSlice(null, ip1);
139  }
140  // name image stacks and show them.
141  it = C_Set.iterator();
142  while (it.hasNext()) {
143  Object theC = it.next();
144  stackName = fileName + " Ch"+ theC;
145  new ImagePlus(stackName, ((ImageStack)img.get(theC))).show();
146  }
147 //- (mb)
148 
149 //if (arg.equals("")) show();
150 
151 }
-
-
-
The documentation for this class was generated from the following file: -
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- - diff --git a/html/classZVI__Reader__coll__graph.dot b/html/classZVI__Reader__coll__graph.dot deleted file mode 100644 index faee8175..00000000 --- a/html/classZVI__Reader__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "ZVI_Reader" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="ZVI_Reader",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classZVI__Reader__coll__graph.md5 b/html/classZVI__Reader__coll__graph.md5 deleted file mode 100644 index 56dda24f..00000000 --- a/html/classZVI__Reader__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -3b6e6baa7ea90877e588ee26a4301bb9 \ No newline at end of file diff --git a/html/classZVI__Reader__inherit__graph.dot b/html/classZVI__Reader__inherit__graph.dot deleted file mode 100644 index 352097ae..00000000 --- a/html/classZVI__Reader__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "ZVI_Reader" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="ZVI_Reader",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classZVI__Reader__inherit__graph.md5 b/html/classZVI__Reader__inherit__graph.md5 deleted file mode 100644 index 36312323..00000000 --- a/html/classZVI__Reader__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -f5215c58c1020afca8aadb13c4a9e401 \ No newline at end of file diff --git a/html/classes.html b/html/classes.html deleted file mode 100644 index c52d7056..00000000 --- a/html/classes.html +++ /dev/null @@ -1,158 +0,0 @@ - - - - - - - -Xmipp: Class Index - - - - - - - - - -
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LIBSVM_VERSIONlibsvm.svmstatic
randlibsvm.svmstatic
svm_check_parameter(svm_problem prob, svm_parameter param)libsvm.svminlinestatic
svm_check_probability_model(svm_model model)libsvm.svminlinestatic
svm_cross_validation(svm_problem prob, svm_parameter param, int nr_fold, double[] target)libsvm.svminlinestatic
svm_get_labels(svm_model model, int[] label)libsvm.svminlinestatic
svm_get_nr_class(svm_model model)libsvm.svminlinestatic
svm_get_nr_sv(svm_model model)libsvm.svminlinestatic
svm_get_sv_indices(svm_model model, int[] indices)libsvm.svminlinestatic
svm_get_svm_type(svm_model model)libsvm.svminlinestatic
svm_get_svr_probability(svm_model model)libsvm.svminlinestatic
svm_load_model(String model_file_name)libsvm.svminlinestatic
svm_load_model(BufferedReader fp)libsvm.svminlinestatic
svm_predict(svm_model model, svm_node[] x)libsvm.svminlinestatic
svm_predict_probability(svm_model model, svm_node[] x, double[] prob_estimates)libsvm.svminlinestatic
svm_predict_values(svm_model model, svm_node[] x, double[] dec_values)libsvm.svminlinestatic
svm_save_model(String model_file_name, svm_model model)libsvm.svminlinestatic
svm_set_print_string_function(svm_print_interface print_func)libsvm.svminlinestatic
svm_train(svm_problem prob, svm_parameter param)libsvm.svminlinestatic
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class  decision_function
 
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-Static Public Member Functions

static svm_model svm_train (svm_problem prob, svm_parameter param)
 
static void svm_cross_validation (svm_problem prob, svm_parameter param, int nr_fold, double[] target)
 
static int svm_get_svm_type (svm_model model)
 
static int svm_get_nr_class (svm_model model)
 
static void svm_get_labels (svm_model model, int[] label)
 
static void svm_get_sv_indices (svm_model model, int[] indices)
 
static int svm_get_nr_sv (svm_model model)
 
static double svm_get_svr_probability (svm_model model)
 
static double svm_predict_values (svm_model model, svm_node[] x, double[] dec_values)
 
static double svm_predict (svm_model model, svm_node[] x)
 
static double svm_predict_probability (svm_model model, svm_node[] x, double[] prob_estimates)
 
static void svm_save_model (String model_file_name, svm_model model) throws IOException
 
static svm_model svm_load_model (String model_file_name) throws IOException
 
static svm_model svm_load_model (BufferedReader fp) throws IOException
 
static String svm_check_parameter (svm_problem prob, svm_parameter param)
 
static int svm_check_probability_model (svm_model model)
 
static void svm_set_print_string_function (svm_print_interface print_func)
 
- - - - - -

-Static Public Attributes

static final int LIBSVM_VERSION =325
 
static final Random rand = new Random()
 
-

Detailed Description

-
-

Definition at line 1294 of file svm.java.

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Member Function Documentation

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◆ svm_check_parameter()

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static String libsvm.svm.svm_check_parameter (svm_problem prob,
svm_parameter param 
)
- 		-inlinestatic
-
- -

Definition at line 2726 of file svm.java.

-
2727  {
2728  // svm_type
2729 
2730  int svm_type = param.svm_type;
2731  if(svm_type != svm_parameter.C_SVC &&
2732  svm_type != svm_parameter.NU_SVC &&
2733  svm_type != svm_parameter.ONE_CLASS &&
2734  svm_type != svm_parameter.EPSILON_SVR &&
2735  svm_type != svm_parameter.NU_SVR)
2736  return "unknown svm type";
2737 
2738  // kernel_type, degree
2739 
2740  int kernel_type = param.kernel_type;
2741  if(kernel_type != svm_parameter.LINEAR &&
2742  kernel_type != svm_parameter.POLY &&
2743  kernel_type != svm_parameter.RBF &&
2744  kernel_type != svm_parameter.SIGMOID &&
2745  kernel_type != svm_parameter.PRECOMPUTED)
2746  return "unknown kernel type";
2747 
2748  if((kernel_type == svm_parameter.POLY ||
2749  kernel_type == svm_parameter.RBF ||
2750  kernel_type == svm_parameter.SIGMOID) &&
2751  param.gamma < 0)
2752  return "gamma < 0";
2753 
2754  if(kernel_type == svm_parameter.POLY && param.degree < 0)
2755  return "degree of polynomial kernel < 0";
2756 
2757  // cache_size,eps,C,nu,p,shrinking
2758 
2759  if(param.cache_size <= 0)
2760  return "cache_size <= 0";
2761 
2762  if(param.eps <= 0)
2763  return "eps <= 0";
2764 
2765  if(svm_type == svm_parameter.C_SVC ||
2766  svm_type == svm_parameter.EPSILON_SVR ||
2767  svm_type == svm_parameter.NU_SVR)
2768  if(param.C <= 0)
2769  return "C <= 0";
2770 
2771  if(svm_type == svm_parameter.NU_SVC ||
2772  svm_type == svm_parameter.ONE_CLASS ||
2773  svm_type == svm_parameter.NU_SVR)
2774  if(param.nu <= 0 || param.nu > 1)
2775  return "nu <= 0 or nu > 1";
2776 
2777  if(svm_type == svm_parameter.EPSILON_SVR)
2778  if(param.p < 0)
2779  return "p < 0";
2780 
2781  if(param.shrinking != 0 &&
2782  param.shrinking != 1)
2783  return "shrinking != 0 and shrinking != 1";
2784 
2785  if(param.probability != 0 &&
2786  param.probability != 1)
2787  return "probability != 0 and probability != 1";
2788 
2789  if(param.probability == 1 &&
2790  svm_type == svm_parameter.ONE_CLASS)
2791  return "one-class SVM probability output not supported yet";
2792 
2793  // check whether nu-svc is feasible
2794 
2795  if(svm_type == svm_parameter.NU_SVC)
2796  {
2797  int l = prob.l;
2798  int max_nr_class = 16;
2799  int nr_class = 0;
2800  int[] label = new int[max_nr_class];
2801  int[] count = new int[max_nr_class];
2802 
2803  int i;
2804  for(i=0;i<l;i++)
2805  {
2806  int this_label = (int)prob.y[i];
2807  int j;
2808  for(j=0;j<nr_class;j++)
2809  if(this_label == label[j])
2810  {
2811  ++count[j];
2812  break;
2813  }
2814 
2815  if(j == nr_class)
2816  {
2817  if(nr_class == max_nr_class)
2818  {
2819  max_nr_class *= 2;
2820  int[] new_data = new int[max_nr_class];
2821  System.arraycopy(label,0,new_data,0,label.length);
2822  label = new_data;
2823 
2824  new_data = new int[max_nr_class];
2825  System.arraycopy(count,0,new_data,0,count.length);
2826  count = new_data;
2827  }
2828  label[nr_class] = this_label;
2829  count[nr_class] = 1;
2830  ++nr_class;
2831  }
2832  }
2833 
2834  for(i=0;i<nr_class;i++)
2835  {
2836  int n1 = count[i];
2837  for(int j=i+1;j<nr_class;j++)
2838  {
2839  int n2 = count[j];
2840  if(param.nu*(n1+n2)/2 > Math.min(n1,n2))
2841  return "specified nu is infeasible";
2842  }
2843  }
2844  }
2845 
2846  return null;
2847  }
-
-
- -

◆ svm_check_probability_model()

- -
-
- - - - - -
- - - - - - - - -
static int libsvm.svm.svm_check_probability_model (svm_model model)
- 		-inlinestatic
-
- -

Definition at line 2849 of file svm.java.

-
2850  {
2851  if (((model.param.svm_type == svm_parameter.C_SVC || model.param.svm_type == svm_parameter.NU_SVC) &&
2852  model.probA!=null && model.probB!=null) ||
2853  ((model.param.svm_type == svm_parameter.EPSILON_SVR || model.param.svm_type == svm_parameter.NU_SVR) &&
2854  model.probA!=null))
2855  return 1;
2856  else
2857  return 0;
2858  }
-
-
- -

◆ svm_cross_validation()

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-
- - - - - -
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static void libsvm.svm.svm_cross_validation (svm_problem prob,
svm_parameter param,
int nr_fold,
double [] target 
)
- 		-inlinestatic
-
- -

Definition at line 2175 of file svm.java.

-
2176  {
2177  int i;
2178  int[] fold_start = new int[nr_fold+1];
2179  int l = prob.l;
2180  int[] perm = new int[l];
2181 
2182  // stratified cv may not give leave-one-out rate
2183  // Each class to l folds -> some folds may have zero elements
2184  if((param.svm_type == svm_parameter.C_SVC ||
2185  param.svm_type == svm_parameter.NU_SVC) && nr_fold < l)
2186  {
2187  int[] tmp_nr_class = new int[1];
2188  int[][] tmp_label = new int[1][];
2189  int[][] tmp_start = new int[1][];
2190  int[][] tmp_count = new int[1][];
2191 
2192  svm_group_classes(prob,tmp_nr_class,tmp_label,tmp_start,tmp_count,perm);
2193 
2194  int nr_class = tmp_nr_class[0];
2195  int[] start = tmp_start[0];
2196  int[] count = tmp_count[0];
2197 
2198  // random shuffle and then data grouped by fold using the array perm
2199  int[] fold_count = new int[nr_fold];
2200  int c;
2201  int[] index = new int[l];
2202  for(i=0;i<l;i++)
2203  index[i]=perm[i];
2204  for (c=0; c<nr_class; c++)
2205  for(i=0;i<count[c];i++)
2206  {
2207  int j = i+rand.nextInt(count[c]-i);
2208  do {int tmp=index[start[c]+j]; index[start[c]+j]=index[start[c]+i]; index[start[c]+i]=tmp;} while(false);
2209  }
2210  for(i=0;i<nr_fold;i++)
2211  {
2212  fold_count[i] = 0;
2213  for (c=0; c<nr_class;c++)
2214  fold_count[i]+=(i+1)*count[c]/nr_fold-i*count[c]/nr_fold;
2215  }
2216  fold_start[0]=0;
2217  for (i=1;i<=nr_fold;i++)
2218  fold_start[i] = fold_start[i-1]+fold_count[i-1];
2219  for (c=0; c<nr_class;c++)
2220  for(i=0;i<nr_fold;i++)
2221  {
2222  int begin = start[c]+i*count[c]/nr_fold;
2223  int end = start[c]+(i+1)*count[c]/nr_fold;
2224  for(int j=begin;j<end;j++)
2225  {
2226  perm[fold_start[i]] = index[j];
2227  fold_start[i]++;
2228  }
2229  }
2230  fold_start[0]=0;
2231  for (i=1;i<=nr_fold;i++)
2232  fold_start[i] = fold_start[i-1]+fold_count[i-1];
2233  }
2234  else
2235  {
2236  for(i=0;i<l;i++) perm[i]=i;
2237  for(i=0;i<l;i++)
2238  {
2239  int j = i+rand.nextInt(l-i);
2240  do {int tmp=perm[i]; perm[i]=perm[j]; perm[j]=tmp;} while(false);
2241  }
2242  for(i=0;i<=nr_fold;i++)
2243  fold_start[i]=i*l/nr_fold;
2244  }
2245 
2246  for(i=0;i<nr_fold;i++)
2247  {
2248  int begin = fold_start[i];
2249  int end = fold_start[i+1];
2250  int j,k;
2251  svm_problem subprob = new svm_problem();
2252 
2253  subprob.l = l-(end-begin);
2254  subprob.x = new svm_node[subprob.l][];
2255  subprob.y = new double[subprob.l];
2256 
2257  k=0;
2258  for(j=0;j<begin;j++)
2259  {
2260  subprob.x[k] = prob.x[perm[j]];
2261  subprob.y[k] = prob.y[perm[j]];
2262  ++k;
2263  }
2264  for(j=end;j<l;j++)
2265  {
2266  subprob.x[k] = prob.x[perm[j]];
2267  subprob.y[k] = prob.y[perm[j]];
2268  ++k;
2269  }
2270  svm_model submodel = svm_train(subprob,param);
2271  if(param.probability==1 &&
2272  (param.svm_type == svm_parameter.C_SVC ||
2273  param.svm_type == svm_parameter.NU_SVC))
2274  {
2275  double[] prob_estimates= new double[svm_get_nr_class(submodel)];
2276  for(j=begin;j<end;j++)
2277  target[perm[j]] = svm_predict_probability(submodel,prob.x[perm[j]],prob_estimates);
2278  }
2279  else
2280  for(j=begin;j<end;j++)
2281  target[perm[j]] = svm_predict(submodel,prob.x[perm[j]]);
2282  }
2283  }
libsvm.svm.svm_train
static svm_model svm_train(svm_problem prob, svm_parameter param)
Definition: svm.java:1938
-
libsvm.svm.svm_predict_probability
static double svm_predict_probability(svm_model model, svm_node[] x, double[] prob_estimates)
Definition: svm.java:2413
-
libsvm.svm.rand
static final Random rand
Definition: svm.java:1299
-
libsvm.svm.svm_get_nr_class
static int svm_get_nr_class(svm_model model)
Definition: svm.java:2290
-
libsvm.svm.svm_predict
static double svm_predict(svm_model model, svm_node[] x)
Definition: svm.java:2399
-
-
-
- -

◆ svm_get_labels()

- -
-
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- - - - - - - - - - - - - - - - - - -
static void libsvm.svm.svm_get_labels (svm_model model,
int [] label 
)
- 		-inlinestatic
-
- -

Definition at line 2295 of file svm.java.

-
2296  {
2297  if (model.label != null)
2298  for(int i=0;i<model.nr_class;i++)
2299  label[i] = model.label[i];
2300  }
-
-
- -

◆ svm_get_nr_class()

- -
-
- - - - - -
- - - - - - - - -
static int libsvm.svm.svm_get_nr_class (svm_model model)
- 		-inlinestatic
-
- -

Definition at line 2290 of file svm.java.

-
2291  {
2292  return model.nr_class;
2293  }
-
-
- -

◆ svm_get_nr_sv()

- -
-
- - - - - -
- - - - - - - - -
static int libsvm.svm.svm_get_nr_sv (svm_model model)
- 		-inlinestatic
-
- -

Definition at line 2309 of file svm.java.

-
2310  {
2311  return model.l;
2312  }
-
-
- -

◆ svm_get_sv_indices()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
static void libsvm.svm.svm_get_sv_indices (svm_model model,
int [] indices 
)
- 		-inlinestatic
-
- -

Definition at line 2302 of file svm.java.

-
2303  {
2304  if (model.sv_indices != null)
2305  for(int i=0;i<model.l;i++)
2306  indices[i] = model.sv_indices[i];
2307  }
-
-
- -

◆ svm_get_svm_type()

- -
-
- - - - - -
- - - - - - - - -
static int libsvm.svm.svm_get_svm_type (svm_model model)
- 		-inlinestatic
-
- -

Definition at line 2285 of file svm.java.

-
2286  {
2287  return model.param.svm_type;
2288  }
-
-
- -

◆ svm_get_svr_probability()

- -
-
- - - - - -
- - - - - - - - -
static double libsvm.svm.svm_get_svr_probability (svm_model model)
- 		-inlinestatic
-
- -

Definition at line 2314 of file svm.java.

-
2315  {
2316  if ((model.param.svm_type == svm_parameter.EPSILON_SVR || model.param.svm_type == svm_parameter.NU_SVR) &&
2317  model.probA!=null)
2318  return model.probA[0];
2319  else
2320  {
2321  System.err.print("Model doesn't contain information for SVR probability inference\n");
2322  return 0;
2323  }
2324  }
-
-
- -

◆ svm_load_model() [1/2]

- -
-
- - - - - -
- - - - - - - - -
static svm_model libsvm.svm.svm_load_model (String model_file_name) throws IOException
- 		-inlinestatic
-
- -

Definition at line 2675 of file svm.java.

-
2676  {
2677  return svm_load_model(new BufferedReader(new FileReader(model_file_name)));
2678  }
libsvm.svm.svm_load_model
static svm_model svm_load_model(String model_file_name)
Definition: svm.java:2675
-
-
-
- -

◆ svm_load_model() [2/2]

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-
- - - - - -
- - - - - - - - -
static svm_model libsvm.svm.svm_load_model (BufferedReader fp) throws IOException
- 		-inlinestatic
-
- -

Definition at line 2680 of file svm.java.

-
2681  {
2682  // read parameters
2683 
2684  svm_model model = new svm_model();
2685  model.rho = null;
2686  model.probA = null;
2687  model.probB = null;
2688  model.label = null;
2689  model.nSV = null;
2690 
2691  // read header
2692  if (!read_model_header(fp, model))
2693  {
2694  System.err.print("ERROR: failed to read model\n");
2695  return null;
2696  }
2697 
2698  // read sv_coef and SV
2699 
2700  int m = model.nr_class - 1;
2701  int l = model.l;
2702  model.sv_coef = new double[m][l];
2703  model.SV = new svm_node[l][];
2704 
2705  for(int i=0;i<l;i++)
2706  {
2707  String line = fp.readLine();
2708  StringTokenizer st = new StringTokenizer(line," \t\n\r\f:");
2709 
2710  for(int k=0;k<m;k++)
2711  model.sv_coef[k][i] = atof(st.nextToken());
2712  int n = st.countTokens()/2;
2713  model.SV[i] = new svm_node[n];
2714  for(int j=0;j<n;j++)
2715  {
2716  model.SV[i][j] = new svm_node();
2717  model.SV[i][j].index = atoi(st.nextToken());
2718  model.SV[i][j].value = atof(st.nextToken());
2719  }
2720  }
2721 
2722  fp.close();
2723  return model;
2724  }
-
-
- -

◆ svm_predict()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
static double libsvm.svm.svm_predict (svm_model model,
svm_node [] x 
)
- 		-inlinestatic
-
- -

Definition at line 2399 of file svm.java.

-
2400  {
2401  int nr_class = model.nr_class;
2402  double[] dec_values;
2403  if(model.param.svm_type == svm_parameter.ONE_CLASS ||
2404  model.param.svm_type == svm_parameter.EPSILON_SVR ||
2405  model.param.svm_type == svm_parameter.NU_SVR)
2406  dec_values = new double[1];
2407  else
2408  dec_values = new double[nr_class*(nr_class-1)/2];
2409  double pred_result = svm_predict_values(model, x, dec_values);
2410  return pred_result;
2411  }
libsvm.svm.svm_predict_values
static double svm_predict_values(svm_model model, svm_node[] x, double[] dec_values)
Definition: svm.java:2326
-
-
-
- -

◆ svm_predict_probability()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - -
static double libsvm.svm.svm_predict_probability (svm_model model,
svm_node [] x,
double [] prob_estimates 
)
- 		-inlinestatic
-
- -

Definition at line 2413 of file svm.java.

-
2414  {
2415  if ((model.param.svm_type == svm_parameter.C_SVC || model.param.svm_type == svm_parameter.NU_SVC) &&
2416  model.probA!=null && model.probB!=null)
2417  {
2418  int i;
2419  int nr_class = model.nr_class;
2420  double[] dec_values = new double[nr_class*(nr_class-1)/2];
2421  svm_predict_values(model, x, dec_values);
2422 
2423  double min_prob=1e-7;
2424  double[][] pairwise_prob=new double[nr_class][nr_class];
2425 
2426  int k=0;
2427  for(i=0;i<nr_class;i++)
2428  for(int j=i+1;j<nr_class;j++)
2429  {
2430  pairwise_prob[i][j]=Math.min(Math.max(sigmoid_predict(dec_values[k],model.probA[k],model.probB[k]),min_prob),1-min_prob);
2431  pairwise_prob[j][i]=1-pairwise_prob[i][j];
2432  k++;
2433  }
2434  if (nr_class == 2)
2435  {
2436  prob_estimates[0] = pairwise_prob[0][1];
2437  prob_estimates[1] = pairwise_prob[1][0];
2438  }
2439  else
2440  multiclass_probability(nr_class,pairwise_prob,prob_estimates);
2441 
2442  int prob_max_idx = 0;
2443  for(i=1;i<nr_class;i++)
2444  if(prob_estimates[i] > prob_estimates[prob_max_idx])
2445  prob_max_idx = i;
2446  return model.label[prob_max_idx];
2447  }
2448  else
2449  return svm_predict(model, x);
2450  }
libsvm.svm.svm_predict
static double svm_predict(svm_model model, svm_node[] x)
Definition: svm.java:2399
-
libsvm.svm.svm_predict_values
static double svm_predict_values(svm_model model, svm_node[] x, double[] dec_values)
Definition: svm.java:2326
-
-
-
- -

◆ svm_predict_values()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - -
static double libsvm.svm.svm_predict_values (svm_model model,
svm_node [] x,
double [] dec_values 
)
- 		-inlinestatic
-
- -

Definition at line 2326 of file svm.java.

-
2327  {
2328  int i;
2329  if(model.param.svm_type == svm_parameter.ONE_CLASS ||
2330  model.param.svm_type == svm_parameter.EPSILON_SVR ||
2331  model.param.svm_type == svm_parameter.NU_SVR)
2332  {
2333  double[] sv_coef = model.sv_coef[0];
2334  double sum = 0;
2335  for(i=0;i<model.l;i++)
2336  sum += sv_coef[i] * Kernel.k_function(x,model.SV[i],model.param);
2337  sum -= model.rho[0];
2338  dec_values[0] = sum;
2339 
2340  if(model.param.svm_type == svm_parameter.ONE_CLASS)
2341  return (sum>0)?1:-1;
2342  else
2343  return sum;
2344  }
2345  else
2346  {
2347  int nr_class = model.nr_class;
2348  int l = model.l;
2349 
2350  double[] kvalue = new double[l];
2351  for(i=0;i<l;i++)
2352  kvalue[i] = Kernel.k_function(x,model.SV[i],model.param);
2353 
2354  int[] start = new int[nr_class];
2355  start[0] = 0;
2356  for(i=1;i<nr_class;i++)
2357  start[i] = start[i-1]+model.nSV[i-1];
2358 
2359  int[] vote = new int[nr_class];
2360  for(i=0;i<nr_class;i++)
2361  vote[i] = 0;
2362 
2363  int p=0;
2364  for(i=0;i<nr_class;i++)
2365  for(int j=i+1;j<nr_class;j++)
2366  {
2367  double sum = 0;
2368  int si = start[i];
2369  int sj = start[j];
2370  int ci = model.nSV[i];
2371  int cj = model.nSV[j];
2372 
2373  int k;
2374  double[] coef1 = model.sv_coef[j-1];
2375  double[] coef2 = model.sv_coef[i];
2376  for(k=0;k<ci;k++)
2377  sum += coef1[si+k] * kvalue[si+k];
2378  for(k=0;k<cj;k++)
2379  sum += coef2[sj+k] * kvalue[sj+k];
2380  sum -= model.rho[p];
2381  dec_values[p] = sum;
2382 
2383  if(dec_values[p] > 0)
2384  ++vote[i];
2385  else
2386  ++vote[j];
2387  p++;
2388  }
2389 
2390  int vote_max_idx = 0;
2391  for(i=1;i<nr_class;i++)
2392  if(vote[i] > vote[vote_max_idx])
2393  vote_max_idx = i;
2394 
2395  return model.label[vote_max_idx];
2396  }
2397  }
-
-
- -

◆ svm_save_model()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
static void libsvm.svm.svm_save_model (String model_file_name,
svm_model model 
) throws IOException
- 		-inlinestatic
-
- -

Definition at line 2462 of file svm.java.

-
2463  {
2464  DataOutputStream fp = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(model_file_name)));
2465 
2466  svm_parameter param = model.param;
2467 
2468  fp.writeBytes("svm_type "+svm_type_table[param.svm_type]+"\n");
2469  fp.writeBytes("kernel_type "+kernel_type_table[param.kernel_type]+"\n");
2470 
2471  if(param.kernel_type == svm_parameter.POLY)
2472  fp.writeBytes("degree "+param.degree+"\n");
2473 
2474  if(param.kernel_type == svm_parameter.POLY ||
2475  param.kernel_type == svm_parameter.RBF ||
2476  param.kernel_type == svm_parameter.SIGMOID)
2477  fp.writeBytes("gamma "+param.gamma+"\n");
2478 
2479  if(param.kernel_type == svm_parameter.POLY ||
2480  param.kernel_type == svm_parameter.SIGMOID)
2481  fp.writeBytes("coef0 "+param.coef0+"\n");
2482 
2483  int nr_class = model.nr_class;
2484  int l = model.l;
2485  fp.writeBytes("nr_class "+nr_class+"\n");
2486  fp.writeBytes("total_sv "+l+"\n");
2487 
2488  {
2489  fp.writeBytes("rho");
2490  for(int i=0;i<nr_class*(nr_class-1)/2;i++)
2491  fp.writeBytes(" "+model.rho[i]);
2492  fp.writeBytes("\n");
2493  }
2494 
2495  if(model.label != null)
2496  {
2497  fp.writeBytes("label");
2498  for(int i=0;i<nr_class;i++)
2499  fp.writeBytes(" "+model.label[i]);
2500  fp.writeBytes("\n");
2501  }
2502 
2503  if(model.probA != null) // regression has probA only
2504  {
2505  fp.writeBytes("probA");
2506  for(int i=0;i<nr_class*(nr_class-1)/2;i++)
2507  fp.writeBytes(" "+model.probA[i]);
2508  fp.writeBytes("\n");
2509  }
2510  if(model.probB != null)
2511  {
2512  fp.writeBytes("probB");
2513  for(int i=0;i<nr_class*(nr_class-1)/2;i++)
2514  fp.writeBytes(" "+model.probB[i]);
2515  fp.writeBytes("\n");
2516  }
2517 
2518  if(model.nSV != null)
2519  {
2520  fp.writeBytes("nr_sv");
2521  for(int i=0;i<nr_class;i++)
2522  fp.writeBytes(" "+model.nSV[i]);
2523  fp.writeBytes("\n");
2524  }
2525 
2526  fp.writeBytes("SV\n");
2527  double[][] sv_coef = model.sv_coef;
2528  svm_node[][] SV = model.SV;
2529 
2530  for(int i=0;i<l;i++)
2531  {
2532  for(int j=0;j<nr_class-1;j++)
2533  fp.writeBytes(sv_coef[j][i]+" ");
2534 
2535  svm_node[] p = SV[i];
2536  if(param.kernel_type == svm_parameter.PRECOMPUTED)
2537  fp.writeBytes("0:"+(int)(p[0].value));
2538  else
2539  for(int j=0;j<p.length;j++)
2540  fp.writeBytes(p[j].index+":"+p[j].value+" ");
2541  fp.writeBytes("\n");
2542  }
2543 
2544  fp.close();
2545  }
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◆ svm_set_print_string_function()

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Definition at line 2860 of file svm.java.

-
2861  {
2862  if (print_func == null)
2863  svm_print_string = svm_print_stdout;
2864  else
2865  svm_print_string = print_func;
2866  }
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static svm_model libsvm.svm.svm_train (svm_problem prob,
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Definition at line 1938 of file svm.java.

-
1939  {
1940  svm_model model = new svm_model();
1941  model.param = param;
1942 
1943  if(param.svm_type == svm_parameter.ONE_CLASS ||
1944  param.svm_type == svm_parameter.EPSILON_SVR ||
1945  param.svm_type == svm_parameter.NU_SVR)
1946  {
1947  // regression or one-class-svm
1948  model.nr_class = 2;
1949  model.label = null;
1950  model.nSV = null;
1951  model.probA = null; model.probB = null;
1952  model.sv_coef = new double[1][];
1953 
1954  if(param.probability == 1 &&
1955  (param.svm_type == svm_parameter.EPSILON_SVR ||
1956  param.svm_type == svm_parameter.NU_SVR))
1957  {
1958  model.probA = new double[1];
1959  model.probA[0] = svm_svr_probability(prob,param);
1960  }
1961 
1962  decision_function f = svm_train_one(prob,param,0,0);
1963  model.rho = new double[1];
1964  model.rho[0] = f.rho;
1965 
1966  int nSV = 0;
1967  int i;
1968  for(i=0;i<prob.l;i++)
1969  if(Math.abs(f.alpha[i]) > 0) ++nSV;
1970  model.l = nSV;
1971  model.SV = new svm_node[nSV][];
1972  model.sv_coef[0] = new double[nSV];
1973  model.sv_indices = new int[nSV];
1974  int j = 0;
1975  for(i=0;i<prob.l;i++)
1976  if(Math.abs(f.alpha[i]) > 0)
1977  {
1978  model.SV[j] = prob.x[i];
1979  model.sv_coef[0][j] = f.alpha[i];
1980  model.sv_indices[j] = i+1;
1981  ++j;
1982  }
1983  }
1984  else
1985  {
1986  // classification
1987  int l = prob.l;
1988  int[] tmp_nr_class = new int[1];
1989  int[][] tmp_label = new int[1][];
1990  int[][] tmp_start = new int[1][];
1991  int[][] tmp_count = new int[1][];
1992  int[] perm = new int[l];
1993 
1994  // group training data of the same class
1995  svm_group_classes(prob,tmp_nr_class,tmp_label,tmp_start,tmp_count,perm);
1996  int nr_class = tmp_nr_class[0];
1997  int[] label = tmp_label[0];
1998  int[] start = tmp_start[0];
1999  int[] count = tmp_count[0];
2000 
2001  if(nr_class == 1)
2002  svm.info("WARNING: training data in only one class. See README for details.\n");
2003 
2004  svm_node[][] x = new svm_node[l][];
2005  int i;
2006  for(i=0;i<l;i++)
2007  x[i] = prob.x[perm[i]];
2008 
2009  // calculate weighted C
2010 
2011  double[] weighted_C = new double[nr_class];
2012  for(i=0;i<nr_class;i++)
2013  weighted_C[i] = param.C;
2014  for(i=0;i<param.nr_weight;i++)
2015  {
2016  int j;
2017  for(j=0;j<nr_class;j++)
2018  if(param.weight_label[i] == label[j])
2019  break;
2020  if(j == nr_class)
2021  System.err.print("WARNING: class label "+param.weight_label[i]+" specified in weight is not found\n");
2022  else
2023  weighted_C[j] *= param.weight[i];
2024  }
2025 
2026  // train k*(k-1)/2 models
2027 
2028  boolean[] nonzero = new boolean[l];
2029  for(i=0;i<l;i++)
2030  nonzero[i] = false;
2031  decision_function[] f = new decision_function[nr_class*(nr_class-1)/2];
2032 
2033  double[] probA=null,probB=null;
2034  if (param.probability == 1)
2035  {
2036  probA=new double[nr_class*(nr_class-1)/2];
2037  probB=new double[nr_class*(nr_class-1)/2];
2038  }
2039 
2040  int p = 0;
2041  for(i=0;i<nr_class;i++)
2042  for(int j=i+1;j<nr_class;j++)
2043  {
2044  svm_problem sub_prob = new svm_problem();
2045  int si = start[i], sj = start[j];
2046  int ci = count[i], cj = count[j];
2047  sub_prob.l = ci+cj;
2048  sub_prob.x = new svm_node[sub_prob.l][];
2049  sub_prob.y = new double[sub_prob.l];
2050  int k;
2051  for(k=0;k<ci;k++)
2052  {
2053  sub_prob.x[k] = x[si+k];
2054  sub_prob.y[k] = +1;
2055  }
2056  for(k=0;k<cj;k++)
2057  {
2058  sub_prob.x[ci+k] = x[sj+k];
2059  sub_prob.y[ci+k] = -1;
2060  }
2061 
2062  if(param.probability == 1)
2063  {
2064  double[] probAB=new double[2];
2065  svm_binary_svc_probability(sub_prob,param,weighted_C[i],weighted_C[j],probAB);
2066  probA[p]=probAB[0];
2067  probB[p]=probAB[1];
2068  }
2069 
2070  f[p] = svm_train_one(sub_prob,param,weighted_C[i],weighted_C[j]);
2071  for(k=0;k<ci;k++)
2072  if(!nonzero[si+k] && Math.abs(f[p].alpha[k]) > 0)
2073  nonzero[si+k] = true;
2074  for(k=0;k<cj;k++)
2075  if(!nonzero[sj+k] && Math.abs(f[p].alpha[ci+k]) > 0)
2076  nonzero[sj+k] = true;
2077  ++p;
2078  }
2079 
2080  // build output
2081 
2082  model.nr_class = nr_class;
2083 
2084  model.label = new int[nr_class];
2085  for(i=0;i<nr_class;i++)
2086  model.label[i] = label[i];
2087 
2088  model.rho = new double[nr_class*(nr_class-1)/2];
2089  for(i=0;i<nr_class*(nr_class-1)/2;i++)
2090  model.rho[i] = f[i].rho;
2091 
2092  if(param.probability == 1)
2093  {
2094  model.probA = new double[nr_class*(nr_class-1)/2];
2095  model.probB = new double[nr_class*(nr_class-1)/2];
2096  for(i=0;i<nr_class*(nr_class-1)/2;i++)
2097  {
2098  model.probA[i] = probA[i];
2099  model.probB[i] = probB[i];
2100  }
2101  }
2102  else
2103  {
2104  model.probA=null;
2105  model.probB=null;
2106  }
2107 
2108  int total_sv = 0;
2109  int[] nz_count = new int[nr_class];
2110  model.nSV = new int[nr_class];
2111  for(i=0;i<nr_class;i++)
2112  {
2113  int nSV = 0;
2114  for(int j=0;j<count[i];j++)
2115  if(nonzero[start[i]+j])
2116  {
2117  ++nSV;
2118  ++total_sv;
2119  }
2120  model.nSV[i] = nSV;
2121  nz_count[i] = nSV;
2122  }
2123 
2124  svm.info("Total nSV = "+total_sv+"\n");
2125 
2126  model.l = total_sv;
2127  model.SV = new svm_node[total_sv][];
2128  model.sv_indices = new int[total_sv];
2129  p = 0;
2130  for(i=0;i<l;i++)
2131  if(nonzero[i])
2132  {
2133  model.SV[p] = x[i];
2134  model.sv_indices[p++] = perm[i] + 1;
2135  }
2136 
2137  int[] nz_start = new int[nr_class];
2138  nz_start[0] = 0;
2139  for(i=1;i<nr_class;i++)
2140  nz_start[i] = nz_start[i-1]+nz_count[i-1];
2141 
2142  model.sv_coef = new double[nr_class-1][];
2143  for(i=0;i<nr_class-1;i++)
2144  model.sv_coef[i] = new double[total_sv];
2145 
2146  p = 0;
2147  for(i=0;i<nr_class;i++)
2148  for(int j=i+1;j<nr_class;j++)
2149  {
2150  // classifier (i,j): coefficients with
2151  // i are in sv_coef[j-1][nz_start[i]...],
2152  // j are in sv_coef[i][nz_start[j]...]
2153 
2154  int si = start[i];
2155  int sj = start[j];
2156  int ci = count[i];
2157  int cj = count[j];
2158 
2159  int q = nz_start[i];
2160  int k;
2161  for(k=0;k<ci;k++)
2162  if(nonzero[si+k])
2163  model.sv_coef[j-1][q++] = f[p].alpha[k];
2164  q = nz_start[j];
2165  for(k=0;k<cj;k++)
2166  if(nonzero[sj+k])
2167  model.sv_coef[i][q++] = f[p].alpha[ci+k];
2168  ++p;
2169  }
2170  }
2171  return model;
2172  }
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Member Data Documentation

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◆ LIBSVM_VERSION

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Definition at line 1298 of file svm.java.

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Definition at line 1299 of file svm.java.

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svm_parameter param
 
int nr_class
 
int l
 
svm_node [][] SV
 
double [][] sv_coef
 
double [] rho
 
double [] probA
 
double [] probB
 
int [] sv_indices
 
int [] label
 
int [] nSV
 
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Definition at line 5 of file svm_model.java.

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Member Data Documentation

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◆ l

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Definition at line 9 of file svm_model.java.

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Definition at line 19 of file svm_model.java.

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Definition at line 8 of file svm_model.java.

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Definition at line 20 of file svm_model.java.

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svm_parameter libsvm.svm_model.param
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Definition at line 7 of file svm_model.java.

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Definition at line 14 of file svm_model.java.

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Definition at line 12 of file svm_model.java.

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◆ SV

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Definition at line 11 of file svm_model.java.

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Definition at line 15 of file svm_model.java.

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int index
 
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Definition at line 2 of file svm_node.java.

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Definition at line 4 of file svm_node.java.

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Definition at line 5 of file svm_node.java.

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Object clone ()
 
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int svm_type
 
int kernel_type
 
int degree
 
double gamma
 
double coef0
 
double cache_size
 
double eps
 
double C
 
int nr_weight
 
int [] weight_label
 
double [] weight
 
double nu
 
double p
 
int shrinking
 
int probability
 
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static final int C_SVC = 0
 
static final int NU_SVC = 1
 
static final int ONE_CLASS = 2
 
static final int EPSILON_SVR = 3
 
static final int NU_SVR = 4
 
static final int LINEAR = 0
 
static final int POLY = 1
 
static final int RBF = 2
 
static final int SIGMOID = 3
 
static final int PRECOMPUTED = 4
 
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Definition at line 2 of file svm_parameter.java.

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Definition at line 36 of file svm_parameter.java.

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Definition at line 27 of file svm_parameter.java.

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Definition at line 5 of file svm_parameter.java.

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Definition at line 26 of file svm_parameter.java.

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Definition at line 21 of file svm_parameter.java.

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Definition at line 19 of file svm_parameter.java.

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Definition at line 12 of file svm_parameter.java.

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Definition at line 28 of file svm_parameter.java.

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Definition at line 31 of file svm_parameter.java.

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Definition at line 6 of file svm_parameter.java.

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Definition at line 7 of file svm_parameter.java.

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Definition at line 32 of file svm_parameter.java.

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Definition at line 13 of file svm_parameter.java.

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Definition at line 16 of file svm_parameter.java.

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Definition at line 34 of file svm_parameter.java.

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Definition at line 14 of file svm_parameter.java.

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Definition at line 33 of file svm_parameter.java.

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Definition at line 15 of file svm_parameter.java.

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Definition at line 18 of file svm_parameter.java.

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Definition at line 30 of file svm_parameter.java.

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Definition at line 29 of file svm_parameter.java.

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Definition at line 2 of file svm_problem.java.

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Definition at line 4 of file svm_problem.java.

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Definition at line 5 of file svm_problem.java.

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Definition at line 8 of file svm_toy.java.

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48  setSize(getSize());
49 
50  final Button button_change = new Button("Change");
51  Button button_run = new Button("Run");
52  Button button_clear = new Button("Clear");
53  Button button_save = new Button("Save");
54  Button button_load = new Button("Load");
55  final TextField input_line = new TextField(DEFAULT_PARAM);
56 
57  BorderLayout layout = new BorderLayout();
58  this.setLayout(layout);
59 
60  Panel p = new Panel();
61  GridBagLayout gridbag = new GridBagLayout();
62  p.setLayout(gridbag);
63 
64  GridBagConstraints c = new GridBagConstraints();
65  c.fill = GridBagConstraints.HORIZONTAL;
66  c.weightx = 1;
67  c.gridwidth = 1;
68  gridbag.setConstraints(button_change,c);
69  gridbag.setConstraints(button_run,c);
70  gridbag.setConstraints(button_clear,c);
71  gridbag.setConstraints(button_save,c);
72  gridbag.setConstraints(button_load,c);
73  c.weightx = 5;
74  c.gridwidth = 5;
75  gridbag.setConstraints(input_line,c);
76 
77  button_change.setBackground(colors[current_value]);
78 
79  p.add(button_change);
80  p.add(button_run);
81  p.add(button_clear);
82  p.add(button_save);
83  p.add(button_load);
84  p.add(input_line);
85  this.add(p,BorderLayout.SOUTH);
86 
87  button_change.addActionListener(new ActionListener()
88  { public void actionPerformed (ActionEvent e)
89  { button_change_clicked(); button_change.setBackground(colors[current_value]); }});
90 
91  button_run.addActionListener(new ActionListener()
92  { public void actionPerformed (ActionEvent e)
93  { button_run_clicked(input_line.getText()); }});
94 
95  button_clear.addActionListener(new ActionListener()
96  { public void actionPerformed (ActionEvent e)
97  { button_clear_clicked(); }});
98 
99  button_save.addActionListener(new ActionListener()
100  { public void actionPerformed (ActionEvent e)
101  { button_save_clicked(input_line.getText()); }});
102 
103  button_load.addActionListener(new ActionListener()
104  { public void actionPerformed (ActionEvent e)
105  { button_load_clicked(); }});
106 
107  input_line.addActionListener(new ActionListener()
108  { public void actionPerformed (ActionEvent e)
109  { button_run_clicked(input_line.getText()); }});
110 
111  this.enableEvents(AWTEvent.MOUSE_EVENT_MASK);
112  }
svm_toy.setSize
void setSize(Dimension d)
Definition: svm_toy.java:472
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481  {
482  new AppletFrame("svm_toy",new svm_toy(),500,500+50);
483  }
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Definition at line 458 of file svm_toy.java.

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459  {
460  // create buffer first time
461  if(buffer == null) {
462  buffer = this.createImage(XLEN,YLEN);
463  buffer_gc = buffer.getGraphics();
464  buffer_gc.setColor(colors[0]);
465  buffer_gc.fillRect(0,0,XLEN,YLEN);
466  }
467  g.drawImage(buffer,0,0,this);
468  }
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446  {
447  if(e.getID() == MouseEvent.MOUSE_PRESSED)
448  {
449  if(e.getX() >= XLEN || e.getY() >= YLEN) return;
450  point p = new point((double)e.getX()/XLEN,
451  (double)e.getY()/YLEN,
452  current_value);
453  point_list.addElement(p);
454  draw_point(p);
455  }
456  }
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473  {
474  super.setSize(w,h);
475  XLEN = w;
476  YLEN = h-50;
477  clear_all();
478  }
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- - diff --git a/html/classsvm__toy__coll__graph.dot b/html/classsvm__toy__coll__graph.dot deleted file mode 100644 index 199bce0c..00000000 --- a/html/classsvm__toy__coll__graph.dot +++ /dev/null @@ -1,16 +0,0 @@ -digraph "svm_toy" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="svm_toy",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="Applet",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node4 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" colors" ,fontname="Helvetica"]; - Node4 [label="Color",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" point_list" ,fontname="Helvetica"]; - Node5 [label="Vector\< point \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" buffer_gc" ,fontname="Helvetica"]; - Node6 [label="Graphics",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" buffer" ,fontname="Helvetica"]; - Node7 [label="Image",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classsvm__toy__coll__graph.md5 b/html/classsvm__toy__coll__graph.md5 deleted file mode 100644 index 05b83447..00000000 --- a/html/classsvm__toy__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -a248b28ce0ba7c574204befde5faff44 \ No newline at end of file diff --git a/html/classsvm__toy__inherit__graph.dot b/html/classsvm__toy__inherit__graph.dot deleted file mode 100644 index 9ffedb0d..00000000 --- a/html/classsvm__toy__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "svm_toy" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="svm_toy",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="Applet",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classsvm__toy__inherit__graph.md5 b/html/classsvm__toy__inherit__graph.md5 deleted file mode 100644 index 0c03d53c..00000000 --- a/html/classsvm__toy__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -988ed94792e8b2eecd51cc5150c32384 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame-members.html b/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame-members.html deleted file mode 100644 index b4f919a7..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame-members.html +++ /dev/null @@ -1,93 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.ij.commons.DesignMaskJFrame Member List
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This is the complete list of members for xmipp.ij.commons.DesignMaskJFrame, including all inherited members.

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actionPerformed(ActionEvent ae)xmipp.ij.commons.DesignMaskJFrameinline
createDefaultMask()xmipp.ij.commons.DesignMaskJFrameinlineprotected
DesignMaskJFrame(XmippImageWindow iw)xmipp.ij.commons.DesignMaskJFrameinline
initComponents()xmipp.ij.commons.DesignMaskJFrameinlineprotected
isAddRoi()xmipp.ij.commons.DesignMaskJFrameinline
isInvert()xmipp.ij.commons.DesignMaskJFrameinline
isSmooth()xmipp.ij.commons.DesignMaskJFrameinline
maskxmipp.ij.commons.DesignMaskJFrameprotected
refreshMask()xmipp.ij.commons.DesignMaskJFrameinline
registerMask()xmipp.ij.commons.DesignMaskJFrameinlineprotected
widthxmipp.ij.commons.DesignMaskJFrameprotected
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xmipp.ij.commons.DesignMaskJFrame Class Reference
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-Public Member Functions

 DesignMaskJFrame (XmippImageWindow iw)
 
boolean isInvert ()
 
boolean isSmooth ()
 
boolean isAddRoi ()
 
void refreshMask ()
 
void actionPerformed (ActionEvent ae)
 
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-Protected Member Functions

void initComponents ()
 
void registerMask ()
 
void createDefaultMask ()
 
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-Protected Attributes

ImagePlus mask
 
int width
 
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Detailed Description

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Author
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Definition at line 43 of file DesignMaskJFrame.java.

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◆ DesignMaskJFrame()

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xmipp.ij.commons.DesignMaskJFrame.DesignMaskJFrame (XmippImageWindow iw)
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Definition at line 56 of file DesignMaskJFrame.java.

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57  {
58  this.iw = iw;
59  createMask();
60  XmippUtil.showImageJ(Tool.VIEWER);
61  IJ.setTool(Toolbar.OVAL);
62  initComponents();
63  }
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◆ actionPerformed()

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void xmipp.ij.commons.DesignMaskJFrame.actionPerformed (ActionEvent ae)
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Definition at line 224 of file DesignMaskJFrame.java.

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224  {
225  smoothtf.setEnabled(isSmooth());
226  createMask();
227  imagepn.setMask(mask, width, height);
228 
229  }
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void setMask(ImagePlus mask, int width, int height)
Definition: ImageJPanel.java:46
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void xmipp.ij.commons.DesignMaskJFrame.createDefaultMask ()
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Definition at line 208 of file DesignMaskJFrame.java.

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209  {
210  FloatProcessor processor = new FloatProcessor(imp.getWidth(), imp.getHeight());
211  mask = new ImagePlus("Mask", processor);
212 
213 
214  }
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Definition at line 65 of file DesignMaskJFrame.java.

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66  {
67  setTitle("Design Mask");
68  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
69 
70  GridBagConstraints constraints = new GridBagConstraints();
71  constraints.insets = new Insets(0, 5, 0, 5);
72  constraints.anchor = GridBagConstraints.WEST;
73  setLayout(new GridBagLayout());
74  JToolBar optionspn = new JToolBar();
75 
76  optionspn.setFloatable(false);
77  add(optionspn, XmippWindowUtil.getConstraints(constraints, 0, 0));
78  refreshbt = XmippWindowUtil.getIconButton("fa-refresh.png", new ActionListener()
79  {
80 
81  @Override
82  public void actionPerformed(ActionEvent e)
83  {
84  refreshMask();
85 
86  }
87  });
88  optionspn.add(refreshbt);
89  invertbt = new JCheckBox("Invert:");
90  invertbt.addActionListener(this);
91  optionspn.add(invertbt);
92 
93  smoothbt = new JCheckBox("Smooth:");
94  smoothbt.addActionListener(this);
95  optionspn.add(smoothbt);
96  smoothtf = new JFormattedTextField(NumberFormat.getIntegerInstance());
97  smoothtf.setColumns(2);
98  smoothtf.setValue(2);
99  smoothtf.addActionListener(this);
100  smoothtf.setEnabled(false);
101  optionspn.add(smoothtf);
102  imagepn = new ImageJPanel(mask, width, height);
103  add(imagepn, XmippWindowUtil.getConstraints(constraints, 0, 1));
104 
105 
106  JPanel commandspn = new JPanel(new FlowLayout(FlowLayout.RIGHT));
107  add(commandspn, XmippWindowUtil.getConstraints(constraints, 0, 2, 1, 1, GridBagConstraints.HORIZONTAL));
108 
109 
110  registerbt = XmippWindowUtil.getScipionIconButton("Create Mask");
111  registerbt.addActionListener(new ActionListener() {
112 
113  @Override
114  public void actionPerformed(ActionEvent ae) {
115  registerMask();
116  }
117 
118  });
119 
120  commandspn.add(registerbt);
121  registerbt.setVisible(XmippApplication.isScipion());
122  pack();
123  setVisible(true);
124 
125  }
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Definition at line 201 of file DesignMaskJFrame.java.

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202  {
203  if(addbt == null)
204  return false;
205  return addbt.isSelected();
206  }
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Definition at line 187 of file DesignMaskJFrame.java.

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188  {
189  if(invertbt == null)
190  return false;
191  return invertbt.isSelected();
192  }
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Definition at line 194 of file DesignMaskJFrame.java.

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195  {
196  if(smoothbt == null)
197  return false;
198  return smoothbt.isSelected();
199  }
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Definition at line 216 of file DesignMaskJFrame.java.

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217  {
218  createMask();
219  imagepn.setMask(mask, width, height);
220  pack();
221  }
xmipp.ij.commons.ImageJPanel.setMask
void setMask(ImagePlus mask, int width, int height)
Definition: ImageJPanel.java:46
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Definition at line 127 of file DesignMaskJFrame.java.

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127  {
128  HashMap<String, String> msgfields = new HashMap<String, String>();
129  String field = "Run name:";
130  msgfields.put(field, "create mask");
131  InputFieldsMessageDialog dlg = new InputFieldsMessageDialog(this, "Question", "Are you sure you want to register mask?", msgfields);
132  int create = dlg.action;
133  boolean register = (create == InputFieldsMessageDialog.OK_OPTION);
134  if (register)
135  try {
136  String path = "mask.spi";
137  ImageGeneric ig = XmippImageConverter.convertToImageGeneric(mask);
138  ig.write(path);
139  ScipionParams params = (ScipionParams)iw.getParams();
140  String label = dlg.getFieldValue(field);
141  String command = String.format("run protocol ProtCreateMask inputObj=%s maskFile='%s' label='%s'", params.inputid, path, label);
142  XmippWindowUtil.runCommand(command, params.port);
143 // String[] command = new String[]{params.python, params.getRegisterMaskScript(), params.projectid, params.inputid, path, label};
144 // String output = XmippWindowUtil.executeCommand(command, true);
145 // System.out.println(output);
146  } catch (Exception ex) {
147  ex.printStackTrace();
148  Logger.getLogger(DesignMaskJFrame.class.getName()).log(Level.SEVERE, null, ex);
149  }
150  }
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◆ mask

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Definition at line 44 of file DesignMaskJFrame.java.

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Definition at line 47 of file DesignMaskJFrame.java.

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The documentation for this class was generated from the following file: -
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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__coll__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__coll__graph.dot deleted file mode 100644 index 2c7e2e6f..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__coll__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.ij.commons.DesignMaskJFrame" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="xmipp.ij.commons.DesignMask\lJFrame",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mask" ,fontname="Helvetica"]; - Node6 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__coll__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__coll__graph.md5 deleted file mode 100644 index 738310de..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -86a197c8c1687349d6c89878bd9a5fda \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__inherit__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__inherit__graph.dot deleted file mode 100644 index ff28d962..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.ij.commons.DesignMaskJFrame" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.ij.commons.DesignMask\lJFrame",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__inherit__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__inherit__graph.md5 deleted file mode 100644 index 19f8d4c6..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1DesignMaskJFrame__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -a917d44bed46b4f7b32c057b8565d8c1 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1Geometry-members.html b/html/classxmipp_1_1ij_1_1commons_1_1Geometry-members.html deleted file mode 100644 index 15d7089d..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1Geometry-members.html +++ /dev/null @@ -1,89 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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flipxmipp.ij.commons.Geometry
Geometry(double shiftx, double shifty, double psiangle, boolean flip, double scaleFactor)xmipp.ij.commons.Geometryinline
Geometry(String matrixString)xmipp.ij.commons.Geometryinline
getMatrix()xmipp.ij.commons.Geometryinline
hasMatrix()xmipp.ij.commons.Geometryinline
scaleFactorxmipp.ij.commons.Geometry
shiftxxmipp.ij.commons.Geometry
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 Geometry (double shiftx, double shifty, double psiangle, boolean flip, double scaleFactor)
 
 Geometry (String matrixString)
 
String getMatrix ()
 
boolean hasMatrix ()
 
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double shiftx
 
boolean flip
 
double scaleFactor = 1
 
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Definition at line 13 of file Geometry.java.

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Definition at line 21 of file Geometry.java.

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22  {
23  this.shiftx = shiftx;
24  this.shifty = shifty;
25  this.psiangle = psiangle;
26  this.flip = flip;
27  this.matrixString = null;
28  this.scaleFactor = scaleFactor;
29  }
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Definition at line 32 of file Geometry.java.

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33  {
34  this.matrixString = matrixString;
35  }
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Definition at line 37 of file Geometry.java.

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39  return this.matrixString;
40  }
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Definition at line 42 of file Geometry.java.

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44  return this.matrixString != null;
45  }
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getCommand()xmipp.ij.commons.IJCommandinline
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getString(String mdstring)xmipp.ij.commons.IJCommandinlinestatic
IJCommand(String command, String options)xmipp.ij.commons.IJCommandinline
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-Public Member Functions

 IJCommand (String command, String options)
 
String getCommand ()
 
void setCommand (String command)
 
String getOptions ()
 
void setOptions (String options)
 
String getMdCommand ()
 
String getMdOptions ()
 
String toString ()
 
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Definition at line 3 of file IJCommand.java.

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Definition at line 9 of file IJCommand.java.

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11  this.command = command;
12  this.options = options;
13  }
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Definition at line 15 of file IJCommand.java.

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17  return command;
18  }
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Definition at line 32 of file IJCommand.java.

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34  return command.replace('_', '&').replace(' ', '_');
35  }
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Definition at line 37 of file IJCommand.java.

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38  {
39  return (options == null || options.equals("")) ? "NULL" :options.replace('_', '&').replace(' ', '_');
40  }
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43  {
44  return mdstring.replace('_', ' ').replace('&', '_');
45  }
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21  this.command = command;
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29  this.options = options;
30  }
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Definition at line 48 of file IJCommand.java.

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49  {
50  return command + " " + options;
51  }
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getPreferredSize()xmipp.ij.commons.ImageJPanelinline
ImageJPanel(ImagePlus image, int width, int height)xmipp.ij.commons.ImageJPanelinline
impxmipp.ij.commons.ImageJPanelprotected
paintComponent(Graphics g)xmipp.ij.commons.ImageJPanelinlineprotected
setMask(ImagePlus mask, int width, int height)xmipp.ij.commons.ImageJPanelinline
widthxmipp.ij.commons.ImageJPanelprotected
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 ImageJPanel (ImagePlus image, int width, int height)
 
Dimension getPreferredSize ()
 
void setMask (ImagePlus mask, int width, int height)
 
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void paintComponent (Graphics g)
 
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ImagePlus imp
 
int width
 
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Definition at line 21 of file ImageJPanel.java.

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Definition at line 26 of file ImageJPanel.java.

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26  {
27  this.imp = image;
28  this.width = width;
29  this.height = height;
30  }
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35  return new Dimension(width, height);
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37  }
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Definition at line 40 of file ImageJPanel.java.

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40  {
41  super.paintComponent(g);
42 
43  g.drawImage(imp.getImage().getScaledInstance(width, height, Image.SCALE_SMOOTH), 0, 0, null); // see javadoc for more info on the parameters
44  }
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Definition at line 46 of file ImageJPanel.java.

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47  {
48  this.imp = mask;
49  this.width = width;
50  this.height = height;
51  setSize(new Dimension(width, height));
52  repaint();
53 
54  }
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Definition at line 23 of file ImageJPanel.java.

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Definition at line 24 of file ImageJPanel.java.

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checkInvertY()xmipp.ij.commons.ImagePlusReaderinlineprotected
checkResizeAndGeo()xmipp.ij.commons.ImagePlusReaderinline
geometryxmipp.ij.commons.ImagePlusReaderprotected
getAllowsPoll()xmipp.ij.commons.ImagePlusFromFileinline
getFileName()xmipp.ij.commons.ImagePlusFromFileinline
getImagePlus()xmipp.ij.commons.ImagePlusReaderinline
getName()xmipp.ij.commons.ImagePlusFromFileinline
getUseGeometry()xmipp.ij.commons.ImagePlusReaderinline
hasChanged()xmipp.ij.commons.ImagePlusFromFileinline
hasIndex()xmipp.ij.commons.ImagePlusReaderinline
igxmipp.ij.commons.ImagePlusReaderprotected
ImagePlusFromFile(String fileName)xmipp.ij.commons.ImagePlusFromFileinline
ImagePlusFromFile(String fileName, ImagePlus imp, ImageGeneric ig)xmipp.ij.commons.ImagePlusFromFileinline
impxmipp.ij.commons.ImagePlusReaderprotected
indexxmipp.ij.commons.ImagePlusReaderprotected
invertyxmipp.ij.commons.ImagePlusReaderprotected
isInvertY()xmipp.ij.commons.ImagePlusReaderinline
isVolume()xmipp.ij.commons.ImagePlusReaderinline
isWrap()xmipp.ij.commons.ImagePlusReaderinline
loadImagePlus()xmipp.ij.commons.ImagePlusFromFileinline
normalizexmipp.ij.commons.ImagePlusReaderprotected
normalize_maxxmipp.ij.commons.ImagePlusReaderprotected
normalize_minxmipp.ij.commons.ImagePlusReaderprotected
setDimension(int width, int height)xmipp.ij.commons.ImagePlusReaderinline
setGeometry(Geometry geometry)xmipp.ij.commons.ImagePlusReaderinline
setInvertY(boolean inverty)xmipp.ij.commons.ImagePlusReaderinline
setNormalize(double normalize_min, double normalize_max)xmipp.ij.commons.ImagePlusReaderinline
setUseGeometry(boolean value)xmipp.ij.commons.ImagePlusReaderinline
setWrap(boolean value)xmipp.ij.commons.ImagePlusReaderinline
useGeometryxmipp.ij.commons.ImagePlusReaderprotected
widthxmipp.ij.commons.ImagePlusReaderprotected
wrapxmipp.ij.commons.ImagePlusReaderprotected
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 ImagePlusFromFile (String fileName)
 
 ImagePlusFromFile (String fileName, ImagePlus imp, ImageGeneric ig)
 
ImagePlus loadImagePlus ()
 
boolean hasChanged ()
 
String getFileName ()
 
boolean getAllowsPoll ()
 
String getName ()
 
- Public Member Functions inherited from xmipp.ij.commons.ImagePlusReader
abstract boolean getAllowsPoll ()
 
ImagePlus getImagePlus ()
 
ImagePlus loadImagePlus ()
 
void checkResizeAndGeo ()
 
void setNormalize (double normalize_min, double normalize_max)
 
void setInvertY (boolean inverty)
 
boolean isVolume ()
 
boolean hasIndex ()
 
abstract String getName ()
 
void setGeometry (Geometry geometry)
 
boolean getUseGeometry ()
 
void setUseGeometry (boolean value)
 
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boolean isWrap ()
 
boolean isInvertY ()
 
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void checkInvertY ()
 
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ImagePlus imp
 
ImageGeneric ig
 
boolean useGeometry
 
boolean wrap
 
long modified
 
long index = -2
 
boolean normalize
 
double normalize_min
 
double normalize_max
 
Geometry geometry
 
int width
 
boolean inverty
 
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Definition at line 18 of file ImagePlusFromFile.java.

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Definition at line 24 of file ImagePlusFromFile.java.

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25  {
26  if (fileName == null || fileName.equals(""))
27  throw new IllegalArgumentException("empty file");
28  this.fileName = fileName;
29  this.modified = new File(fileName).lastModified();
30 
31  }
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Definition at line 33 of file ImagePlusFromFile.java.

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34  {
35  this(fileName);
36  this.imp = imp;
37  this.ig = ig;
38  }
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Definition at line 116 of file ImagePlusFromFile.java.

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117  return true;
118  }
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Definition at line 110 of file ImagePlusFromFile.java.

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112  return fileName;
113  }
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Definition at line 121 of file ImagePlusFromFile.java.

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121  {
122 
123  String name = fileName;
124  if(!name.contains("@"))
125  name = Filename.getBaseName(name);
126  else
127  name = Filename.getPrefix(name) + Filename.SEPARATOR + Filename.getBaseName(Filename.getFilename(name));
128 
129  if(index != -2)
130  name = String.format("%d@%s", index, name);
131  return name;
132 
133  }
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Definition at line 104 of file ImagePlusFromFile.java.

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105  {
106  return new File(fileName).lastModified() > modified;
107  }
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Definition at line 42 of file ImagePlusFromFile.java.

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43  {
44 
45  imp = null;
46  try
47  {
48  if (ig == null || hasChanged())
49  {
50  if(Filename.isXmippSupported(fileName))
51  try
52  {
53  ig = new ImageGeneric(fileName);//to read again file
54  }
55  catch(Exception e)
56  {
57  imp = new ImagePlus(fileName);
58  }
59  else
60  imp = new ImagePlus(fileName);
61  if(ig != null && !hasIndex())
62  {
63  imp = XmippImageConverter.readToImagePlus(ig);
64  }
65  else if(ig != null)
66  {
67  if(ig.isStack())
68  imp = XmippImageConverter.readToImagePlus(ig, index, ImageGeneric.ALL_SLICES);//read image or volume on indexn
69  else
70  imp = XmippImageConverter.readToImagePlus(ig, (int)index);//read image slice on volume
71  }
72  }
73  else if(ig != null)
74  {
75  if(index == -2 || !ig.isStackOrVolume())//if index is not -2 ig read it already
76  imp = XmippImageConverter.convertToImagePlus(ig);
77  else
78  {
79  if(ig.isStack())
80  imp = XmippImageConverter.convertToImagePlus(ig, index);//read image or volume on index
81  else
82  imp = XmippImageConverter.convertToImagePlus(ig, ImageGeneric.FIRST_IMAGE, (int)index);//read image slice on volume
83  }
84  }
85  checkResizeAndGeo();
86  checkInvertY();
87  if(normalize)
88  {
89  imp.getProcessor().setMinAndMax(normalize_min, normalize_max);
90  imp.updateImage();
91  }
92  return imp;
93 
94  }
95  catch (Exception e)
96  {
97  e.printStackTrace();
98  }
99  return imp;
100  }
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__coll__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__coll__graph.dot deleted file mode 100644 index 9a53cda7..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__coll__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.ij.commons.ImagePlusFromFile" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.ij.commons.ImagePlus\lFromFile",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.ij.commons.ImagePlus\lReader",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html"]; - Node4 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" imp" ,fontname="Helvetica"]; - Node4 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" geometry" ,fontname="Helvetica"]; - Node5 [label="xmipp.ij.commons.Geometry",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1Geometry.html"]; - Node6 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ig" ,fontname="Helvetica"]; - Node6 [label="xmipp.jni.ImageGeneric",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1ImageGeneric.html"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__coll__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__coll__graph.md5 deleted file mode 100644 index 9b8585c8..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -273997e4e6b8b7eab005a5b8aa039e2b \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__inherit__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__inherit__graph.dot deleted file mode 100644 index d68408a8..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.ij.commons.ImagePlusFromFile" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.ij.commons.ImagePlus\lFromFile",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.ij.commons.ImagePlus\lReader",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__inherit__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__inherit__graph.md5 deleted file mode 100644 index f56a2e3d..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ffa06ae4383b0952d4baf2719d999c26 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader-members.html b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader-members.html deleted file mode 100644 index 6dc911e0..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader-members.html +++ /dev/null @@ -1,112 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.ij.commons.ImagePlusLoader Member List
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This is the complete list of members for xmipp.ij.commons.ImagePlusLoader, including all inherited members.

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allowsPoll()xmipp.ij.commons.ImagePlusLoaderinline
existsFile()xmipp.ij.commons.ImagePlusLoaderinline
getFile(ImagePlus imp)xmipp.ij.commons.ImagePlusLoaderinlinestatic
getFile(ImageGeneric ig)xmipp.ij.commons.ImagePlusLoaderinlinestatic
getImagePlus()xmipp.ij.commons.ImagePlusLoaderinline
getName()xmipp.ij.commons.ImagePlusLoaderinline
getUseGeometry()xmipp.ij.commons.ImagePlusLoaderinline
hasGeometry()xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(ImagePlus imp)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(ImagePlus imp, boolean inverty)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(ImageGeneric ig, boolean inverty)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(int index, ImageGeneric ig)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(int index, ImageGeneric ig, boolean inverty)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(String fileName, boolean inverty)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(String fileName)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(String fileName, boolean useGeometry, boolean wrap, boolean inverty)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(String fileName, ImagePlus imp, ImageGeneric ig, boolean useGeo, boolean wrap, boolean inverty, int index)xmipp.ij.commons.ImagePlusLoaderinline
ImagePlusLoader(ImageGeneric ig)xmipp.ij.commons.ImagePlusLoaderinline
impreaderxmipp.ij.commons.ImagePlusLoaderprotected
isInvertY()xmipp.ij.commons.ImagePlusLoaderinline
isStackOrVolume()xmipp.ij.commons.ImagePlusLoaderinline
isVolume()xmipp.ij.commons.ImagePlusLoaderinline
isWrap()xmipp.ij.commons.ImagePlusLoaderinline
loadImagePlus()xmipp.ij.commons.ImagePlusLoaderinline
setDimension(int width, int height)xmipp.ij.commons.ImagePlusLoaderinline
setGeometry(Geometry geometry)xmipp.ij.commons.ImagePlusLoaderinline
setInvertY(boolean invert)xmipp.ij.commons.ImagePlusLoaderinline
setNormalize(double normalize_min, double normalize_max)xmipp.ij.commons.ImagePlusLoaderinline
setUseGeometry(boolean value)xmipp.ij.commons.ImagePlusLoaderinline
setWrap(boolean value)xmipp.ij.commons.ImagePlusLoaderinline
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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader.html b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader.html deleted file mode 100644 index 42fa7a0b..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader.html +++ /dev/null @@ -1,1173 +0,0 @@ - - - - - - - -Xmipp: xmipp.ij.commons.ImagePlusLoader Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Static Public Member Functions | -Protected Attributes | -List of all members
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xmipp.ij.commons.ImagePlusLoader Class Reference
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-Collaboration diagram for xmipp.ij.commons.ImagePlusLoader:
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-Public Member Functions

 ImagePlusLoader (ImagePlus imp)
 
 ImagePlusLoader (ImagePlus imp, boolean inverty)
 
 ImagePlusLoader (ImageGeneric ig, boolean inverty)
 
 ImagePlusLoader (int index, ImageGeneric ig)
 
 ImagePlusLoader (int index, ImageGeneric ig, boolean inverty)
 
 ImagePlusLoader (String fileName, boolean inverty)
 
 ImagePlusLoader (String fileName)
 
 ImagePlusLoader (String fileName, boolean useGeometry, boolean wrap, boolean inverty)
 
 ImagePlusLoader (String fileName, ImagePlus imp, ImageGeneric ig, boolean useGeo, boolean wrap, boolean inverty, int index)
 
 ImagePlusLoader (ImageGeneric ig)
 
void setNormalize (double normalize_min, double normalize_max)
 
void setInvertY (boolean invert)
 
ImagePlus getImagePlus ()
 
void setWrap (boolean value)
 
boolean isWrap ()
 
boolean allowsPoll ()
 
String getName ()
 
ImagePlus loadImagePlus ()
 
boolean existsFile ()
 
boolean isVolume ()
 
boolean isStackOrVolume ()
 
boolean getUseGeometry ()
 
void setUseGeometry (boolean value)
 
void setGeometry (Geometry geometry)
 
boolean hasGeometry ()
 
void setDimension (int width, int height)
 
boolean isInvertY ()
 
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-Static Public Member Functions

static String getFile (ImagePlus imp)
 
static String getFile (ImageGeneric ig)
 
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-Protected Attributes

ImagePlusReader impreader
 
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Detailed Description

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Definition at line 34 of file ImagePlusLoader.java.

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◆ ImagePlusLoader() [1/10]

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xmipp.ij.commons.ImagePlusLoader.ImagePlusLoader (ImagePlus imp)
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Definition at line 39 of file ImagePlusLoader.java.

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39  {
40  this(getFile(imp), imp, null, false, false, false, -2);
41  }
xmipp.ij.commons.ImagePlusLoader.getFile
static String getFile(ImagePlus imp)
Definition: ImagePlusLoader.java:120
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Definition at line 43 of file ImagePlusLoader.java.

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43  {
44  this(getFile(imp), imp, null, false, false, inverty, -2);
45  }
xmipp.ij.commons.ImagePlusLoader.getFile
static String getFile(ImagePlus imp)
Definition: ImagePlusLoader.java:120
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Definition at line 47 of file ImagePlusLoader.java.

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47  {
48  this(getFile(ig), null, ig, false, false, inverty, -2);
49  }
xmipp.ij.commons.ImagePlusLoader.getFile
static String getFile(ImagePlus imp)
Definition: ImagePlusLoader.java:120
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Definition at line 51 of file ImagePlusLoader.java.

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51  {
52  this(getFile(ig), null, ig, false, false, false, index);
53  }
xmipp.ij.commons.ImagePlusLoader.getFile
static String getFile(ImagePlus imp)
Definition: ImagePlusLoader.java:120
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Definition at line 55 of file ImagePlusLoader.java.

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55  {
56  this(getFile(ig), null, ig, false, false, inverty, index);
57  }
xmipp.ij.commons.ImagePlusLoader.getFile
static String getFile(ImagePlus imp)
Definition: ImagePlusLoader.java:120
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Definition at line 59 of file ImagePlusLoader.java.

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59  {
60  this(fileName, null, null, false, false, inverty, -2);
61  }
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Definition at line 63 of file ImagePlusLoader.java.

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63  {
64  this(fileName, null, null, false, false, false, -2);
65  }
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Definition at line 67 of file ImagePlusLoader.java.

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67  {
68  this(fileName, null, null, useGeometry, wrap, inverty, -2);
69  }
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Definition at line 71 of file ImagePlusLoader.java.

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71  {
72 
73  if (fileName != null) {
74  String path = Filename.findImagePath(fileName, null, true);//check if file exists dismissing preffix and suffix
75  existsfile = path != null;
76  }
77  if (existsfile)
78  impreader = new ImagePlusFromFile(fileName, imp, ig);
79  else
80  {
81 
82  if(fileName != null)
83  throw new IllegalArgumentException(XmippMessage.getPathNotExistsMsg(fileName));
84  impreader = new ImagePlusNotFromFile(imp, ig);
85  }
86 //
87  impreader.setIndex(index);
88  impreader.setUseGeometry(useGeo);
89  setWrap(wrap);
90  setInvertY(inverty);
91  }
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Definition at line 93 of file ImagePlusLoader.java.

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93  {
94  this(-1, ig);
95  }
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◆ allowsPoll()

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Definition at line 138 of file ImagePlusLoader.java.

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138  {
139  return impreader.getAllowsPoll();
140  }
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Definition at line 150 of file ImagePlusLoader.java.

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150  {
151  return existsfile;
152  }
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Definition at line 120 of file ImagePlusLoader.java.

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120  {
121  String file = null;
122 
123  if (imp != null && imp.getOriginalFileInfo() != null) {
124  file = imp.getOriginalFileInfo().directory + File.separator + imp.getOriginalFileInfo().fileName;
125  }
126 
127  return file;
128  }
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Definition at line 130 of file ImagePlusLoader.java.

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130  {
131  String file = null;
132  if (ig != null && ig.getFilename() != null) {
133  file = ig.getFilename();
134  }
135  return file;
136  }
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Definition at line 107 of file ImagePlusLoader.java.

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107  {
108  return impreader.getImagePlus();
109  }
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Definition at line 142 of file ImagePlusLoader.java.

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142  {
143  return impreader.getName();
144  }
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Definition at line 163 of file ImagePlusLoader.java.

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163  {
164  return impreader.getUseGeometry();
165  }
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Definition at line 177 of file ImagePlusLoader.java.

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178  {
179  return impreader.geometry != null;
180  }
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Definition at line 188 of file ImagePlusLoader.java.

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188  {
189  return impreader.isInvertY();
190  }
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Definition at line 159 of file ImagePlusLoader.java.

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159  {
160  return impreader.isStackOrVolume();
161  }
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Definition at line 154 of file ImagePlusLoader.java.

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154  {
155  return impreader.isVolume();
156  }
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Definition at line 116 of file ImagePlusLoader.java.

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116  {
117  return impreader.isWrap();
118  }
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Definition at line 146 of file ImagePlusLoader.java.

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146  {
147  return impreader.loadImagePlus();
148  }
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Definition at line 183 of file ImagePlusLoader.java.

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184  {
185  impreader.setDimension(width, height);
186  }
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void setDimension(int width, int height)
Definition: ImagePlusReader.java:179
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Definition at line 172 of file ImagePlusLoader.java.

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173  {
174  impreader.setGeometry(geometry);
175  }
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void setGeometry(Geometry geometry)
Definition: ImagePlusReader.java:165
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Definition at line 102 of file ImagePlusLoader.java.

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102  {
103  impreader.setInvertY(invert);
104 
105  }
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double normalize_max 
)
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Definition at line 97 of file ImagePlusLoader.java.

-
97  {
98  impreader.setNormalize(normalize_min, normalize_max);
99 
100  }
xmipp.ij.commons.ImagePlusReader.setNormalize
void setNormalize(double normalize_min, double normalize_max)
Definition: ImagePlusReader.java:115
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Definition at line 167 of file ImagePlusLoader.java.

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167  {
168  impreader.setUseGeometry(value);
169 
170  }
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Definition at line 111 of file ImagePlusLoader.java.

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111  {
112  impreader.setWrap(value);
113 
114  }
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◆ impreader

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Definition at line 36 of file ImagePlusLoader.java.

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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader__coll__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader__coll__graph.dot deleted file mode 100644 index c34ba960..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader__coll__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.ij.commons.ImagePlusLoader" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node1 [label="xmipp.ij.commons.ImagePlus\lLoader",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node2 -> Node1 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" impreader" ,fontname="Helvetica"]; - Node2 [label="xmipp.ij.commons.ImagePlus\lReader",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html"]; - Node3 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" imp" ,fontname="Helvetica"]; - Node3 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node4 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" geometry" ,fontname="Helvetica"]; - Node4 [label="xmipp.ij.commons.Geometry",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1Geometry.html"]; - Node5 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ig" ,fontname="Helvetica"]; - Node5 [label="xmipp.jni.ImageGeneric",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1ImageGeneric.html"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader__coll__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader__coll__graph.md5 deleted file mode 100644 index c8b9999b..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusLoader__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -5116cbad4f78618a6e0b842628850c13 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile-members.html b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile-members.html deleted file mode 100644 index efef08d6..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile-members.html +++ /dev/null @@ -1,112 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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checkInvertY()xmipp.ij.commons.ImagePlusReaderinlineprotected
checkResizeAndGeo()xmipp.ij.commons.ImagePlusReaderinline
geometryxmipp.ij.commons.ImagePlusReaderprotected
getAllowsPoll()xmipp.ij.commons.ImagePlusNotFromFileinline
getImagePlus()xmipp.ij.commons.ImagePlusReaderinline
getName()xmipp.ij.commons.ImagePlusNotFromFileinline
getUseGeometry()xmipp.ij.commons.ImagePlusReaderinline
hasIndex()xmipp.ij.commons.ImagePlusReaderinline
igxmipp.ij.commons.ImagePlusReaderprotected
ImagePlusNotFromFile(ImagePlus imp, ImageGeneric ig)xmipp.ij.commons.ImagePlusNotFromFileinline
impxmipp.ij.commons.ImagePlusReaderprotected
indexxmipp.ij.commons.ImagePlusReaderprotected
invertyxmipp.ij.commons.ImagePlusReaderprotected
isInvertY()xmipp.ij.commons.ImagePlusReaderinline
isVolume()xmipp.ij.commons.ImagePlusReaderinline
isWrap()xmipp.ij.commons.ImagePlusReaderinline
loadImagePlus()xmipp.ij.commons.ImagePlusReaderinline
modifiedxmipp.ij.commons.ImagePlusReaderprotected
normalizexmipp.ij.commons.ImagePlusReaderprotected
normalize_maxxmipp.ij.commons.ImagePlusReaderprotected
normalize_minxmipp.ij.commons.ImagePlusReaderprotected
setDimension(int width, int height)xmipp.ij.commons.ImagePlusReaderinline
setGeometry(Geometry geometry)xmipp.ij.commons.ImagePlusReaderinline
setInvertY(boolean inverty)xmipp.ij.commons.ImagePlusReaderinline
setNormalize(double normalize_min, double normalize_max)xmipp.ij.commons.ImagePlusReaderinline
setUseGeometry(boolean value)xmipp.ij.commons.ImagePlusReaderinline
setWrap(boolean value)xmipp.ij.commons.ImagePlusReaderinline
useGeometryxmipp.ij.commons.ImagePlusReaderprotected
widthxmipp.ij.commons.ImagePlusReaderprotected
wrapxmipp.ij.commons.ImagePlusReaderprotected
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile.html b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile.html deleted file mode 100644 index 7db2acbc..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile.html +++ /dev/null @@ -1,277 +0,0 @@ - - - - - - - -Xmipp: xmipp.ij.commons.ImagePlusNotFromFile Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.ij.commons.ImagePlusNotFromFile Class Reference
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-Inheritance diagram for xmipp.ij.commons.ImagePlusNotFromFile:
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-Public Member Functions

 ImagePlusNotFromFile (ImagePlus imp, ImageGeneric ig)
 
boolean getAllowsPoll ()
 
String getName ()
 
- Public Member Functions inherited from xmipp.ij.commons.ImagePlusReader
abstract boolean getAllowsPoll ()
 
ImagePlus getImagePlus ()
 
ImagePlus loadImagePlus ()
 
void checkResizeAndGeo ()
 
void setNormalize (double normalize_min, double normalize_max)
 
void setInvertY (boolean inverty)
 
boolean isVolume ()
 
boolean hasIndex ()
 
abstract String getName ()
 
void setGeometry (Geometry geometry)
 
boolean getUseGeometry ()
 
void setUseGeometry (boolean value)
 
void setDimension (int width, int height)
 
void setWrap (boolean value)
 
boolean isWrap ()
 
boolean isInvertY ()
 
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-Additional Inherited Members

- Protected Member Functions inherited from xmipp.ij.commons.ImagePlusReader
void checkInvertY ()
 
- Protected Attributes inherited from xmipp.ij.commons.ImagePlusReader
ImagePlus imp
 
ImageGeneric ig
 
boolean useGeometry
 
boolean wrap
 
long modified
 
long index = -2
 
boolean normalize
 
double normalize_min
 
double normalize_max
 
Geometry geometry
 
int width
 
boolean inverty
 
-

Detailed Description

-
Author
airen
- -

Definition at line 18 of file ImagePlusNotFromFile.java.

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Constructor & Destructor Documentation

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◆ ImagePlusNotFromFile()

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xmipp.ij.commons.ImagePlusNotFromFile.ImagePlusNotFromFile (ImagePlus imp,
ImageGeneric ig 
)
- 		-inline
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Definition at line 21 of file ImagePlusNotFromFile.java.

-
21  {
22  if(imp == null && ig == null)
23  throw new IllegalArgumentException(XmippMessage.getEmptyFieldMsg("image") );
24  this.imp = imp;
25  this.ig = ig;
26  }
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Member Function Documentation

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◆ getAllowsPoll()

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boolean xmipp.ij.commons.ImagePlusNotFromFile.getAllowsPoll ()
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Definition at line 31 of file ImagePlusNotFromFile.java.

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31  {
32  return false;
33  }
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◆ getName()

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String xmipp.ij.commons.ImagePlusNotFromFile.getName ()
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Definition at line 38 of file ImagePlusNotFromFile.java.

-
38  {
39 
40  if(imp == null && ig == null)
41  return null;
42  String name = (ig != null)? Filename.getBaseName(ig.getFilename()): imp.getTitle();
43 
44  if(index != -2)
45  name = String.format("%d@%s", index, name);
46  return name;
47  }
- - - -
-
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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__coll__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__coll__graph.dot deleted file mode 100644 index 1337f036..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__coll__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.ij.commons.ImagePlusNotFromFile" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.ij.commons.ImagePlus\lNotFromFile",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.ij.commons.ImagePlus\lReader",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html"]; - Node4 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" imp" ,fontname="Helvetica"]; - Node4 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" geometry" ,fontname="Helvetica"]; - Node5 [label="xmipp.ij.commons.Geometry",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1Geometry.html"]; - Node6 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ig" ,fontname="Helvetica"]; - Node6 [label="xmipp.jni.ImageGeneric",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1ImageGeneric.html"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__coll__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__coll__graph.md5 deleted file mode 100644 index 17f8954f..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -d06375af9184f2e6ad3e34f66d5a4710 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__inherit__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__inherit__graph.dot deleted file mode 100644 index c3841e9f..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.ij.commons.ImagePlusNotFromFile" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.ij.commons.ImagePlus\lNotFromFile",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.ij.commons.ImagePlus\lReader",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__inherit__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__inherit__graph.md5 deleted file mode 100644 index a0561747..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -4fa7d4b184d890079e8e3fafeabe5ce7 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader-members.html b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader-members.html deleted file mode 100644 index 4b23d1e8..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader-members.html +++ /dev/null @@ -1,111 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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checkInvertY()xmipp.ij.commons.ImagePlusReaderinlineprotected
checkResizeAndGeo()xmipp.ij.commons.ImagePlusReaderinline
geometryxmipp.ij.commons.ImagePlusReaderprotected
getAllowsPoll()xmipp.ij.commons.ImagePlusReader
getImagePlus()xmipp.ij.commons.ImagePlusReaderinline
getName()xmipp.ij.commons.ImagePlusReader
getUseGeometry()xmipp.ij.commons.ImagePlusReaderinline
hasIndex()xmipp.ij.commons.ImagePlusReaderinline
igxmipp.ij.commons.ImagePlusReaderprotected
impxmipp.ij.commons.ImagePlusReaderprotected
indexxmipp.ij.commons.ImagePlusReaderprotected
invertyxmipp.ij.commons.ImagePlusReaderprotected
isInvertY()xmipp.ij.commons.ImagePlusReaderinline
isVolume()xmipp.ij.commons.ImagePlusReaderinline
isWrap()xmipp.ij.commons.ImagePlusReaderinline
loadImagePlus()xmipp.ij.commons.ImagePlusReaderinline
modifiedxmipp.ij.commons.ImagePlusReaderprotected
normalizexmipp.ij.commons.ImagePlusReaderprotected
normalize_maxxmipp.ij.commons.ImagePlusReaderprotected
normalize_minxmipp.ij.commons.ImagePlusReaderprotected
setDimension(int width, int height)xmipp.ij.commons.ImagePlusReaderinline
setGeometry(Geometry geometry)xmipp.ij.commons.ImagePlusReaderinline
setInvertY(boolean inverty)xmipp.ij.commons.ImagePlusReaderinline
setNormalize(double normalize_min, double normalize_max)xmipp.ij.commons.ImagePlusReaderinline
setUseGeometry(boolean value)xmipp.ij.commons.ImagePlusReaderinline
setWrap(boolean value)xmipp.ij.commons.ImagePlusReaderinline
useGeometryxmipp.ij.commons.ImagePlusReaderprotected
widthxmipp.ij.commons.ImagePlusReaderprotected
wrapxmipp.ij.commons.ImagePlusReaderprotected
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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html deleted file mode 100644 index 8bc9260c..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html +++ /dev/null @@ -1,984 +0,0 @@ - - - - - - - -Xmipp: xmipp.ij.commons.ImagePlusReader Class Reference - - - - - - - - - -
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-Public Member Functions

abstract boolean getAllowsPoll ()
 
ImagePlus getImagePlus ()
 
ImagePlus loadImagePlus ()
 
void checkResizeAndGeo ()
 
void setNormalize (double normalize_min, double normalize_max)
 
void setInvertY (boolean inverty)
 
boolean isVolume ()
 
boolean hasIndex ()
 
abstract String getName ()
 
void setGeometry (Geometry geometry)
 
boolean getUseGeometry ()
 
void setUseGeometry (boolean value)
 
void setDimension (int width, int height)
 
void setWrap (boolean value)
 
boolean isWrap ()
 
boolean isInvertY ()
 
- - - -

-Protected Member Functions

void checkInvertY ()
 
- - - - - - - - - - - - - - - - - - - - - - - - - -

-Protected Attributes

ImagePlus imp
 
ImageGeneric ig
 
boolean useGeometry
 
boolean wrap
 
long modified
 
long index = -2
 
boolean normalize
 
double normalize_min
 
double normalize_max
 
Geometry geometry
 
int width
 
boolean inverty
 
-

Detailed Description

-
Author
airen
- -

Definition at line 18 of file ImagePlusReader.java.

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Member Function Documentation

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◆ checkInvertY()

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void xmipp.ij.commons.ImagePlusReader.checkInvertY ()
- 		-inlineprotected
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Definition at line 106 of file ImagePlusReader.java.

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106  {
107  if(inverty)
108  {
109  imp.getProcessor().flipVertical();
110  imp.updateImage();
111  }
112  }
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Definition at line 80 of file ImagePlusReader.java.

-
81  {
82  if(useGeometry && geometry != null)
83  {
84  try {
85 
86  ImageGeneric tempig = XmippImageConverter.convertToImageGeneric(imp);
87  if (geometry.hasMatrix())
88  tempig.applyGeoMatrix(geometry.getMatrix(), wrap);
89  else
90  tempig.applyGeo(geometry.shiftx, geometry.shifty, geometry.psiangle, geometry.flip, wrap, geometry.scaleFactor);
91  imp = XmippImageConverter.convertToImagePlus(tempig);
92  } catch (Exception ex) {
93  Logger.getLogger(ImagePlusReader.class.getName()).log(Level.SEVERE, null, ex);
94  }
95  }
96  ImageProcessor processor = imp.getProcessor();
97  if(width != 0 && height != 0 && imp != null && processor != null)
98  {
99  processor.setInterpolate(true);
100  processor = processor.resize(width, height);
101  imp = new ImagePlus("", processor);
102  }
103  }
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Definition at line 37 of file ImagePlusReader.java.

-
37  {
38  if (imp == null) {
39  imp = loadImagePlus();
40  }
41  return imp;
42  }
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Definition at line 170 of file ImagePlusReader.java.

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170  {
171  return useGeometry;
172  }
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Definition at line 150 of file ImagePlusReader.java.

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151  {
152  return index != -2;
153  }
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Definition at line 193 of file ImagePlusReader.java.

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193  {
194  return inverty;
195  }
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Definition at line 129 of file ImagePlusReader.java.

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130  {
131  try
132  {
133  if(imp != null)
134  return imp.getStackSize() > 1;
135  loadImagePlus();
136  return isVolume();
137 
138  }
139  catch (Exception e)
140  {
141  throw new IllegalArgumentException(e.getMessage());
142  }
143  }
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Definition at line 189 of file ImagePlusReader.java.

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189  {
190  return wrap;
191  }
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Definition at line 44 of file ImagePlusReader.java.

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45  {
46  imp = null;
47  try
48  {
49  if(ig != null)
50  {
51 
52  if(!hasIndex() )
53  imp = XmippImageConverter.convertToImagePlus(ig);
54  else
55  {
56  if(ig.isStack())
57  imp = XmippImageConverter.convertToImagePlus(ig, index);//read image or volume on index
58  else
59  imp = XmippImageConverter.convertToImagePlus(ig, ImageGeneric.FIRST_IMAGE, (int)index);//read image slice on volume
60  }
61  }
62  checkResizeAndGeo();
63  checkInvertY();
64  if(normalize)
65  {
66  imp.getProcessor().setMinAndMax(normalize_min, normalize_max);
67  imp.updateImage();
68  }
69 
70  return imp;
71  }
72  catch (Exception e)
73  {
74  e.printStackTrace();
75  throw new IllegalArgumentException(e);
76  }
77 
78  }
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Definition at line 179 of file ImagePlusReader.java.

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179  {
180  this.width = width;
181  this.height = height;
182  }
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Definition at line 165 of file ImagePlusReader.java.

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166  {
167  this.geometry = geometry;
168  }
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Definition at line 123 of file ImagePlusReader.java.

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124  {
125  this.inverty = inverty;
126 
127  }
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Definition at line 115 of file ImagePlusReader.java.

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116  {
117  this.normalize = true;
118  this.normalize_min = normalize_min;
119  this.normalize_max = normalize_max;
120 
121  }
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Definition at line 174 of file ImagePlusReader.java.

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174  {
175  useGeometry = value;
176 
177  }
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Definition at line 184 of file ImagePlusReader.java.

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184  {
185  wrap = value;
186 
187  }
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Definition at line 30 of file ImagePlusReader.java.

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Definition at line 21 of file ImagePlusReader.java.

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Definition at line 20 of file ImagePlusReader.java.

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Definition at line 26 of file ImagePlusReader.java.

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Definition at line 32 of file ImagePlusReader.java.

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Definition at line 24 of file ImagePlusReader.java.

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Definition at line 27 of file ImagePlusReader.java.

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Definition at line 29 of file ImagePlusReader.java.

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Definition at line 28 of file ImagePlusReader.java.

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Definition at line 22 of file ImagePlusReader.java.

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Definition at line 31 of file ImagePlusReader.java.

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Definition at line 23 of file ImagePlusReader.java.

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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__coll__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__coll__graph.dot deleted file mode 100644 index 38d4ff7e..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__coll__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.ij.commons.ImagePlusReader" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="xmipp.ij.commons.ImagePlus\lReader",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" imp" ,fontname="Helvetica"]; - Node4 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" geometry" ,fontname="Helvetica"]; - Node5 [label="xmipp.ij.commons.Geometry",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1Geometry.html"]; - Node6 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ig" ,fontname="Helvetica"]; - Node6 [label="xmipp.jni.ImageGeneric",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1ImageGeneric.html"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__coll__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__coll__graph.md5 deleted file mode 100644 index 752f81d2..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -4c5ff2d83109ff360c41ecb5ff6b67d3 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__inherit__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__inherit__graph.dot deleted file mode 100644 index 7909322f..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.ij.commons.ImagePlusReader" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.ij.commons.ImagePlus\lReader",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node0 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.ij.commons.ImagePlus\lFromFile",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1ImagePlusFromFile.html"]; - Node0 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.ij.commons.ImagePlus\lNotFromFile",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1ImagePlusNotFromFile.html"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__inherit__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__inherit__graph.md5 deleted file mode 100644 index 38318ee0..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1ImagePlusReader__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -dce62dc09f934a794c2e9c4d295ed1ea \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1InputFieldsMessageDialog-members.html b/html/classxmipp_1_1ij_1_1commons_1_1InputFieldsMessageDialog-members.html deleted file mode 100644 index 4f091320..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1InputFieldsMessageDialog-members.html +++ /dev/null @@ -1,91 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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actionxmipp.ij.commons.InputFieldsMessageDialog
actionPerformed(ActionEvent ae)xmipp.ij.commons.InputFieldsMessageDialoginline
CANCEL_OPTIONxmipp.ij.commons.InputFieldsMessageDialogstatic
close()xmipp.ij.commons.InputFieldsMessageDialoginline
getFieldValue(String field)xmipp.ij.commons.InputFieldsMessageDialoginline
initComponents(String title)xmipp.ij.commons.InputFieldsMessageDialoginlineprotected
InputFieldsMessageDialog(JFrame parent, String title, String msg, Map< String, String > fields)xmipp.ij.commons.InputFieldsMessageDialoginline
InputFieldsMessageDialog(JFrame parent, String title, String msg)xmipp.ij.commons.InputFieldsMessageDialoginline
OK_OPTIONxmipp.ij.commons.InputFieldsMessageDialogstatic
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-Public Member Functions

 InputFieldsMessageDialog (JFrame parent, String title, String msg, Map< String, String > fields)
 
 InputFieldsMessageDialog (JFrame parent, String title, String msg)
 
void close ()
 
void actionPerformed (ActionEvent ae)
 
String getFieldValue (String field)
 
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-Public Attributes

int action
 
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-Static Public Attributes

static final int OK_OPTION = 1
 
static final int CANCEL_OPTION = 0
 
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-Protected Member Functions

void initComponents (String title)
 
-

Detailed Description

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Author
airen
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Definition at line 34 of file InputFieldsMessageDialog.java.

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◆ InputFieldsMessageDialog() [1/2]

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xmipp.ij.commons.InputFieldsMessageDialog.InputFieldsMessageDialog (JFrame parent,
String title,
String msg,
Map< String, String > fields 
)
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Definition at line 47 of file InputFieldsMessageDialog.java.

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48  {
49  super(parent, true);
50  this.msg = msg;
51  this.fields = fields;
52  fieldstfs = new HashMap<String, JTextField>();
53  initComponents(title);
54 
55  }
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xmipp.ij.commons.InputFieldsMessageDialog.InputFieldsMessageDialog (JFrame parent,
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Definition at line 57 of file InputFieldsMessageDialog.java.

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58  {
59  this(parent, title, msg, null);
60  }
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Definition at line 119 of file InputFieldsMessageDialog.java.

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119  {
120  action = OK_OPTION;
121  close();
122  }
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Definition at line 112 of file InputFieldsMessageDialog.java.

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113  {
114  setVisible(false);
115  dispose();
116  }
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Definition at line 124 of file InputFieldsMessageDialog.java.

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125  {
126  return fieldstfs.get(field).getText();
127  }
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Definition at line 62 of file InputFieldsMessageDialog.java.

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63  {
64  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
65  setTitle(title);
66  setLayout(new GridBagLayout());
67  GridBagConstraints constraints = new GridBagConstraints();
68  constraints.insets = new Insets(5, 5, 5, 5);
69  JLabel msgLb = new JLabel(msg);
70  add(msgLb, XmippWindowUtil.getConstraints(constraints, 0, 0, 2));
71  int index = 1;
72  JTextField tf;
73  if(fields != null)
74  for(Map.Entry<String, String> e: fields.entrySet())
75  {
76 
77  add(new JLabel(e.getKey()), XmippWindowUtil.getConstraints(constraints, 0, index));
78  tf = new JTextField(e.getValue());
79  tf.setColumns(20);
80  fieldstfs.put(e.getKey(), tf);
81  add(tf, XmippWindowUtil.getConstraints(constraints, 1, index));
82  index ++;
83  }
84  JPanel buttonspn = new JPanel();
85  cancelbt = new JButton("Cancel");
86  cancelbt.addActionListener(new ActionListener() {
87 
88  @Override
89  public void actionPerformed(ActionEvent ae) {
90  action = CANCEL_OPTION;
91  close();
92  }
93  });
94  buttonspn.add(cancelbt);
95  okbt = new JButton("Ok");
96  okbt.setBackground(XmippWindowUtil.firebrick);
97  okbt.setForeground(Color.WHITE);
98  okbt.addActionListener(this);
99 
100  buttonspn.add(okbt);
101  add(buttonspn, XmippWindowUtil.getConstraints(constraints, 0, index, GridBagConstraints.HORIZONTAL));
102  pack();
103  if (getParent() != null)
104  XmippWindowUtil.centerWindows(this, getParent());
105  setVisible(true);
106 
107  }
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Definition at line 39 of file InputFieldsMessageDialog.java.

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Definition at line 42 of file InputFieldsMessageDialog.java.

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Definition at line 41 of file InputFieldsMessageDialog.java.

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PollTimer(final XmippIJWindow xp)xmipp.ij.commons.PollTimerinline
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 PollTimer (final XmippIJWindow xp)
 
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Definition at line 8 of file PollTimer.java.

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◆ PollTimer()

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xmipp.ij.commons.PollTimer.PollTimer (final XmippIJWindow xp)
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Definition at line 13 of file PollTimer.java.

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14  {
15  super(PERIOD, new ActionListener()
16  {
17 
18  @Override
19  public void actionPerformed(ActionEvent e)
20  {
21  xp.loadData();
22  }
23  });
24  this.xp = xp;
25  }
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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__coll__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__coll__graph.dot deleted file mode 100644 index 9c6d730b..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.ij.commons.PollTimer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.ij.commons.PollTimer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="Timer",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__coll__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__coll__graph.md5 deleted file mode 100644 index 78dc3247..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -9e462290eb3e88b20874c2672054144f \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__inherit__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__inherit__graph.dot deleted file mode 100644 index 22d88bbf..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.ij.commons.PollTimer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.ij.commons.PollTimer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="Timer",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__inherit__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__inherit__graph.md5 deleted file mode 100644 index a2be4a4e..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1PollTimer__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -376857eceb7bd82a4563750e38274ec5 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippApplication-members.html b/html/classxmipp_1_1ij_1_1commons_1_1XmippApplication-members.html deleted file mode 100644 index 5fb2648c..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippApplication-members.html +++ /dev/null @@ -1,87 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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addInstance(boolean isijwindow)xmipp.ij.commons.XmippApplicationinlinestatic
getInstances()xmipp.ij.commons.XmippApplicationinlinestatic
isScipion()xmipp.ij.commons.XmippApplicationinlinestatic
removeInstance(boolean isijwindow)xmipp.ij.commons.XmippApplicationinlinestatic
setIsScipion(boolean isscipion)xmipp.ij.commons.XmippApplicationinlinestatic
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static short getInstances ()
 
static void addInstance (boolean isijwindow)
 
static void removeInstance (boolean isijwindow)
 
static boolean isScipion ()
 
static void setIsScipion (boolean isscipion)
 
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Definition at line 5 of file XmippApplication.java.

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◆ addInstance()

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static void xmipp.ij.commons.XmippApplication.addInstance (boolean isijwindow)
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Definition at line 18 of file XmippApplication.java.

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19  {
20  instances ++;
21  if(isijwindow)
22  ijwindows ++;
23  //System.out.printf("instances:%s\n", instances);
24  }
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Definition at line 13 of file XmippApplication.java.

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15  return instances;
16  }
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Definition at line 43 of file XmippApplication.java.

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44  {
45  return isscipion;
46  }
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Definition at line 28 of file XmippApplication.java.

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29  {
30  instances --;
31  if(isijwindow)
32  {
33  ijwindows --;
34  if(XmippUtil.getXmippImageJ() != null && ijwindows == 0)
35  XmippUtil.getXmippImageJ().setVisible(false);//if ImageJ is not shared hide it
36  }
37  //System.out.printf("instances %s\n", instances);
38  if (instances == 0)
39  System.exit(0);
40 
41  }
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Definition at line 48 of file XmippApplication.java.

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49  {
50  XmippApplication.isscipion = isscipion;
51  }
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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippImageCanvas-members.html b/html/classxmipp_1_1ij_1_1commons_1_1XmippImageCanvas-members.html deleted file mode 100644 index 4ad80927..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippImageCanvas-members.html +++ /dev/null @@ -1,104 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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adjustMagnification()xmipp.ij.commons.XmippImageCanvasinline
customScrollSetup(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
getPreferredMagnification()xmipp.ij.commons.XmippImageCanvasinline
getTool()xmipp.ij.commons.XmippImageCanvasinline
getXOnImage(int x)xmipp.ij.commons.XmippImageCanvasinline
getYOnImage(int y)xmipp.ij.commons.XmippImageCanvasinline
isDragImage(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinlineprotected
isKeyPressed(int keyCode)xmipp.ij.commons.XmippImageCanvasinlineprotected
keyPressed(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyReleased(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyTyped(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
loadData(XmippIJWindow xiw)xmipp.ij.commons.XmippImageCanvasinline
mouseDragged(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseMoved(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mousePressed(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseReleased(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseWheelMoved(MouseWheelEvent e)xmipp.ij.commons.XmippImageCanvasinline
offScreenX(int x)xmipp.ij.commons.XmippImageCanvasinline
offScreenY(int y)xmipp.ij.commons.XmippImageCanvasinline
setInvertX(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setInvertY(boolean value)xmipp.ij.commons.XmippImageCanvasinline
XmippImageCanvas(ImagePlus imp)xmipp.ij.commons.XmippImageCanvasinline
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Tool getTool ()
 
 XmippImageCanvas (ImagePlus imp)
 
void mousePressed (MouseEvent e)
 
void customScrollSetup (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void mouseWheelMoved (MouseWheelEvent e)
 
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int offScreenX (int x)
 
int offScreenY (int y)
 
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void keyPressed (KeyEvent keyEvent)
 
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boolean isDragImage (MouseEvent e)
 
boolean isKeyPressed (int keyCode)
 
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Definition at line 12 of file XmippImageCanvas.java.

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Definition at line 27 of file XmippImageCanvas.java.

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28  {
29  super(imp);
30  addMouseWheelListener(this);
31 
32 
33  }
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Definition at line 195 of file XmippImageCanvas.java.

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196  {
197  double currmagnif = getMagnification();
198  double prefmagnif = getPreferredMagnification();
199  if (currmagnif < prefmagnif)
200  {
201  setMagnification(prefmagnif);
202  setDrawingSize((int) (getSrcRect().getWidth() * magnification), (int) (getSrcRect().getHeight() * magnification));
203  repaint();
204  if (getParent() != null)
205  {
206  ImageWindow iw = (ImageWindow) getParent();
207  iw.pack();
208  }
209  }
210  }
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Definition at line 55 of file XmippImageCanvas.java.

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55  {
56 
57  int x = super.offScreenX(e.getX());
58  int y = super.offScreenY(e.getY());
59 
60  setupScroll(x, y);
61 
62  }
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Definition at line 184 of file XmippImageCanvas.java.

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185  {
186  double magnification = getMagnification();
187  int min = 200;
188  while (Math.min(getSrcRect().getWidth() * magnification, getSrcRect().getHeight() * magnification) < min)
189  {
190  magnification = 2 * magnification;
191  }
192  return magnification;
193  }
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Definition at line 19 of file XmippImageCanvas.java.

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20  {
21 
22  if (IJ.getInstance() == null || !IJ.getInstance().isVisible())
23  return Tool.PICKER;
24  return Tool.getTool(IJ.getToolName());
25  }
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Definition at line 97 of file XmippImageCanvas.java.

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98  {
99  int x0 = (int) getSrcRect().getX();
100  return (int) ((x - x0) * magnification);
101  }
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Definition at line 103 of file XmippImageCanvas.java.

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104  {
105  int y0 = (int) getSrcRect().getY();
106  return (int) ((y - y0) * magnification);
107  }
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Definition at line 64 of file XmippImageCanvas.java.

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65  {
66  return (SwingUtilities.isRightMouseButton(e) && !e.isControlDown());
67  }
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Definition at line 238 of file XmippImageCanvas.java.

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238  {
239  if (keyCode < keys.length){
240  return keys[keyCode];
241  }
242  return false;
243  }
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Definition at line 228 of file XmippImageCanvas.java.

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228  {
229 
230  keys[keyEvent.getKeyCode()] = true;
231  }
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Definition at line 234 of file XmippImageCanvas.java.

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234  {
235  keys[keyEvent.getKeyCode()] = false;
236  }
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void xmipp.ij.commons.XmippImageCanvas.keyTyped (KeyEvent keyEvent)
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Definition at line 223 of file XmippImageCanvas.java.

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223  {
224 
225  }
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void xmipp.ij.commons.XmippImageCanvas.loadData (XmippIJWindow xiw)
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Definition at line 161 of file XmippImageCanvas.java.

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162  {
163  double currmagnif = getMagnification();
164  Rectangle rect = getSrcRect();
165  imp = xiw.getImagePlusLoader().loadImagePlus();
166  imp.setTitle(xiw.getImagePlusLoader().getName());
167  ImageWindow iw = (ImageWindow) xiw;
168  iw.setImage(getImage());
169  iw.updateImage(getImage());
170 
171  setSourceRect(rect);
172  double prefmagnif = getPreferredMagnification();
173  if (currmagnif < prefmagnif)
174  setMagnification(prefmagnif);
175  else
176  setMagnification(currmagnif);
177  setDrawingSize((int) (rect.getWidth() * magnification), (int) (rect.getHeight() * magnification));
178 
179  repaint();
180  iw.pack();
181 
182  }
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void xmipp.ij.commons.XmippImageCanvas.mouseDragged (MouseEvent e)
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Definition at line 69 of file XmippImageCanvas.java.

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70  {
71 
72  if (getTool() == Tool.IMAGEJ)
73  {
74  super.mouseDragged(e);
75  return;
76  }
77  if (isDragImage(e))
78  {
79  scroll(e.getX(), e.getY());
80  return;
81  }
82  }
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Definition at line 126 of file XmippImageCanvas.java.

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127  {
128  int x = offScreenX(e.getX());
129  int y = offScreenY(e.getY());
130 
131  if(getParent() instanceof XmippImageWindow)
132  {
133  int[] pixels = imp.getPixel(x, y);
134  if(pixels != null)
135  ((XmippImageWindow)getParent()).showPixels(x, y, pixels);
136  }
137  if (getTool() == Tool.IMAGEJ)
138  super.mouseMoved(e);
139 
140  imp.mouseMoved(x, y);
141  imp.updateStatusbarValue();
142 
143  }
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Definition at line 35 of file XmippImageCanvas.java.

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36  {
37  if (getTool() == Tool.IMAGEJ)
38  {
39  super.mousePressed(e);
40  return;
41  }
42  if (isDragImage(e))
43  {
44  customScrollSetup(e);
45  return;
46  }
47  if(e.isControlDown())
48  {
49  if (SwingUtilities.isLeftMouseButton(e))
50  zoomIn(e.getX(), e.getY());
51  if (SwingUtilities.isRightMouseButton(e))
52  zoomOut(e.getX(), e.getY());
53  }
54  }
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Definition at line 87 of file XmippImageCanvas.java.

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88  {
89  if (getTool() == Tool.IMAGEJ)// do nothing for ImageJ tool is mine is selected
90  {
91  super.mouseReleased(e);
92  return;
93  }
94 
95  }
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Definition at line 110 of file XmippImageCanvas.java.

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111  {
112  if (!e.isShiftDown())
113  return;
114 
115  int x = e.getX();
116  int y = e.getY();
117  int rotation = e.getWheelRotation();
118  if (rotation < 0)
119  zoomIn(x, y);
120  else
121  zoomOut(x, y);
122 
123 
124  }
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Definition at line 145 of file XmippImageCanvas.java.

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146  {
147  x = super.offScreenX(x);
148  if(invertx)
149  x = imp.getWidth() - x;
150  return x;
151  }
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Definition at line 153 of file XmippImageCanvas.java.

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154  {
155  y = super.offScreenY(y);
156  if(inverty)
157  y = imp.getHeight() - y;
158  return y;
159  }
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Definition at line 212 of file XmippImageCanvas.java.

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213  {
214  invertx = value;
215  }
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void xmipp.ij.commons.XmippImageCanvas.setInvertY (boolean value)
- 		-inline
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Definition at line 217 of file XmippImageCanvas.java.

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218  {
219  inverty = value;
220  }
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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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xmipp.ij.commons.XmippImageConverter Member List
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This is the complete list of members for xmipp.ij.commons.XmippImageConverter, including all inherited members.

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buildImagePlus(String filename, ImageStack is)xmipp.ij.commons.XmippImageConverterinlinestatic
convertToImageGeneric(ImagePlus imp)xmipp.ij.commons.XmippImageConverterinlinestatic
convertToImagePlus(ImageGeneric image)xmipp.ij.commons.XmippImageConverterinlinestatic
convertToImagePlus(ImageGeneric image, long select_image)xmipp.ij.commons.XmippImageConverterinlinestatic
convertToImagePlus(ImageGeneric image, long select_image, int slice)xmipp.ij.commons.XmippImageConverterinlinestatic
loadImage(String filename)xmipp.ij.commons.XmippImageConverterinlinestatic
loadImage(String filename, int zoom)xmipp.ij.commons.XmippImageConverterinlinestatic
normalizeImagePlus(ImagePlus imp)xmipp.ij.commons.XmippImageConverterinlinestatic
readMdRowToImagePlus(String fn, MetaData md, long objId, int width, int height, boolean useGeo, boolean wrap)xmipp.ij.commons.XmippImageConverterinlinestatic
readMdRowToImagePlus(String fn, MetaData md, long objId, boolean useGeo, boolean wrap)xmipp.ij.commons.XmippImageConverterinlinestatic
readMetadataToImagePlus(int label, MetaData md, boolean useGeo, boolean wrap, boolean inverty)xmipp.ij.commons.XmippImageConverterinlinestatic
readToImagePlus(ImageGeneric image)xmipp.ij.commons.XmippImageConverterinlinestatic
readToImagePlus(ImageGeneric image, int nslice)xmipp.ij.commons.XmippImageConverterinlinestatic
readToImagePlus(ImageGeneric image, long nimage, int nslice)xmipp.ij.commons.XmippImageConverterinlinestatic
readToImagePlus(ImageGeneric image, long nimage)xmipp.ij.commons.XmippImageConverterinlinestatic
readToImagePlus(ImageGeneric image, int width, int height)xmipp.ij.commons.XmippImageConverterinlinestatic
readToImagePlus(ImageGeneric image, int width, int height, int nslice)xmipp.ij.commons.XmippImageConverterinlinestatic
readToImagePlus(ImageGeneric image, int width, int height, long nimage)xmipp.ij.commons.XmippImageConverterinlinestatic
readToImagePlus(ImageGeneric image, int width, int height, int slice, long select_image)xmipp.ij.commons.XmippImageConverterinlinestatic
revert(ImagePlus imp, String path)xmipp.ij.commons.XmippImageConverterinlinestatic
writeImagePlus(ImagePlus imp, String filename)xmipp.ij.commons.XmippImageConverterinlinestatic
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippImageConverter.html b/html/classxmipp_1_1ij_1_1commons_1_1XmippImageConverter.html deleted file mode 100644 index 8fc36312..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippImageConverter.html +++ /dev/null @@ -1,1032 +0,0 @@ - - - - - - - -Xmipp: xmipp.ij.commons.XmippImageConverter Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Static Public Member Functions | -List of all members
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xmipp.ij.commons.XmippImageConverter Class Reference
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-Static Public Member Functions

static ImagePlus loadImage (String filename) throws Exception
 
static ImagePlus loadImage (String filename, int zoom) throws Exception
 
static ImagePlus readToImagePlus (ImageGeneric image) throws Exception
 
static ImagePlus readToImagePlus (ImageGeneric image, int nslice) throws Exception
 
static ImagePlus readToImagePlus (ImageGeneric image, long nimage, int nslice) throws Exception
 
static ImagePlus readToImagePlus (ImageGeneric image, long nimage) throws Exception
 
static ImagePlus readToImagePlus (ImageGeneric image, int width, int height) throws Exception
 
static ImagePlus readToImagePlus (ImageGeneric image, int width, int height, int nslice) throws Exception
 
static ImagePlus readToImagePlus (ImageGeneric image, int width, int height, long nimage) throws Exception
 
static ImagePlus readToImagePlus (ImageGeneric image, int width, int height, int slice, long select_image) throws Exception
 
static ImagePlus convertToImagePlus (ImageGeneric image) throws Exception
 
static ImagePlus convertToImagePlus (ImageGeneric image, long select_image) throws Exception
 
static ImagePlus convertToImagePlus (ImageGeneric image, long select_image, int slice) throws Exception
 
static ImagePlus readMdRowToImagePlus (String fn, MetaData md, long objId, int width, int height, boolean useGeo, boolean wrap) throws Exception
 
static ImagePlus readMdRowToImagePlus (String fn, MetaData md, long objId, boolean useGeo, boolean wrap) throws Exception
 
static ImagePlus readMetadataToImagePlus (int label, MetaData md, boolean useGeo, boolean wrap, boolean inverty) throws Exception
 
static ImagePlus buildImagePlus (String filename, ImageStack is)
 
static void normalizeImagePlus (ImagePlus imp)
 
static void revert (ImagePlus imp, String path) throws Exception
 
static ImageGeneric convertToImageGeneric (ImagePlus imp) throws Exception
 
static boolean writeImagePlus (ImagePlus imp, String filename) throws Exception
 
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Detailed Description

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Definition at line 47 of file XmippImageConverter.java.

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Member Function Documentation

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◆ buildImagePlus()

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static ImagePlus xmipp.ij.commons.XmippImageConverter.buildImagePlus (String filename,
ImageStack is 
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Definition at line 264 of file XmippImageConverter.java.

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264  {
265  ImagePlus imp = new ImagePlus(filename, is);
266 
267  if (filename != null) {
268  // Sets associated file info.
269  File f = new File(filename);
270  FileInfo fi = new FileInfo();
271  String absPath = f.getAbsolutePath();
272  fi.directory = absPath.substring(0,
273  absPath.lastIndexOf(File.separator));
274  fi.fileName = f.getName();
275  imp.setFileInfo(fi);
276  }
277 
278  return imp;
279  }
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◆ convertToImageGeneric()

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static ImageGeneric xmipp.ij.commons.XmippImageConverter.convertToImageGeneric (ImagePlus imp) throws Exception
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This will convert an ImagePlus to ImageGeneric. NOTE: This can be used now with images or volumes

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Definition at line 297 of file XmippImageConverter.java.

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298  {
299  ImageGeneric image = new ImageGeneric();
300  DataSetter ds = createDataSetter(image, imp.getType());
301  image.resize(imp.getWidth(), imp.getHeight(), imp.getStackSize());
302 
303  ImageStack is = imp.getStack();
304  for (int nslice = ImageGeneric.FIRST_SLICE; nslice <= is.getSize(); nslice++) {
305  ds.setArray(image, is.getProcessor(nslice).getPixels(),
306  ImageGeneric.FIRST_IMAGE, nslice);
307  }
308 
309  return image;
310  }
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static ImagePlus xmipp.ij.commons.XmippImageConverter.convertToImagePlus (ImageGeneric image) throws Exception
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Converts an ImageGeneric to ImageJ WARNING!: Use this when converting images from memory.

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Definition at line 148 of file XmippImageConverter.java.

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149  {
150  return convertToImagePlus(image, ImageGeneric.ALL_IMAGES,
151  ImageGeneric.ALL_SLICES);
152  }
xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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static ImagePlus xmipp.ij.commons.XmippImageConverter.convertToImagePlus (ImageGeneric image,
long select_image 
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Converts an ImageGeneric to ImageJ WARNING!: Use this when converting images from memory.

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Definition at line 158 of file XmippImageConverter.java.

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159  {
160  return convertToImagePlus(image, select_image, ImageGeneric.ALL_SLICES);
161  }
xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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◆ convertToImagePlus() [3/3]

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static ImagePlus xmipp.ij.commons.XmippImageConverter.convertToImagePlus (ImageGeneric image,
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Definition at line 163 of file XmippImageConverter.java.

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164  {
165  int width = image.getXDim();
166  int height = image.getYDim();
167 
168  ImageStack is = new ImageStack(width, height);
169  ProcessorCreator pc = createProcessorCreator(image);
170  long lastImage = select_image;
171 
172  if (select_image == ImageGeneric.ALL_IMAGES) {
173  select_image = ImageGeneric.FIRST_IMAGE;
174  lastImage = image.getNDim();
175  }
176  for (; select_image <= lastImage; select_image++) {
177  addSlicesToStack(image, select_image, slice, is, pc);
178  }
179  return buildImagePlus(image.getFilename(), is);
180  }
xmipp.ij.commons.XmippImageConverter.buildImagePlus
static ImagePlus buildImagePlus(String filename, ImageStack is)
Definition: XmippImageConverter.java:264
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◆ loadImage() [1/2]

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static ImagePlus xmipp.ij.commons.XmippImageConverter.loadImage (String filename) throws Exception
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Definition at line 49 of file XmippImageConverter.java.

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49  {
50  return loadImage(filename, 100);
51  }
xmipp.ij.commons.XmippImageConverter.loadImage
static ImagePlus loadImage(String filename)
Definition: XmippImageConverter.java:49
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◆ loadImage() [2/2]

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static ImagePlus xmipp.ij.commons.XmippImageConverter.loadImage (String filename,
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Definition at line 53 of file XmippImageConverter.java.

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54  {
55  ImageGeneric image = new ImageGeneric(filename);
56 
57  double scale = zoom / 100.0;
58  int w = (int) (image.getXDim() * scale);
59  int h = (int) (image.getYDim() * scale);
60 
61  ImagePlus imp;
62  /*
63  * if (Filename.hasPrefix(filename)) { String name =
64  * Filename.getFilename(filename); long nimage =
65  * Filename.getNimage(filename);
66  *
67  * image = new ImageGeneric(name); imp = convertToImageJ(image, nimage);
68  * } else {
69  */
70  long select_image = Filename.getNimage(filename);
71  imp = readToImagePlus(image, w, h, select_image);
72  // }
73 
74  image.destroy();
75  return imp;
76  }
xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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Definition at line 281 of file XmippImageConverter.java.

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281  {
282  StackStatistics ss = new StackStatistics(imp);
283  imp.getProcessor().setMinAndMax(ss.min, ss.max);
284  }
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static ImagePlus xmipp.ij.commons.XmippImageConverter.readMdRowToImagePlus (String fn,
MetaData md,
long objId,
int width,
int height,
boolean useGeo,
boolean wrap 
) throws Exception
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Definition at line 198 of file XmippImageConverter.java.

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200  {
201  ImageGeneric image = new ImageGeneric();
202  if (useGeo)
203  image.readApplyGeo(fn, md, objId, width, height, wrap);
204  else
205  image.read(fn, width, height);
206 
207  ImagePlus ip = convertToImagePlus(image);
208 
209  image.destroy();
210  return ip;
211  }
xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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MetaData md,
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Definition at line 213 of file XmippImageConverter.java.

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214  {
215  ImageGeneric image = new ImageGeneric();
216  if (useGeo)
217  image.readApplyGeo(fn, md, objId, wrap);
218  else
219  image.read(fn, true);
220  ImagePlus ip = convertToImagePlus(image, ImageGeneric.ALL_IMAGES);
221  image.destroy();
222  return ip;
223  }
xmipp.ij.commons.XmippImageConverter.convertToImagePlus
static ImagePlus convertToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:148
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static ImagePlus xmipp.ij.commons.XmippImageConverter.readMetadataToImagePlus (int label,
MetaData md,
boolean useGeo,
boolean wrap,
boolean inverty 
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Read the entries on the metadata and create an ImagePlus

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Definition at line 226 of file XmippImageConverter.java.

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227  {
228  LinkedList<String> missing = new LinkedList<String>();
229  ImagePlus imp = null;
230 
231  if (md.containsLabel(label)) {
232  ImageStack is = null;
233  long ids[] = md.findObjects();
234 
235  for (long id : ids) {
236  String filename = md.getValueString(label, id, true);
237 
238  try {
239  ImagePlus slice = readMdRowToImagePlus(filename, md, id, useGeo, wrap);
240  if(inverty)
241  slice = new ImagePlusLoader(slice, inverty).getImagePlus();
242  if (is == null)
243  is = new ImageStack(slice.getWidth(), slice.getHeight());
244  is.addSlice(filename, slice.getProcessor());
245  } catch (Exception ex) {
246  ex.printStackTrace(System.err);
247  missing.add(filename);
248  }
249  }
250  imp = buildImagePlus(md.getFilename(), is);
251  }
252  // Tells user about missing files.
253  if (!missing.isEmpty()) {
254  String message = "There are missing files:\n";
255  for (int i = 0; i < missing.size(); i++) {
256  message += missing.get(i) + "\n";
257  }
258  IJ.error(message);
259  }
260 
261  return imp;
262  }//function readMetadataToImagePlus
xmipp.ij.commons.XmippImageConverter.buildImagePlus
static ImagePlus buildImagePlus(String filename, ImageStack is)
Definition: XmippImageConverter.java:264
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xmipp.ij.commons.XmippImageConverter.readMdRowToImagePlus
static ImagePlus readMdRowToImagePlus(String fn, MetaData md, long objId, int width, int height, boolean useGeo, boolean wrap)
Definition: XmippImageConverter.java:198
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Definition at line 82 of file XmippImageConverter.java.

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83  {
84  return readToImagePlus(image, ImageGeneric.ALL_SLICES);
85  }
xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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Definition at line 87 of file XmippImageConverter.java.

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88  {
89  return readToImagePlus(image, image.getXDim(), image.getYDim(), nslice);
90  }
xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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Definition at line 92 of file XmippImageConverter.java.

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93  {
94  return readToImagePlus(image, image.getXDim(), image.getYDim(), nslice, nimage);
95  }
xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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Definition at line 97 of file XmippImageConverter.java.

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98  {
99  return readToImagePlus(image, image.getXDim(), image.getYDim(), nimage);
100  }
xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
Definition: XmippImageConverter.java:82
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Definition at line 102 of file XmippImageConverter.java.

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103  {
104  return readToImagePlus(image, width, height, ImageGeneric.ALL_SLICES,
105  ImageGeneric.ALL_IMAGES);
106  }
xmipp.ij.commons.XmippImageConverter.readToImagePlus
static ImagePlus readToImagePlus(ImageGeneric image)
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Definition at line 108 of file XmippImageConverter.java.

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109  {
110  return readToImagePlus(image, width, height, nslice,
111  ImageGeneric.ALL_IMAGES);
112  }
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static ImagePlus readToImagePlus(ImageGeneric image)
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Definition at line 114 of file XmippImageConverter.java.

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115  {
116  return readToImagePlus(image, width, height, ImageGeneric.ALL_SLICES,
117  nimage);
118  }
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static ImagePlus readToImagePlus(ImageGeneric image)
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static ImagePlus xmipp.ij.commons.XmippImageConverter.readToImagePlus (ImageGeneric image,
int width,
int height,
int slice,
long select_image 
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In this function is supposed the the ImageGeneric is read only the header and the data will be read from disk

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Definition at line 124 of file XmippImageConverter.java.

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125  {
126  ImageStack is = new ImageStack(width, height);
127  ProcessorCreator pc = createProcessorCreator(image);
128  long lastImage = select_image;
129 
130  if (select_image == ImageGeneric.ALL_IMAGES) {
131  select_image = ImageGeneric.FIRST_IMAGE;
132  lastImage = image.getNDim();
133  }
134  else if (select_image == -1)
135  select_image = lastImage = image.getNDim()/2;
136  for (; select_image <= lastImage; select_image++) {
137  image.read(width, height, select_image);
138  addSlicesToStack(image, ImageGeneric.FIRST_IMAGE, slice, is, pc);
139  }
140 
141  return buildImagePlus(image.getFilename(), is);
142  }
xmipp.ij.commons.XmippImageConverter.buildImagePlus
static ImagePlus buildImagePlus(String filename, ImageStack is)
Definition: XmippImageConverter.java:264
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Definition at line 286 of file XmippImageConverter.java.

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286  {
287  ImagePlus imp2 = XmippImageConverter.loadImage(path);
288  imp2.setTitle("Revert!!: " + System.currentTimeMillis());
289  imp2.show();
290  imp.setStack(imp.getTitle(), imp2.getImageStack());
291  }
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Definition at line 312 of file XmippImageConverter.java.

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313  {
314  ImageGeneric image = new ImageGeneric();
315 
316  int width = imp.getWidth();
317  int height = imp.getHeight();
318  int depth = imp.getStackSize();
319  int image_index = 1;
320 
321  boolean storeAllImages = Filename.hasStackExtension(filename);
322  boolean storeAllSlices = !storeAllImages;// =
323  // Filename.hasVolumeExtension(filename);
324 
325  // TODO: Add support for hyperstacks and remove this "if".
326  if (storeAllImages) {
327  image_index = depth;
328  depth = 1;
329  }
330 
331  DataSetter ds = createDataSetter(image, imp.getType());
332 
333  for (long nimage = ImageGeneric.FIRST_IMAGE; nimage <= image_index; nimage++) {
334  image.mapFile2Write(width, height, depth, filename, nimage);
335 
336  // Store volume.
337  for (int nslice = ImageGeneric.FIRST_SLICE; nslice <= depth; nslice++) {
338  Object data = imp.getStack()
339  .getProcessor((int) nimage * nslice).getPixels();
340 
341  // image.setData...
342  ds.setArray(image, data, ImageGeneric.FIRST_IMAGE, nslice);
343 
344  // If just one image, breaks loop.
345  if (!storeAllSlices) {
346  break;
347  }
348  }
349 
350  image.write(filename);
351 
352  // If just one image, breaks loop.
353  if (!storeAllImages) {
354  break;
355  }
356  }
357 
358  image.destroy();
359  return true;
360  }
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anisotropicDiffFilterxmipp.ij.commons.XmippImageJstatic
bandPassFilterxmipp.ij.commons.XmippImageJstatic
brightnessContrastFilterxmipp.ij.commons.XmippImageJstatic
duplicateFilterxmipp.ij.commons.XmippImageJstatic
enhanceContrastFilterxmipp.ij.commons.XmippImageJstatic
gaussianBlurFilterxmipp.ij.commons.XmippImageJstatic
invertLUTFilterxmipp.ij.commons.XmippImageJstatic
substractBackgroundFilterxmipp.ij.commons.XmippImageJstatic
windowClosing(WindowEvent e)xmipp.ij.commons.XmippImageJinline
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-Public Member Functions

void windowClosing (WindowEvent e)
 
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-Static Public Attributes

static final String duplicateFilter = "Duplicate"
 
static final String bandPassFilter = "Bandpass Filter..."
 
static final String anisotropicDiffFilter = "Anisotropic Diffusion..."
 
static final String substractBackgroundFilter = "Subtract Background..."
 
static final String gaussianBlurFilter = "Gaussian Blur..."
 
static final String brightnessContrastFilter = "Brightness/Contrast..."
 
static final String invertLUTFilter = "Invert LUT"
 
static final String enhanceContrastFilter = "Enhance Contrast..."
 
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Definition at line 7 of file XmippImageJ.java.

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◆ windowClosing()

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void xmipp.ij.commons.XmippImageJ.windowClosing (WindowEvent e)
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Definition at line 20 of file XmippImageJ.java.

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20  {
21  setVisible(false);
22  }
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◆ anisotropicDiffFilter

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final String xmipp.ij.commons.XmippImageJ.anisotropicDiffFilter = "Anisotropic Diffusion..."
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Definition at line 12 of file XmippImageJ.java.

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Definition at line 11 of file XmippImageJ.java.

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final String xmipp.ij.commons.XmippImageJ.brightnessContrastFilter = "Brightness/Contrast..."
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Definition at line 15 of file XmippImageJ.java.

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Definition at line 10 of file XmippImageJ.java.

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Definition at line 17 of file XmippImageJ.java.

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Definition at line 14 of file XmippImageJ.java.

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Definition at line 13 of file XmippImageJ.java.

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close()xmipp.ij.commons.XmippImageWindowinline
closingxmipp.ij.commons.XmippImageWindowprotected
getCanvas()xmipp.ij.commons.XmippImageWindowinline
getImagePlusLoader()xmipp.ij.commons.XmippImageWindowinline
getParams()xmipp.ij.commons.XmippImageWindowinline
initComponents()xmipp.ij.commons.XmippImageWindowinlineprotected
iplxmipp.ij.commons.XmippImageWindowprotected
isClosing()xmipp.ij.commons.XmippImageWindowinline
isStack()xmipp.ij.commons.XmippImageWindowinline
isVolume()xmipp.ij.commons.XmippImageWindowinline
loadData()xmipp.ij.commons.XmippImageWindowinline
loadMaskFrame()xmipp.ij.commons.XmippImageWindowinlineprotected
menuxmipp.ij.commons.XmippImageWindowprotected
myClose()xmipp.ij.commons.XmippImageWindowinline
openMaskToolbar()xmipp.ij.commons.XmippImageWindowinline
paramsxmipp.ij.commons.XmippImageWindowprotected
pixelslbxmipp.ij.commons.XmippImageWindowprotected
pixelsToString(ImagePlus imp, int x, int y, int[] pixels)xmipp.ij.commons.XmippImageWindowinlinestatic
saveData()xmipp.ij.commons.XmippImageWindowinline
saveDataAs(String file)xmipp.ij.commons.XmippImageWindowinline
showPixels(int x, int y, int[] pixels)xmipp.ij.commons.XmippImageWindowinline
windowActivated(WindowEvent e)xmipp.ij.commons.XmippImageWindowinline
windowClosing(WindowEvent e)xmipp.ij.commons.XmippImageWindowinline
XmippImageWindow(ImagePlusLoader ipl, Params params)xmipp.ij.commons.XmippImageWindowinline
XmippImageWindow(ImagePlus imp, Params params)xmipp.ij.commons.XmippImageWindowinline
XmippImageWindow(ImagePlus imp, ImageCanvas canvas, Params params)xmipp.ij.commons.XmippImageWindowinline
XmippImageWindow(ImagePlusLoader ipl, String title, Params params)xmipp.ij.commons.XmippImageWindowinline
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Xmipp -  v20.07 -
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-Public Member Functions | -Static Public Member Functions | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.ij.commons.XmippImageWindow Class Reference
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-Public Member Functions

 XmippImageWindow (ImagePlusLoader ipl, Params params)
 
 XmippImageWindow (ImagePlus imp, Params params)
 
 XmippImageWindow (ImagePlus imp, ImageCanvas canvas, Params params)
 
 XmippImageWindow (ImagePlusLoader ipl, String title, Params params)
 
void openMaskToolbar ()
 
void loadData ()
 
void saveDataAs (String file) throws Exception
 
void saveData () throws Exception
 
ImagePlusLoader getImagePlusLoader ()
 
boolean isVolume ()
 
boolean isStack ()
 
void windowActivated (WindowEvent e)
 
XmippImageCanvas getCanvas ()
 
void showPixels (int x, int y, int[] pixels)
 
void windowClosing (WindowEvent e)
 
synchronized void myClose ()
 
boolean close ()
 
Params getParams ()
 
synchronized boolean isClosing ()
 
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-Static Public Member Functions

static String pixelsToString (ImagePlus imp, int x, int y, int[] pixels)
 
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-Protected Member Functions

void initComponents ()
 
void loadMaskFrame ()
 
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-Protected Attributes

XmippMenuBar menu
 
ImagePlusLoader ipl
 
Label pixelslb
 
Params params
 
boolean closing = false
 
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Detailed Description

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Definition at line 24 of file XmippImageWindow.java.

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Constructor & Destructor Documentation

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◆ XmippImageWindow() [1/4]

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xmipp.ij.commons.XmippImageWindow.XmippImageWindow (ImagePlusLoader ipl,
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Definition at line 35 of file XmippImageWindow.java.

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36  {
37  this(ipl, ipl.getName(), params);
38  }
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xmipp.ij.commons.XmippImageWindow.XmippImageWindow (ImagePlus imp,
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Definition at line 40 of file XmippImageWindow.java.

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41  {
42  this(imp, new XmippImageCanvas(imp), params);
43  }
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xmipp.ij.commons.XmippImageWindow.XmippImageWindow (ImagePlus imp,
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Definition at line 45 of file XmippImageWindow.java.

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46  {
47  super(imp, canvas);
48  this.ipl = new ImagePlusLoader(imp);
49  this.params = params;
50  XmippApplication.addInstance(true);
51  initComponents();
52  XmippWindowUtil.setScipionImageIcon(this);
53  }
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xmipp.ij.commons.XmippImageWindow.XmippImageWindow (ImagePlusLoader ipl,
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Definition at line 56 of file XmippImageWindow.java.

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57  {
58  super(ipl.getImagePlus(), new XmippImageCanvas(ipl.getImagePlus()));
59  this.ipl = ipl;
60  imp.setTitle(title);
61  this.params = params;
62  XmippApplication.addInstance(true);
63  initComponents();
64  XmippWindowUtil.setScipionImageIcon(this);
65  }
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◆ close()

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boolean xmipp.ij.commons.XmippImageWindow.close ()
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Definition at line 218 of file XmippImageWindow.java.

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219  {
220  boolean result = super.close();
221  myClose();
222  return result;
223  }
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Definition at line 154 of file XmippImageWindow.java.

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155  {
156  return ((XmippImageCanvas) super.getCanvas());
157  }
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Definition at line 122 of file XmippImageWindow.java.

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123  {
124  return ipl;
125  }
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Definition at line 226 of file XmippImageWindow.java.

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227  {
228  return params;
229  }
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Definition at line 67 of file XmippImageWindow.java.

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68  {
69 
70  menu = new XmippMenuBar(this);
71  if(params != null)//otherwise is picker window
72  {
73  setMenuBar(menu);
74  if(XmippApplication.isScipion())
75  {
76  MenuItem createMaskmi = new MenuItem("Design Mask");
77  createMaskmi.addActionListener(new ActionListener() {
78 
79  @Override
80  public void actionPerformed(ActionEvent ae) {
81  loadMaskFrame();
82  }
83  });
84  menu.advancedmn.add(createMaskmi);
85  if(params!= null && params.isMask())
86  loadMaskFrame();
87  }
88  }
89  pixelslb = new Label(" ");
90  add(pixelslb);
91 
92 
93  }
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boolean isMask()
Definition: Params.java:328
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Definition at line 282 of file XmippImageWindow.java.

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283  {
284  // TODO Auto-generated method stub
285  return closing;
286  }
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Definition at line 134 of file XmippImageWindow.java.

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135  {
136  return false;
137  }
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Definition at line 128 of file XmippImageWindow.java.

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129  {
130  return false;
131  }
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Definition at line 102 of file XmippImageWindow.java.

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103  {
104  getCanvas().loadData(this);
105  if(params != null)//otherwise is picker window
106  menu.applyFilters();
107  }
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Definition at line 232 of file XmippImageWindow.java.

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233  {
234  if(maskfr == null || !maskfr.isVisible())
235  {
236  SwingUtilities.invokeLater(new Runnable() {
237 
238  @Override
239  public void run() {
240  maskfr = new DesignMaskJFrame(XmippImageWindow.this);
241  XmippWindowUtil.setLocation(0.2f, 0.5f, XmippImageWindow.this);
242  XmippWindowUtil.setLocation(0.6f, 0.5f, maskfr);
243  }
244  });
245 
246  imp.getCanvas().addMouseListener(new MouseListener() {
247 
248  @Override
249  public void mouseClicked(MouseEvent me) {
250  }
251 
252  @Override
253  public void mousePressed(MouseEvent me) {
254  }
255 
256  @Override
257  public void mouseReleased(MouseEvent me) {
258  maskfr.refreshMask();
259  }
260 
261  @Override
262  public void mouseEntered(MouseEvent me) {
263  }
264 
265  @Override
266  public void mouseExited(MouseEvent me) {
267  }
268  });
269  imp.getCanvas().addComponentListener(new java.awt.event.ComponentAdapter()
270  {
271  @Override
272  public void componentResized(ComponentEvent e)
273  {
274  maskfr.refreshMask();
275  }
276  });
277 
278  }
279  }
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XmippImageWindow(ImagePlusLoader ipl, Params params)
Definition: XmippImageWindow.java:35
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205  {
206  closing = true;
207  XmippApplication.removeInstance(true);
208  if(maskfr != null)
209  {
210  maskfr.setVisible(false);
211  maskfr.dispose();
212 
213  }
214  }
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97  {
98  menu.runCommand("Masks Tool Bar", new IJRequirement[] { IJRequirement.IMAGEJ });
99  }
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static String xmipp.ij.commons.XmippImageWindow.pixelsToString (ImagePlus imp,
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Definition at line 167 of file XmippImageWindow.java.

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168  {
169  String text = "";
170  String value = "";
171  switch (imp.getType())
172  {
173  case ImagePlus.GRAY8:
174  case ImagePlus.GRAY16:
175  double cValue = imp.getCalibration().getCValue(pixels[0]);
176  if (cValue == pixels[0])
177  value = String.valueOf(pixels[0]);
178  else
179  value = IJ.d2s(cValue) + " (" + pixels[0] + ")";
180  text = String.format("x=%s, y=%s, value=%-5s", x, y, value);
181  break;
182  case ImagePlus.GRAY32:
183  text = String.format("x=%s, y=%s, value=%.2f", x, y, Float.intBitsToFloat(pixels[0]));
184  break;
185  case ImagePlus.COLOR_256:
186  case ImagePlus.COLOR_RGB:
187  value = pixels[0] + "," + pixels[1] + "," + pixels[2];
188  text = String.format("x=%s, y=%s, value=%-15s", x, y, value);
189  break;
190  }
191  return text;
192 
193  }
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Definition at line 116 of file XmippImageWindow.java.

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117  {
118  saveDataAs(imp.getTitle());
119  }
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Definition at line 110 of file XmippImageWindow.java.

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111  {
112  XmippImageConverter.writeImagePlus(imp, file);
113  }
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Definition at line 159 of file XmippImageWindow.java.

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160  {
161  if(pixelslb == null)//avoid error running showPixels before initialization
162  return;
163  pixelslb.setText(pixelsToString(imp, x, y, pixels));
164 
165  }
xmipp.ij.commons.XmippImageWindow.pixelsToString
static String pixelsToString(ImagePlus imp, int x, int y, int[] pixels)
Definition: XmippImageWindow.java:167
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Definition at line 141 of file XmippImageWindow.java.

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142  {
143  // if (IJ.isMacintosh())
144  // this.setMenuBar(Menus.getMenuBar());
145 
146  if (!closed)
147  {
148  //ic.requestFocus();
149  WindowManager.setCurrentWindow(this);
150  }
151  }
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Definition at line 197 of file XmippImageWindow.java.

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197  {
198 
199  super.windowClosing(e);
200  myClose();
201  imp.flush();
202  }
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Definition at line 29 of file XmippImageWindow.java.

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- Node21 -> Node20 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" impreader" ,fontname="Helvetica"]; - Node21 [label="xmipp.ij.commons.ImagePlus\lReader",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1ImagePlusReader.html"]; - Node22 -> Node21 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" imp" ,fontname="Helvetica"]; - Node22 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node23 -> Node21 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" geometry" ,fontname="Helvetica"]; - Node23 [label="xmipp.ij.commons.Geometry",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1Geometry.html"]; - Node24 -> Node21 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ig" ,fontname="Helvetica"]; - Node24 [label="xmipp.jni.ImageGeneric",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1ImageGeneric.html"]; 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- Node29 [label="CommandLine",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node20 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ipl" ,fontname="Helvetica"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippImageWindow__coll__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1XmippImageWindow__coll__graph.md5 deleted file mode 100644 index 03894299..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippImageWindow__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -02173cdf67252633b7e23ef0fa031aa1 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippImageWindow__inherit__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1XmippImageWindow__inherit__graph.dot deleted file mode 100644 index 305db0c7..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippImageWindow__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.ij.commons.XmippImageWindow" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; 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xmipp.ij.commons.XmippMenuBar Member List
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This is the complete list of members for xmipp.ij.commons.XmippMenuBar, including all inherited members.

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activemixmipp.ij.commons.XmippMenuBarprotected
addCheckCommand(CheckboxMenuItem mi, String command, final IJRequirement... requirements)xmipp.ij.commons.XmippMenuBarinlineprotected
addCommand(MenuItem mi, String command, final IJRequirement... requirements)xmipp.ij.commons.XmippMenuBarinlineprotected
addFilterAppliedListener()xmipp.ij.commons.XmippMenuBarinlineprotected
addIJCheckMenuItem(Menu mn, String command, IJRequirement... requirements)xmipp.ij.commons.XmippMenuBarinlineprotected
addIJCheckMenuItem(Menu mn, String name, String command, IJRequirement... requirements)xmipp.ij.commons.XmippMenuBarinlineprotected
addIJMenuItem(Menu mn, String name, String command, IJRequirement... requirements)xmipp.ij.commons.XmippMenuBarinlineprotected
advancedmnxmipp.ij.commons.XmippMenuBarprotected
applyFilters()xmipp.ij.commons.XmippMenuBarinline
binarymnxmipp.ij.commons.XmippMenuBarprotected
close()xmipp.ij.commons.XmippMenuBarinlineprotected
commandxmipp.ij.commons.XmippMenuBarprotected
drawmnxmipp.ij.commons.XmippMenuBarprotected
exitmixmipp.ij.commons.XmippMenuBarprotected
filemnxmipp.ij.commons.XmippMenuBarprotected
filtersxmipp.ij.commons.XmippMenuBarprotected
getFilter(String command)xmipp.ij.commons.XmippMenuBarinline
getKeyAssist()xmipp.ij.commons.XmippMenuBarinline
helpmnxmipp.ij.commons.XmippMenuBarprotected
imagejmixmipp.ij.commons.XmippMenuBarprotected
imagemnxmipp.ij.commons.XmippMenuBarprotected
infomnxmipp.ij.commons.XmippMenuBarprotected
invertxxmipp.ij.commons.XmippMenuBarprotected
invertyxmipp.ij.commons.XmippMenuBarprotected
iploaderxmipp.ij.commons.XmippMenuBarprotected
keyassistdlgxmipp.ij.commons.XmippMenuBarprotected
keyassistmixmipp.ij.commons.XmippMenuBarprotected
onlinemixmipp.ij.commons.XmippMenuBarprotected
openImagePlusAs3D(ImagePlus ip)xmipp.ij.commons.XmippMenuBarinlinestatic
openwith3dmixmipp.ij.commons.XmippMenuBarprotected
poll()xmipp.ij.commons.XmippMenuBarinlineprotected
pollmixmipp.ij.commons.XmippMenuBarprotected
polltimerxmipp.ij.commons.XmippMenuBarprotected
processmnxmipp.ij.commons.XmippMenuBarprotected
profilemnxmipp.ij.commons.XmippMenuBarprotected
refreshmixmipp.ij.commons.XmippMenuBarprotected
runCommand(String command, IJRequirement... requirements)xmipp.ij.commons.XmippMenuBarinline
saveAs()xmipp.ij.commons.XmippMenuBarinlineprotected
saveasmixmipp.ij.commons.XmippMenuBarprotected
savemixmipp.ij.commons.XmippMenuBarprotected
thresholdingmnxmipp.ij.commons.XmippMenuBarprotected
timerxmipp.ij.commons.XmippMenuBarprotected
transformmnxmipp.ij.commons.XmippMenuBarprotected
ugmixmipp.ij.commons.XmippMenuBarprotected
useGeometry(boolean ug)xmipp.ij.commons.XmippMenuBarinlineprotected
wrap(boolean value)xmipp.ij.commons.XmippMenuBarinlineprotected
wrapmixmipp.ij.commons.XmippMenuBarprotected
XmippMenuBar(XmippIJWindow xw)xmipp.ij.commons.XmippMenuBarinline
xwxmipp.ij.commons.XmippMenuBarprotected
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xmipp.ij.commons.XmippMenuBar Class Reference
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-Inheritance diagram for xmipp.ij.commons.XmippMenuBar:
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-Classes

enum  IJRequirement
 
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-Public Member Functions

 XmippMenuBar (XmippIJWindow xw)
 
void applyFilters ()
 
IJCommand getFilter (String command)
 
void runCommand (String command, IJRequirement... requirements)
 
Map< Object, Object > getKeyAssist ()
 
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-Static Public Member Functions

static void openImagePlusAs3D (ImagePlus ip)
 
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-Protected Member Functions

void addFilterAppliedListener ()
 
void close ()
 
void useGeometry (boolean ug)
 
void saveAs ()
 
void wrap (boolean value)
 
CheckboxMenuItem addIJCheckMenuItem (Menu mn, String command, IJRequirement... requirements)
 
CheckboxMenuItem addIJCheckMenuItem (Menu mn, String name, String command, IJRequirement... requirements)
 
void poll ()
 
void addCheckCommand (CheckboxMenuItem mi, String command, final IJRequirement... requirements)
 
MenuItem addIJMenuItem (Menu mn, String name, String command, IJRequirement... requirements)
 
void addCommand (MenuItem mi, String command, final IJRequirement... requirements)
 
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-Protected Attributes

final XmippIJWindow xw
 
Menu filemn
 
Menu imagemn
 
Menu advancedmn
 
MenuItem savemi
 
MenuItem saveasmi
 
MenuItem openwith3dmi
 
Menu infomn
 
Menu transformmn
 
Menu thresholdingmn
 
Menu binarymn
 
Menu processmn
 
Menu drawmn
 
MenuItem imagejmi
 
Menu profilemn
 
CheckboxMenuItem pollmi
 
Object timer
 
PollTimer polltimer
 
MenuItem refreshmi
 
CheckboxMenuItem wrapmi
 
CheckboxMenuItem ugmi
 
MenuItem exitmi
 
Menu helpmn
 
MenuItem onlinemi
 
MenuItem keyassistmi
 
QuickHelpJDialog keyassistdlg
 
boolean invertx
 
boolean inverty
 
CheckboxMenuItem activemi
 
String command
 
List< IJCommand > filters
 
ImagePlusLoader iploader
 
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Detailed Description

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Author
Juanjo Vega
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Definition at line 46 of file XmippMenuBar.java.

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Constructor & Destructor Documentation

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◆ XmippMenuBar()

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xmipp.ij.commons.XmippMenuBar.XmippMenuBar (XmippIJWindow xw)
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Definition at line 90 of file XmippMenuBar.java.

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91  {
92  filters = new ArrayList<IJCommand>();
93  this.xw = xw;
94  this.iploader = xw.getImagePlusLoader();
95  // menubar menus
96  filemn = new Menu("File");
97  imagemn = new Menu("Image");
98  advancedmn = new Menu("Advanced");
99  helpmn = new Menu("Help");
100 
101  add(filemn);
102  add(imagemn);
103  add(advancedmn);
104  add(helpmn);
105 
106  // menubar file menu
107 // savemi = new MenuItem("Save");
108 // savemi.setShortcut(new MenuShortcut(KeyEvent.VK_S));
109 // savemi.addActionListener(new ActionListener()
110 // {
111 //
112 // @Override
113 // public void actionPerformed(ActionEvent e)
114 // {
115 // try
116 // {
117 // if(XmippMenuBar.this.iploader.existsFile())
118 // XmippMenuBar.this.xw.saveData();
119 // else
120 // XmippMenuBar.this.saveAs();
121 // }
122 // catch (Exception ex)
123 // {
124 // ex.printStackTrace();
125 // XmippDialog.showInfo(null, ex.getMessage());
126 // }
127 //
128 // }
129 // });
130  saveasmi = new MenuItem("Save As...");
131  saveasmi.addActionListener(new ActionListener()
132  {
133 
134  @Override
135  public void actionPerformed(ActionEvent e)
136  {
137  saveAs();
138  }
139  });
140 
141 // openwith3dmi = new MenuItem("Open with 3D Viewer");
142 // openwith3dmi.setEnabled(xw.isVolume());
143 // openwith3dmi.setEnabled(Filename.isVolume(xw.getImageFilePath()));
144 // openwith3dmi.addActionListener(new ActionListener()
145 // {
146 //
147 // @Override
148 // public void actionPerformed(ActionEvent arg0)
149 // {
150 // ImagePlus imp = XmippMenuBar.this.iploader.getImagePlus();
151 // if (imp.getImageStackSize() == 1)
152 // XmippDialog.showInfo(null, "Only for Stack");
153 // else
154 // openImagePlusAs3D(imp);
155 //
156 // }
157 // });
158 // filemn.add(openwith3dmi);
159  MenuItem volviewermi = new MenuItem("Open with Volume Viewer/3D Slicer");
160  volviewermi.setActionCommand("Volume Viewer");
161  volviewermi.setEnabled(xw.isVolume());
162  volviewermi.addActionListener(new ActionListener()
163  {
164 
165  @Override
166  public void actionPerformed(ActionEvent e)
167  {
168  MenuItem mi = (MenuItem) e.getSource();
169  runCommand(mi.getActionCommand());
170 
171  }
172  });
173  filemn.add(volviewermi);
174 // addIJCheckMenuItem(filemn, "Open with Volume Viewer/3D Slicer", "Volume Viewer", IJRequirement.VOLUME);
175 // addIJCheckMenuItem(filemn, "Open with VolumeJ", "VolumeJ ", IJRequirement.VOLUME);
176  refreshmi = new MenuItem("Refresh");
177  refreshmi.setEnabled(iploader.allowsPoll());
178  refreshmi.setShortcut(new MenuShortcut(KeyEvent.VK_F5));
179  refreshmi.addActionListener(new ActionListener()
180  {
181 
182  @Override
183  public void actionPerformed(ActionEvent arg0)
184  {
185  XmippMenuBar.this.xw.loadData();
186 
187  }
188  });
189 
190  pollmi = new CheckboxMenuItem("Poll");
191  pollmi.setEnabled(iploader.allowsPoll());
192  pollmi.addItemListener(new ItemListener()
193  {
194 
195  @Override
196  public void itemStateChanged(ItemEvent e)
197  {
198  boolean poll = pollmi.getState();
199  if (poll)
200  poll();
201  else
202  polltimer.stop();
203  }
204  });
205 
206  ugmi = new CheckboxMenuItem("Use Geometry");
207  ugmi.setEnabled(iploader.hasGeometry());
208  ugmi.setState(iploader.getUseGeometry());
209  ugmi.addItemListener(new ItemListener()
210  {
211 
212  @Override
213  public void itemStateChanged(ItemEvent e)
214  {
215  boolean ug = ugmi.getState();
216  useGeometry(ug);
217 
218  }
219  });
220 
221 
222  wrapmi = new CheckboxMenuItem("Wrap");
223  wrapmi.setEnabled(iploader.hasGeometry());
224  wrapmi.setState(iploader.isWrap());
225  wrapmi.addItemListener(new ItemListener()
226  {
227 
228  @Override
229  public void itemStateChanged(ItemEvent e)
230  {
231  wrap(wrapmi.getState());
232 
233  }
234  });
235 
236 
237  exitmi = new MenuItem("Exit");
238  exitmi.setShortcut(new MenuShortcut(KeyEvent.VK_Q));
239  exitmi.addActionListener(new ActionListener() {
240 
241  @Override
242  public void actionPerformed(ActionEvent e) {
243 
244  close();
245  }
246  });
247 
248 
249 
250 // filemn.add(savemi);
251  filemn.add(saveasmi);
252 // addIJCheckMenuItem(filemn, "Duplicate", "Duplicate...", IJRequirement.IMAGEJ);
253  filemn.add(refreshmi);
254  filemn.add(pollmi);
255  filemn.add(ugmi);
256  filemn.add(wrapmi);
257  filemn.add(exitmi);
258 
259  // menubar image menu
260 // infomn = new Menu("Info");
261 // adjustmn = new Menu("Adjust");
262 // filtersmn = new Menu("Filters");
263 
264 // imagemn.add(infomn);
265 // imagemn.add(adjustmn);
266 // imagemn.add(transformmn);
267 // imagemn.add(filtersmn);
268 
269 
270  // image info menu
271 // addIJCheckMenuItem(infomn, "Show Info", "Show Info...");
272 // addIJCheckMenuItem(infomn, "Properties", "Properties...");
273 // addIJCheckMenuItem(infomn, "Histogram", "Histogram", IJRequirement.IMAGEJ);
274 // addIJCheckMenuItem(infomn, "Plot Profile", "Plot Profile", IJRequirement.IMAGEJ);
275 
276  // image adjust menu
277 
278 // addIJCheckMenuItem(adjustmn, "Crop", "Crop", IJRequirement.IMAGEJ);
279 // addIJCheckMenuItem(adjustmn, "Scale", "Scale...");
280 // addIJCheckMenuItem(adjustmn, "Untilt Stack", "Untilt Stack", IJRequirement.STACK);
281 
282 // addIJCheckMenuItem(adjustmn, "Reslice", "Reslice [/]...", IJRequirement.VOLUME);
283 
284  // image transform menu
285 
286 // addIJCheckMenuItem(transformmn, "Rotate 90 Degrees Left", "Rotate 90 Degrees Left");
287 // addIJCheckMenuItem(transformmn, "Rotate 90 Degrees Right", "Rotate 90 Degrees Right");
288 
289  // image filters menu
290  CheckboxMenuItem gbmi = addIJCheckMenuItem(imagemn, XmippImageJ.gaussianBlurFilter);
291  addIJCheckMenuItem(imagemn, XmippImageJ.bandPassFilter);
292 // addIJCheckMenuItem(imagemn, XmippImageJ.anisotropicDiffFilter, IJRequirement.EIGHTBIT);
293  CheckboxMenuItem ecmi = addIJCheckMenuItem(imagemn, XmippImageJ.enhanceContrastFilter);
294  addIJCheckMenuItem(imagemn, XmippImageJ.brightnessContrastFilter);
295  addIJCheckMenuItem(imagemn, XmippImageJ.invertLUTFilter);
296  addIJCheckMenuItem(imagemn, XmippImageJ.substractBackgroundFilter);
297  // menubar advanced menu
298  imagejmi = new MenuItem("ImageJ");
299  imagejmi.setShortcut(new MenuShortcut(KeyEvent.VK_I));
300  transformmn = new Menu("Transform");
301  thresholdingmn = new Menu("Thresholding");
302  binarymn = new Menu("Binary");
303  processmn = new Menu("Process");
304  drawmn = new Menu("Draw");
305  profilemn = new Menu("Profile");
306 
307  advancedmn.add(imagejmi);
308  advancedmn.add(thresholdingmn);
309  advancedmn.add(binarymn);
310  advancedmn.add(processmn);
311  advancedmn.add(drawmn);
312  advancedmn.add(profilemn);
313 // addIJCheckMenuItem(advancedmn, "Masks Tool Bar", "Masks Tool Bar", IJRequirement.IMAGEJ);// missing
314  // plugin
315  onlinemi = new MenuItem("Online Help");
316  onlinemi.addActionListener(new ActionListener()
317  {
318 
319 
320 
321  @Override
322  public void actionPerformed(ActionEvent arg0)
323  {
324  XmippWindowUtil.openURI("https://github.com/I2PC/scipion/wiki/ShowJ");
325  }
326  });
327  helpmn.add(onlinemi);
328  keyassistmi = new MenuItem("Tips");
329  keyassistmi.addActionListener(new ActionListener()
330  {
331 
332 
333 
334  @Override
335  public void actionPerformed(ActionEvent arg0)
336  {
337  try
338  {
339  if(keyassistdlg == null)
340  keyassistdlg = new QuickHelpJDialog(null, false, "Tips...", getKeyAssist());
341  keyassistdlg.setVisible(true);
342  }
343  catch(Exception e)
344  {
345  XmippDialog.showInfo(null, e.getMessage());
346  }
347  }
348  });
349  helpmn.add(keyassistmi);
350 
351  addIJMenuItem(transformmn, "Flip Horizontally", "Flip Horizontally", IJRequirement.INVERTX);
352  addIJMenuItem(transformmn, "Flip Vertically", "Flip Vertically", IJRequirement.INVERTY);
353 
354  // advanced threshold menu
355  addIJMenuItem(thresholdingmn, "Threshold", "Threshold...");
356  addIJMenuItem(thresholdingmn, "Otsu Threshold", "Otsu Thresholding", IJRequirement.EIGHTBIT);
357  addIJMenuItem(thresholdingmn, "Multi Otsu Threshold", "Multi OtsuThreshold");
358  addIJMenuItem(thresholdingmn, "Maximum Entropy Threshold", "Entropy Threshold", IJRequirement.EIGHTBIT);
359  addIJMenuItem(thresholdingmn, "Mixture Modeling Threshold", "Mixture Modeling", IJRequirement.EIGHTBIT);
360  addIJMenuItem(thresholdingmn, "Robust Automatic Threshold Selection", "RATS ");
361  //addIJMenuItem(thresholdingmn, "Simple Iterative Object Extraction", "SIOX Segmentation", IJRequirement.RGB);
362 
363  // advanced binary menu
364  addIJMenuItem(binarymn, "Voxel Counter", "Voxel Counter", IJRequirement.STACK);// stack required
365  addIJMenuItem(binarymn, "Erode", "Erode", IJRequirement.BINARY);
366  addIJMenuItem(binarymn, "Dilate", "Dilate", IJRequirement.BINARY);
367  addIJMenuItem(binarymn, "Open", "Open", IJRequirement.BINARY);
368  addIJMenuItem(binarymn, "Close", "Close", IJRequirement.BINARY);
369  addIJMenuItem(binarymn, "Float Morphology", "Float Morphology", IJRequirement.THIRTYTWOBIT);// missing plugin
370  addIJMenuItem(binarymn, "Outline", "Outline", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
371  addIJMenuItem(binarymn, "Fill Holes", "Fill Holes", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
372  addIJMenuItem(binarymn, "Skeletonize", "Skeletonize", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
373  addIJMenuItem(binarymn, "Distance Map", "Distance Map", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
374  addIJMenuItem(binarymn, "Ultimate Points", "Ultimate Points", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
375  addIJMenuItem(binarymn, "Watershed", "Watershed");
376  addIJMenuItem(binarymn, "Voronoi", "Voronoi", IJRequirement.BINARY, IJRequirement.EIGHTBIT);
377 
378  // advanced process menu
379 
380 
381  addIJMenuItem(processmn, "Convolve", "Convolve...");
382  addIJMenuItem(processmn, "Median", "Median...");
383  addIJMenuItem(processmn, "FFT", "FFT", IJRequirement.IMAGEJ);// memory error
384  addIJMenuItem(processmn, "Straighten Curved Objects", "Straighten...", IJRequirement.IMAGEJ);
385 
386  // advanced drawn menu
387  addIJMenuItem(drawmn, "Dotted Line", "Dotted Line", IJRequirement.IMAGEJ);
388  addIJMenuItem(drawmn, "Radial Grid", "Radial Grid");
389  addIJMenuItem(drawmn, "Concenctric Circles", "Concentric Circles");
390 
391  // advanced profile menu
392  addIJMenuItem(profilemn, "Line Analyzer", "Plot Profile", IJRequirement.IMAGEJ);
393  addIJMenuItem(profilemn, "Oval Profile Plot", "Oval Profile", IJRequirement.IMAGEJ);
394 // addIJMenuItem(profilemn, "Contour Plotter", "ContourPlotter ");
395 
396  imagejmi.addActionListener(new ActionListener()
397  {
398 
399  @Override
400  public void actionPerformed(ActionEvent e)
401  {
402  XmippUtil.showImageJ(Tool.VIEWER);
403  }
404  });
405  addFilterAppliedListener();
406  ImagePlus imp = iploader.getImagePlus();
407  if(xw.getParams() != null && imp.getWidth() > 1024 && imp.getStackSize() == 1)
408  {
409  String value = System.getenv("SCIPION_MIC_NOGAUSS");
410 
411  if (value == null || !value.equals("1"))
412  {
413  gbmi.setState(true);
414  IJCommand ijcmd = new IJCommand(XmippImageJ.gaussianBlurFilter, "sigma =2");
415  IJ.run(imp, ijcmd.getCommand(), ijcmd.getOptions());
416  filters.add(ijcmd);
417  }
418 
419  value = System.getenv("SCIPION_MIC_NOENHANCE");
420  if (value == null || !value.equals("1"))
421  {
422  ecmi.setState(true);
423  IJCommand ijcmd = new IJCommand(XmippImageJ.enhanceContrastFilter, "saturated=0.4");
424  IJ.run(imp, ijcmd.getCommand(), ijcmd.getOptions());
425  filters.add(ijcmd);
426  }
427  }
428 
429  }
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xmipp.ij.commons.XmippMenuBar.getKeyAssist
Map< Object, Object > getKeyAssist()
Definition: XmippMenuBar.java:704
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xmipp.ij.commons.XmippMenuBar.addIJCheckMenuItem
CheckboxMenuItem addIJCheckMenuItem(Menu mn, String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:543
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xmipp.ij.commons.XmippMenuBar.runCommand
void runCommand(String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:666
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xmipp.ij.commons.XmippMenuBar.addIJMenuItem
MenuItem addIJMenuItem(Menu mn, String name, String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:608
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xmipp.ij.commons.XmippMenuBar.XmippMenuBar
XmippMenuBar(XmippIJWindow xw)
Definition: XmippMenuBar.java:90
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◆ addCheckCommand()

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void xmipp.ij.commons.XmippMenuBar.addCheckCommand (CheckboxMenuItem mi,
String command,
final IJRequirement... requirements 
)
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Definition at line 565 of file XmippMenuBar.java.

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566  {
567  mi.setActionCommand(command);
568  for (IJRequirement requirement : requirements)
569  {
570  if (requirement == IJRequirement.STACK && !xw.isStack())
571  mi.setEnabled(false);
572  if (requirement == IJRequirement.VOLUME && !xw.isVolume())
573  mi.setEnabled(false);
574  }
575  mi.addItemListener(new ItemListener()
576  {
577 
578  @Override
579  public void itemStateChanged(ItemEvent e)
580  {
581  try
582  {
583  CheckboxMenuItem mi = (CheckboxMenuItem) e.getSource();
584  String command = mi.getActionCommand();
585  if(mi.getState())//checked
586  {
587  activemi = mi;
588  mi.setState(false);//confirm selected only after filter applied
589  runCommand(command, requirements);
590 
591  }
592  else
593  {
594  filters.remove(getFilter(command));
595  xw.loadData();
596  applyFilters();
597  }
598 
599  }
600  catch (Exception ex)
601  {
602  ex.printStackTrace();
603  }
604  }
605  });
606  }//function addCommand
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xmipp.ij.commons.XmippMenuBar.runCommand
void runCommand(String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:666
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xmipp.ij.commons.XmippMenuBar.getFilter
IJCommand getFilter(String command)
Definition: XmippMenuBar.java:656
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void xmipp.ij.commons.XmippMenuBar.addCommand (MenuItem mi,
String command,
final IJRequirement... requirements 
)
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Definition at line 617 of file XmippMenuBar.java.

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618  {
619  mi.setActionCommand(command);
620  for (IJRequirement requirement : requirements)
621  {
622  if (requirement == IJRequirement.STACK && !xw.isStack())
623  mi.setEnabled(false);
624  if (requirement == IJRequirement.VOLUME && !xw.isVolume())
625  mi.setEnabled(false);
626  }
627  mi.addActionListener(new ActionListener()
628  {
629 
630  @Override
631  public void actionPerformed(java.awt.event.ActionEvent e) {
632 
633  try
634  {
635  MenuItem mi = (MenuItem) e.getSource();
636  String command = mi.getActionCommand();
637  runCommand(command, requirements);
638 
639  }
640  catch (Exception ex)
641  {
642  ex.printStackTrace();
643  }
644  }
645  });
646  }//function addCommand
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xmipp.ij.commons.XmippMenuBar.runCommand
void runCommand(String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:666
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◆ addFilterAppliedListener()

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void xmipp.ij.commons.XmippMenuBar.addFilterAppliedListener ()
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Definition at line 431 of file XmippMenuBar.java.

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431  {
432 
433  Recorder.record = true;
434  // detecting if a command is thrown by ImageJ
435  Executer.addCommandListener(new CommandListener() {
436  public String commandExecuting(String command) {
437 
438 
439  XmippMenuBar.this.command = command;
440  return command;
441 
442  }
443  });
444 
445  // detecting if a command is thrown by ImageJ
446 
447  ImagePlus.addImageListener(new ImageListener() {
448 
449  @Override
450  public void imageUpdated(ImagePlus imp) {
451  //activemi will contain last filter selected, if its the command runned we confirm selection
452  if(activemi != null && activemi.getActionCommand().equals(command))
453  {
454  activemi.setState(true);
455  String options = Recorder.getCommandOptions();
456  filters.add(new IJCommand(command, options));
457  activemi = null;
458  }
459 
460  }
461 
462  @Override
463  public void imageOpened(ImagePlus arg0) {
464 
465  }
466 
467  @Override
468  public void imageClosed(ImagePlus arg0) {
469  // TODO Auto-generated method stub
470 
471  }
472  });
473  }
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XmippMenuBar(XmippIJWindow xw)
Definition: XmippMenuBar.java:90
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CheckboxMenuItem xmipp.ij.commons.XmippMenuBar.addIJCheckMenuItem (Menu mn,
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Definition at line 543 of file XmippMenuBar.java.

-
544  {
545  return addIJCheckMenuItem(mn, command, command, requirements);
546 
547  }
xmipp.ij.commons.XmippMenuBar.addIJCheckMenuItem
CheckboxMenuItem addIJCheckMenuItem(Menu mn, String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:543
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CheckboxMenuItem xmipp.ij.commons.XmippMenuBar.addIJCheckMenuItem (Menu mn,
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Definition at line 549 of file XmippMenuBar.java.

-
550  {
551  CheckboxMenuItem mi = new CheckboxMenuItem(name);
552  addCheckCommand(mi, command, requirements);
553  mn.add(mi);
554  return mi;
555  }
xmipp.ij.commons.XmippMenuBar.addCheckCommand
void addCheckCommand(CheckboxMenuItem mi, String command, final IJRequirement... requirements)
Definition: XmippMenuBar.java:565
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◆ addIJMenuItem()

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MenuItem xmipp.ij.commons.XmippMenuBar.addIJMenuItem (Menu mn,
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Definition at line 608 of file XmippMenuBar.java.

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609  {
610  MenuItem mi = new MenuItem(name);
611  addCommand(mi, command, requirements);
612  mn.add(mi);
613  return mi;
614  }
xmipp.ij.commons.XmippMenuBar.addCommand
void addCommand(MenuItem mi, String command, final IJRequirement... requirements)
Definition: XmippMenuBar.java:617
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◆ applyFilters()

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Definition at line 648 of file XmippMenuBar.java.

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649  {
650  ImagePlus imp = xw.getImagePlusLoader().getImagePlus();
651  for(IJCommand filter: filters)
652  IJ.run(imp, filter.getCommand(), filter.getOptions());
653  }
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Definition at line 476 of file XmippMenuBar.java.

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477  {
478  Frame w = (Frame)xw;
479  w.setVisible(false);
480  w.dispose();
481  XmippApplication.removeInstance(false);
482  }
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Definition at line 656 of file XmippMenuBar.java.

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657  {
658  for(IJCommand filter: filters)
659  {
660  if(filter.getCommand().equals(command))
661  return filter;
662  }
663  return null;
664  }
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Definition at line 704 of file XmippMenuBar.java.

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705  {
706  Map<Object, Object> map = Collections.synchronizedMap(new LinkedHashMap<Object, Object>());
707  map.put("Shift + scroll up", "Zoom in");
708  map.put("Shift + scroll down", "Zoom out");
709  map.put("Right click + mouse move", "Moves image previously expanded");
710  return map;
711  }
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static void xmipp.ij.commons.XmippMenuBar.openImagePlusAs3D (ImagePlus ip)
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Definition at line 520 of file XmippMenuBar.java.

-
520  {
521  try {
522  int UNIVERSE_W = 400, UNIVERSE_H = 400;
523  // Checks if java3D is available or not.
524  Class.forName("javax.media.j3d.J3DBuffer");
525 
526  new StackConverter(ip).convertToRGB();
527 
528  Image3DUniverse universe = new Image3DUniverse(UNIVERSE_W,
529  UNIVERSE_H);
530 
531  // Adds the sphere image plus to universe.
532  Content c = universe.addSurfacePlot(ip, new Color3f(1f, 165f / 255,
533  82f / 255), "1", 50, new boolean[] { true, true, true }, 1);
534  c.displayAs(Content.SURFACE);
535  c.setColor(new Color3f(1f, 165f / 255, 82f / 255));
536 
537  universe.show(); // Shows...
538  } catch (final ClassNotFoundException e) {
539  IJ.error("Java 3D not found. Please, check your installation.");
540  }
541  }
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Definition at line 558 of file XmippMenuBar.java.

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559  {
560  if (timer == null)
561  polltimer = new PollTimer(xw);
562  polltimer.start();
563  }
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void xmipp.ij.commons.XmippMenuBar.runCommand (String command,
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Run ImageJ command

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Definition at line 666 of file XmippMenuBar.java.

-
666  {
667  if (requirements != null)
668  for (IJRequirement requirement : requirements)
669  switch (requirement)
670  {
671  case IMAGEJ:
672  XmippUtil.showImageJ(Tool.VIEWER);
673  break;
674  case BINARY:
675  IJ.run("Make Binary");
676  XmippDialog.showInfo(null, "make binary applied");
677  break;
678  case EIGHTBIT:
679  IJ.run("8-bit");
680  XmippDialog.showInfo(null, "8-bit applied");
681  break;
682  case THIRTYTWOBIT:
683  IJ.run("32-bit");
684  XmippDialog.showInfo(null, "32-bit applied");
685  break;
686  case RGB:
687  IJ.run("RGB Color");
688  XmippDialog.showInfo(null, "RGB color applied");
689  break;
690  case INVERTX:
691  invertx = !invertx;
692  xw.getCanvas().setInvertX(invertx);
693  break;
694  case INVERTY:
695  inverty = !inverty;
696  xw.getCanvas().setInvertY(inverty);
697  break;
698 
699  }
700  ImagePlus imp = xw.getImagePlusLoader().getImagePlus();
701  IJ.run(imp, command, "");
702  }//function runCommand
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Definition at line 491 of file XmippMenuBar.java.

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492  {
493  XmippFileChooser fc = new XmippFileChooser();
494  int returnVal = fc.showOpenDialog(null);
495 
496  try
497  {
498  if (returnVal == XmippFileChooser.APPROVE_OPTION)
499  {
500  File file = fc.getSelectedFile();
501  XmippMenuBar.this.xw.saveDataAs(file.getAbsolutePath());
502  }
503  }
504  catch (Exception ex)
505  {
506  XmippDialog.showInfo(null, ex.getMessage());
507  }
508  }
xmipp.ij.commons.XmippMenuBar.XmippMenuBar
XmippMenuBar(XmippIJWindow xw)
Definition: XmippMenuBar.java:90
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Definition at line 485 of file XmippMenuBar.java.

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486  {
487  xw.getImagePlusLoader().setUseGeometry(ug);
488  xw.loadData();
489  }
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Definition at line 512 of file XmippMenuBar.java.

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513  {
514  xw.getImagePlusLoader().setWrap(value);
515  xw.loadData();
516  }
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Member Data Documentation

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Definition at line 79 of file XmippMenuBar.java.

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Definition at line 52 of file XmippMenuBar.java.

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Definition at line 61 of file XmippMenuBar.java.

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Definition at line 80 of file XmippMenuBar.java.

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Definition at line 63 of file XmippMenuBar.java.

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Definition at line 50 of file XmippMenuBar.java.

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Definition at line 81 of file XmippMenuBar.java.

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Definition at line 73 of file XmippMenuBar.java.

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Definition at line 64 of file XmippMenuBar.java.

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Definition at line 76 of file XmippMenuBar.java.

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Definition at line 75 of file XmippMenuBar.java.

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Definition at line 74 of file XmippMenuBar.java.

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Definition at line 55 of file XmippMenuBar.java.

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Definition at line 66 of file XmippMenuBar.java.

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Definition at line 68 of file XmippMenuBar.java.

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Definition at line 62 of file XmippMenuBar.java.

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Definition at line 65 of file XmippMenuBar.java.

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Definition at line 69 of file XmippMenuBar.java.

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Definition at line 54 of file XmippMenuBar.java.

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Definition at line 53 of file XmippMenuBar.java.

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Definition at line 60 of file XmippMenuBar.java.

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Definition at line 58 of file XmippMenuBar.java.

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Definition at line 71 of file XmippMenuBar.java.

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Definition at line 70 of file XmippMenuBar.java.

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Definition at line 49 of file XmippMenuBar.java.

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The documentation for this class was generated from the following file: -
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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippMenuBar__coll__graph.dot b/html/classxmipp_1_1ij_1_1commons_1_1XmippMenuBar__coll__graph.dot deleted file mode 100644 index 06ee048f..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippMenuBar__coll__graph.dot +++ /dev/null @@ -1,49 +0,0 @@ -digraph "xmipp.ij.commons.XmippMenuBar" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node2 [label="xmipp.ij.commons.XmippMenuBar",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="MenuBar",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node4 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" filters" ,fontname="Helvetica"]; - Node4 [label="List\< xmipp.ij.commons.IJCommand \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; 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- node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.ij.commons.XmippMenuBar",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="MenuBar",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippMenuBar__inherit__graph.md5 b/html/classxmipp_1_1ij_1_1commons_1_1XmippMenuBar__inherit__graph.md5 deleted file mode 100644 index d897fac2..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippMenuBar__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -d537c21da185da1156621bac64700e59 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippStackWindow-members.html b/html/classxmipp_1_1ij_1_1commons_1_1XmippStackWindow-members.html deleted file mode 100644 index 108d0b08..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippStackWindow-members.html +++ /dev/null @@ -1,96 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.ij.commons.XmippStackWindow Member List
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This is the complete list of members for xmipp.ij.commons.XmippStackWindow, including all inherited members.

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getCanvas()xmipp.ij.commons.XmippStackWindowinline
getImagePlusLoader()xmipp.ij.commons.XmippStackWindowinline
getParams()xmipp.ij.commons.XmippStackWindowinline
isStack()xmipp.ij.commons.XmippStackWindowinline
isVolume()xmipp.ij.commons.XmippStackWindowinline
loadData()xmipp.ij.commons.XmippStackWindowinline
menuxmipp.ij.commons.XmippStackWindowprotected
openMaskToolbar()xmipp.ij.commons.XmippStackWindowinline
paramsxmipp.ij.commons.XmippStackWindowprotected
saveData()xmipp.ij.commons.XmippStackWindowinline
saveDataAs(String file)xmipp.ij.commons.XmippStackWindowinline
windowClosing(WindowEvent e)xmipp.ij.commons.XmippStackWindowinline
XmippStackWindow(ImagePlusLoader ipl, String title, Params params)xmipp.ij.commons.XmippStackWindowinline
XmippStackWindow(ImagePlusLoader ipl, Params params)xmipp.ij.commons.XmippStackWindowinline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippStackWindow.html b/html/classxmipp_1_1ij_1_1commons_1_1XmippStackWindow.html deleted file mode 100644 index 40320305..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippStackWindow.html +++ /dev/null @@ -1,574 +0,0 @@ - - - - - - - -Xmipp: xmipp.ij.commons.XmippStackWindow Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Attributes | -List of all members
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xmipp.ij.commons.XmippStackWindow Class Reference
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-Public Member Functions

 XmippStackWindow (ImagePlusLoader ipl, String title, Params params)
 
 XmippStackWindow (ImagePlusLoader ipl, Params params)
 
void loadData ()
 
void openMaskToolbar ()
 
void saveDataAs (String file) throws Exception
 
void saveData () throws Exception
 
XmippImageCanvas getCanvas ()
 
void windowClosing (WindowEvent e)
 
ImagePlusLoader getImagePlusLoader ()
 
boolean isVolume ()
 
boolean isStack ()
 
Params getParams ()
 
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-Protected Attributes

XmippMenuBar menu
 
Params params
 
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Detailed Description

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Definition at line 11 of file XmippStackWindow.java.

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Constructor & Destructor Documentation

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◆ XmippStackWindow() [1/2]

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xmipp.ij.commons.XmippStackWindow.XmippStackWindow (ImagePlusLoader ipl,
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Definition at line 17 of file XmippStackWindow.java.

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18  {
19  super(ipl.getImagePlus(), new XmippImageCanvas(ipl.getImagePlus()));
20  this.ipl = ipl;
21  imp.setTitle(title);
22  menu = new XmippMenuBar(this);
23  setMenuBar(menu);
24  //getCanvas().adjustMagnification();
25  XmippApplication.addInstance(true);
26  this.params = params;
27 
28  }
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xmipp.ij.commons.XmippStackWindow.XmippStackWindow (ImagePlusLoader ipl,
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Definition at line 30 of file XmippStackWindow.java.

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31  {
32  this(ipl, ipl.getName(), params);
33  }
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Member Function Documentation

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◆ getCanvas()

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XmippImageCanvas xmipp.ij.commons.XmippStackWindow.getCanvas ()
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Definition at line 62 of file XmippStackWindow.java.

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63  {
64  return ((XmippImageCanvas)super.getCanvas());
65  }
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Definition at line 76 of file XmippStackWindow.java.

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77  {
78  return ipl;
79  }
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Definition at line 93 of file XmippStackWindow.java.

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94  {
95  return params;
96  }
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Definition at line 88 of file XmippStackWindow.java.

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89  {
90  return true;
91  }
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Definition at line 82 of file XmippStackWindow.java.

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83  {
84  return getImagePlusLoader().isVolume();
85  }
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Definition at line 39 of file XmippStackWindow.java.

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40  {
41  getCanvas().loadData(this);
42  }
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void xmipp.ij.commons.XmippStackWindow.openMaskToolbar ()
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Definition at line 44 of file XmippStackWindow.java.

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44  {
45  menu.runCommand("Masks Tool Bar", new IJRequirement[]{IJRequirement.IMAGEJ});
46  }
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xmipp.ij.commons.XmippMenuBar.runCommand
void runCommand(String command, IJRequirement... requirements)
Definition: XmippMenuBar.java:666
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◆ saveData()

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void xmipp.ij.commons.XmippStackWindow.saveData () throws Exception
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Definition at line 56 of file XmippStackWindow.java.

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57  {
58  saveDataAs(imp.getTitle());
59 
60  }
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void xmipp.ij.commons.XmippStackWindow.saveDataAs (String file) throws Exception
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Definition at line 49 of file XmippStackWindow.java.

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50  {
51 
52  XmippImageConverter.writeImagePlus(imp, file);
53  }
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void xmipp.ij.commons.XmippStackWindow.windowClosing (WindowEvent e)
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Definition at line 68 of file XmippStackWindow.java.

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68  {
69 
70  super.windowClosing(e);
71  XmippApplication.removeInstance(true);
72 
73  }
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Member Data Documentation

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◆ menu

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XmippMenuBar xmipp.ij.commons.XmippStackWindow.menu
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Definition at line 14 of file XmippStackWindow.java.

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◆ params

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Params xmipp.ij.commons.XmippStackWindow.params
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Definition at line 15 of file XmippStackWindow.java.

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The documentation for this class was generated from the following file: -
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xmipp.ij.commons.XmippUtil Member List
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copyFile(String source, String dest)xmipp.ij.commons.XmippUtilinlinestatic
copyFile(File source, File dest)xmipp.ij.commons.XmippUtilinlinestatic
findFreePort()xmipp.ij.commons.XmippUtilinlinestatic
formatNumbers(String str)xmipp.ij.commons.XmippUtilinlinestatic
getImageIcon(Image imp, int width, int height)xmipp.ij.commons.XmippUtilinlinestatic
getImagePlus(String file)xmipp.ij.commons.XmippUtilinlinestatic
getXmippImageJ()xmipp.ij.commons.XmippUtilinlinestatic
isInPath(String executable)xmipp.ij.commons.XmippUtilinlinestatic
showImageJ(Tool tool)xmipp.ij.commons.XmippUtilinlinestatic
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- - diff --git a/html/classxmipp_1_1ij_1_1commons_1_1XmippUtil.html b/html/classxmipp_1_1ij_1_1commons_1_1XmippUtil.html deleted file mode 100644 index ddf2cf20..00000000 --- a/html/classxmipp_1_1ij_1_1commons_1_1XmippUtil.html +++ /dev/null @@ -1,398 +0,0 @@ - - - - - - - -Xmipp: xmipp.ij.commons.XmippUtil Class Reference - - - - - - - - - -
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xmipp.ij.commons.XmippUtil Class Reference
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-Static Public Member Functions

static XmippImageJ showImageJ (Tool tool)
 
static XmippImageJ getXmippImageJ ()
 
static ImagePlus getImagePlus (String file)
 
static Icon getImageIcon (Image imp, int width, int height)
 
static void copyFile (String source, String dest) throws IOException
 
static void copyFile (File source, File dest) throws IOException
 
static boolean isInPath (String executable)
 
static String formatNumbers (String str)
 
static int findFreePort () throws IOException
 
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Definition at line 24 of file XmippUtil.java.

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◆ copyFile() [1/2]

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static void xmipp.ij.commons.XmippUtil.copyFile (String source,
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Definition at line 84 of file XmippUtil.java.

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85  {
86  copyFile(new File(source), new File(dest));
87  }
xmipp.ij.commons.XmippUtil.copyFile
static void copyFile(String source, String dest)
Definition: XmippUtil.java:84
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static void xmipp.ij.commons.XmippUtil.copyFile (File source,
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Definition at line 89 of file XmippUtil.java.

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90  {
91  InputStream input = null;
92  OutputStream output = null;
93  try {
94  input = new FileInputStream(source);
95  output = new FileOutputStream(dest);
96  byte[] buf = new byte[1024];
97  int bytesRead;
98  while ((bytesRead = input.read(buf)) > 0) {
99  output.write(buf, 0, bytesRead);
100  }
101  } finally {
102  if(input != null)
103  input.close();
104  if(output != null)
105  output.close();
106  }
107  }
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Definition at line 145 of file XmippUtil.java.

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146  {
147  ServerSocket server = new ServerSocket(0);
148  int port = server.getLocalPort();
149  server.close();
150  return port;
151  }
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Definition at line 131 of file XmippUtil.java.

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132  {
133  Pattern p = Pattern.compile("(-?(\\d)+(\\.)?(\\d)*)");
134  Matcher m = p.matcher(str);
135  StringBuffer sb = new StringBuffer(str.length());
136  while(m.find())
137  {
138  String number = m.group(1);
139  m.appendReplacement(sb, String.format("%.2f", Double.parseDouble(number)));
140  }
141  m.appendTail(sb);
142  return sb.toString();
143  }
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Definition at line 70 of file XmippUtil.java.

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71  {
72 
73  Image image = imp.getScaledInstance(width, height, Image.SCALE_SMOOTH);
74  Icon icon = new ImageIcon(image);
75 
76  return icon;
77  }
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Definition at line 55 of file XmippUtil.java.

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55  {
56  try {
57 
58  ImageGeneric ig = new ImageGeneric(file);
59  ig.read(ImageGeneric.FIRST_IMAGE);
60  ImagePlus imp = XmippImageConverter.convertToImagePlus(ig);
61  ig.destroy();
62 
63  return imp;
64  } catch (Exception e) {
65  e.printStackTrace();
66  throw new IllegalArgumentException(e.getMessage());
67  }
68  }
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Definition at line 49 of file XmippUtil.java.

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49  {
50  return xij;
51  }
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Definition at line 109 of file XmippUtil.java.

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110  {
111  String[] paths = System.getenv("PATH").split(Pattern.quote(File.pathSeparator));
112  String exePath;
113  File file, exeFile;
114  for(String path: paths)
115  {
116  file = new File(path);
117  if(file.isDirectory())
118  {
119  exePath = path + File.separator + executable;
120  exeFile = new File(exePath);
121  if(exeFile.exists())
122  return true;
123  }
124  else if(file.getName().equals(executable))
125  return true;
126 
127  }
128  return false;
129  }
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Definition at line 28 of file XmippUtil.java.

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28  {
29  if (IJ.getInstance() == null) {
30  try {
31  xij = new XmippImageJ();
32 
33 //
34  File tempFile = File.createTempFile("macros", ".txt");
35  BufferedWriter writer = new BufferedWriter(new FileWriter(tempFile));
36  writer.write("macro \"Particle Picker Tool - C0a0L18f8L818f\" { }\nmacro \"Xmipp Micrograph Viewer Tool - C0a0L18f8L818f\" { }");
37  writer.close();
38  IJ.run("Install...", "install=" + tempFile.getAbsolutePath());
39  //Tool cannot be set if it is not a default one
40  } catch (Exception ex) {
41  Logger.getLogger(XmippUtil.class.getName()).log(Level.SEVERE, null, ex);
42  throw new IllegalArgumentException(ex);
43  }
44  } else if (!xij.isVisible())
45  xij.setVisible(true);
46  return xij;
47  }
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AboutMasksToolBar()xmipp.ij.plugins.maskstoolbar.AboutMasksToolBarinline
run(String arg)xmipp.ij.plugins.maskstoolbar.AboutMasksToolBarinline
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 AboutMasksToolBar ()
 
void run (String arg)
 
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Definition at line 17 of file AboutMasksToolBar.java.

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◆ AboutMasksToolBar()

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Definition at line 19 of file AboutMasksToolBar.java.

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19  {
20  super("About Masks Tool Bar...");
21 
22  JLabel jlIcon = new JLabel(new ImageIcon(getClass().getResource("/resources/I2PC.png")));
23  JScrollPane jspText = new JScrollPane();
24  JTextPane jtpAbout = new JTextPane();
25 
26  jtpAbout.setContentType("text/html");
27  jtpAbout.setEditable(false);
28  jtpAbout.setText("<html>\nJuanjo Vega (<b>juanjo.vega@gmail.com</b>)<br>"
29  + "Biocomputing Unit.<br>"
30  + "National Center for Biotechnology (CNB/CSIC).<br>"
31  + "Madrid. May 2011.</html>");
32  jspText.setViewportView(jtpAbout);
33 
34  add(jlIcon, java.awt.BorderLayout.WEST);
35  add(jspText, java.awt.BorderLayout.CENTER);
36 
37  pack();
38  setLocationRelativeTo(null);
39  setResizable(false);
40  }
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◆ run()

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Definition at line 43 of file AboutMasksToolBar.java.

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43  {
44  setVisible(true);
45  }
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Xmipp -  v20.07 -
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xmipp.ij.plugins.maskstoolbar.ICONS Member List
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This is the complete list of members for xmipp.ij.plugins.maskstoolbar.ICONS, including all inherited members.

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ACTION_BRUSHSIZExmipp.ij.plugins.maskstoolbar.ICONSstatic
ACTION_CREATEMASKxmipp.ij.plugins.maskstoolbar.ICONSstatic
ACTION_CREATESELECTIONxmipp.ij.plugins.maskstoolbar.ICONSstatic
ACTION_INVERTMASKxmipp.ij.plugins.maskstoolbar.ICONSstatic
ACTION_INVERTSELECTIONxmipp.ij.plugins.maskstoolbar.ICONSstatic
ACTION_SPECIFYSELECTIONxmipp.ij.plugins.maskstoolbar.ICONSstatic
ICONS()xmipp.ij.plugins.maskstoolbar.ICONSinline
MASK_LOCKEDxmipp.ij.plugins.maskstoolbar.ICONSstatic
MASK_UNLOCKEDxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_ACTION_BRUSHSIZExmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_ACTION_CREATEMASKxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_ACTION_CREATESELECTIONxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_ACTION_INVERTMASKxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_ACTION_INVERTSELECTIONxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_ACTION_SPECIFYSELECTIONxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_ICONSxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_MASK_LOCKEDxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_MASK_UNLOCKEDxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_TOOL_BRUSHxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_TOOL_ELLIPSExmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_TOOL_FREEHANDxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_TOOL_OVALxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_TOOL_POLYGONxmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_TOOL_RECTANGLExmipp.ij.plugins.maskstoolbar.ICONSstatic
PATH_TOOL_ROUNDRECTANGLExmipp.ij.plugins.maskstoolbar.ICONSstatic
TOOL_BRUSHxmipp.ij.plugins.maskstoolbar.ICONSstatic
TOOL_ELLIPSExmipp.ij.plugins.maskstoolbar.ICONSstatic
TOOL_FREEHANDxmipp.ij.plugins.maskstoolbar.ICONSstatic
TOOL_OVALxmipp.ij.plugins.maskstoolbar.ICONSstatic
TOOL_POLYGONxmipp.ij.plugins.maskstoolbar.ICONSstatic
TOOL_RECTANGLExmipp.ij.plugins.maskstoolbar.ICONSstatic
TOOL_ROUNDRECTANGLExmipp.ij.plugins.maskstoolbar.ICONSstatic
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- - diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS.html b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS.html deleted file mode 100644 index 371e2ebb..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS.html +++ /dev/null @@ -1,971 +0,0 @@ - - - - - - - -Xmipp: xmipp.ij.plugins.maskstoolbar.ICONS Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Static Public Attributes | -List of all members
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xmipp.ij.plugins.maskstoolbar.ICONS Class Reference
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-Collaboration diagram for xmipp.ij.plugins.maskstoolbar.ICONS:
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[legend]
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-Public Member Functions

 ICONS ()
 
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-Static Public Attributes

static final String PATH_ICONS = Filename.getXmippPath("resources/")
 
static final String PATH_TOOL_RECTANGLE = PATH_ICONS + "rectangle.png"
 
static final String PATH_TOOL_ROUNDRECTANGLE = PATH_ICONS + "roundrectangle.png"
 
static final String PATH_TOOL_ELLIPSE = PATH_ICONS + "ellipse.png"
 
static final String PATH_TOOL_OVAL = PATH_ICONS + "oval.png"
 
static final String PATH_TOOL_POLYGON = PATH_ICONS + "polygon.png"
 
static final String PATH_TOOL_FREEHAND = PATH_ICONS + "freehand.png"
 
static final String PATH_TOOL_BRUSH = PATH_ICONS + "brush.png"
 
static final String PATH_ACTION_CREATEMASK = PATH_ICONS + "create_mask.png"
 
static final String PATH_ACTION_CREATESELECTION = PATH_ICONS + "create_selection.png"
 
static final String PATH_ACTION_INVERTSELECTION = PATH_ICONS + "invert_selection.png"
 
static final String PATH_ACTION_INVERTMASK = PATH_ICONS + "invert_mask.png"
 
static final String PATH_ACTION_SPECIFYSELECTION = PATH_ICONS + "specify_selection.png"
 
static final String PATH_ACTION_BRUSHSIZE = PATH_ICONS + "brush_size.png"
 
static final String PATH_MASK_LOCKED = PATH_ICONS + "locked.png"
 
static final String PATH_MASK_UNLOCKED = PATH_ICONS + "unlocked.png"
 
static ImageIcon TOOL_RECTANGLE
 
static ImageIcon TOOL_ROUNDRECTANGLE
 
static ImageIcon TOOL_ELLIPSE
 
static ImageIcon TOOL_OVAL
 
static ImageIcon TOOL_POLYGON
 
static ImageIcon TOOL_FREEHAND
 
static ImageIcon TOOL_BRUSH
 
static ImageIcon ACTION_CREATEMASK
 
static ImageIcon ACTION_CREATESELECTION
 
static ImageIcon ACTION_INVERTSELECTION
 
static ImageIcon ACTION_INVERTMASK
 
static ImageIcon ACTION_SPECIFYSELECTION
 
static ImageIcon ACTION_BRUSHSIZE
 
static ImageIcon MASK_LOCKED
 
static ImageIcon MASK_UNLOCKED
 
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Detailed Description

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Author
Juanjo Vega
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Definition at line 16 of file ICONS.java.

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Constructor & Destructor Documentation

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◆ ICONS()

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xmipp.ij.plugins.maskstoolbar.ICONS.ICONS ()
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Definition at line 54 of file ICONS.java.

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54  {
55 // TOOL_RECTANGLE = new ImageIcon(getClass().getResource(PATH_TOOL_RECTANGLE));
56 // TOOL_ROUNDRECTANGLE = new ImageIcon(getClass().getResource(PATH_TOOL_ROUNDRECTANGLE));
57 // TOOL_ELLIPSE = new ImageIcon(getClass().getResource(PATH_TOOL_ELLIPSE));
58 // TOOL_OVAL = new ImageIcon(getClass().getResource(PATH_TOOL_OVAL));
59 // TOOL_POLYGON = new ImageIcon(getClass().getResource(PATH_TOOL_POLYGON));
60 // TOOL_FREEHAND = new ImageIcon(getClass().getResource(PATH_TOOL_FREEHAND));
61 // TOOL_BRUSH = new ImageIcon(getClass().getResource(PATH_TOOL_BRUSH));
62 // ACTION_CREATEMASK = new ImageIcon(getClass().getResource(PATH_ACTION_CREATEMASK));
63 // ACTION_CREATESELECTION = new ImageIcon(getClass().getResource(PATH_ACTION_CREATESELECTION));
64 // ACTION_INVERTSELECTION = new ImageIcon(getClass().getResource(PATH_ACTION_INVERTSELECTION));
65 // ACTION_INVERTMASK = new ImageIcon(getClass().getResource(PATH_ACTION_INVERTMASK));
66 // ACTION_SPECIFYSELECTION = new ImageIcon(getClass().getResource(PATH_ACTION_SPECIFYSELECTION));
67 // ACTION_BRUSHSIZE = new ImageIcon(getClass().getResource(PATH_ACTION_BRUSHSIZE));
68 // MASK_LOCKED = new ImageIcon(getClass().getResource(PATH_MASK_LOCKED));
69 // MASK_UNLOCKED = new ImageIcon(getClass().getResource(PATH_MASK_UNLOCKED));
70  TOOL_RECTANGLE = new ImageIcon(PATH_TOOL_RECTANGLE);
71  TOOL_ROUNDRECTANGLE = new ImageIcon(PATH_TOOL_ROUNDRECTANGLE);
72  TOOL_ELLIPSE = new ImageIcon(PATH_TOOL_ELLIPSE);
73  TOOL_OVAL = new ImageIcon(PATH_TOOL_OVAL);
74  TOOL_POLYGON = new ImageIcon(PATH_TOOL_POLYGON);
75  TOOL_FREEHAND = new ImageIcon(PATH_TOOL_FREEHAND);
76  TOOL_BRUSH = new ImageIcon(PATH_TOOL_BRUSH);
77  ACTION_CREATEMASK = new ImageIcon(PATH_ACTION_CREATEMASK);
78  ACTION_CREATESELECTION = new ImageIcon(PATH_ACTION_CREATESELECTION);
79  ACTION_INVERTSELECTION = new ImageIcon(PATH_ACTION_INVERTSELECTION);
80  ACTION_INVERTMASK = new ImageIcon(PATH_ACTION_INVERTMASK);
81  ACTION_SPECIFYSELECTION = new ImageIcon(PATH_ACTION_SPECIFYSELECTION);
82  ACTION_BRUSHSIZE = new ImageIcon(PATH_ACTION_BRUSHSIZE);
83  MASK_LOCKED = new ImageIcon(PATH_MASK_LOCKED);
84  MASK_UNLOCKED = new ImageIcon(PATH_MASK_UNLOCKED);
85  }
xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_RECTANGLE
static ImageIcon TOOL_RECTANGLE
Definition: ICONS.java:34
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_ELLIPSE
static final String PATH_TOOL_ELLIPSE
Definition: ICONS.java:21
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_ELLIPSE
static ImageIcon TOOL_ELLIPSE
Definition: ICONS.java:36
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_ROUNDRECTANGLE
static final String PATH_TOOL_ROUNDRECTANGLE
Definition: ICONS.java:20
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_RECTANGLE
static final String PATH_TOOL_RECTANGLE
Definition: ICONS.java:19
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_INVERTSELECTION
static ImageIcon ACTION_INVERTSELECTION
Definition: ICONS.java:43
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_INVERTSELECTION
static final String PATH_ACTION_INVERTSELECTION
Definition: ICONS.java:28
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_CREATEMASK
static final String PATH_ACTION_CREATEMASK
Definition: ICONS.java:26
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_SPECIFYSELECTION
static final String PATH_ACTION_SPECIFYSELECTION
Definition: ICONS.java:30
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_MASK_LOCKED
static final String PATH_MASK_LOCKED
Definition: ICONS.java:32
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xmipp.ij.plugins.maskstoolbar.ICONS.MASK_UNLOCKED
static ImageIcon MASK_UNLOCKED
Definition: ICONS.java:48
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_OVAL
static final String PATH_TOOL_OVAL
Definition: ICONS.java:22
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_FREEHAND
static ImageIcon TOOL_FREEHAND
Definition: ICONS.java:39
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_INVERTMASK
static final String PATH_ACTION_INVERTMASK
Definition: ICONS.java:29
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_CREATESELECTION
static ImageIcon ACTION_CREATESELECTION
Definition: ICONS.java:42
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_CREATESELECTION
static final String PATH_ACTION_CREATESELECTION
Definition: ICONS.java:27
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_POLYGON
static final String PATH_TOOL_POLYGON
Definition: ICONS.java:23
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_CREATEMASK
static ImageIcon ACTION_CREATEMASK
Definition: ICONS.java:41
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xmipp.ij.plugins.maskstoolbar.ICONS.MASK_LOCKED
static ImageIcon MASK_LOCKED
Definition: ICONS.java:47
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_MASK_UNLOCKED
static final String PATH_MASK_UNLOCKED
Definition: ICONS.java:33
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_INVERTMASK
static ImageIcon ACTION_INVERTMASK
Definition: ICONS.java:44
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_BRUSH
static final String PATH_TOOL_BRUSH
Definition: ICONS.java:25
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_SPECIFYSELECTION
static ImageIcon ACTION_SPECIFYSELECTION
Definition: ICONS.java:45
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_POLYGON
static ImageIcon TOOL_POLYGON
Definition: ICONS.java:38
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_BRUSHSIZE
static final String PATH_ACTION_BRUSHSIZE
Definition: ICONS.java:31
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xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_ROUNDRECTANGLE
static ImageIcon TOOL_ROUNDRECTANGLE
Definition: ICONS.java:35
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xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_FREEHAND
static final String PATH_TOOL_FREEHAND
Definition: ICONS.java:24
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xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_BRUSHSIZE
static ImageIcon ACTION_BRUSHSIZE
Definition: ICONS.java:46
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◆ ACTION_BRUSHSIZE

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ImageIcon xmipp.ij.plugins.maskstoolbar.ICONS.ACTION_BRUSHSIZE
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Definition at line 46 of file ICONS.java.

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Definition at line 41 of file ICONS.java.

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◆ ACTION_CREATESELECTION

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Definition at line 42 of file ICONS.java.

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◆ ACTION_INVERTMASK

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Definition at line 44 of file ICONS.java.

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Definition at line 43 of file ICONS.java.

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Definition at line 45 of file ICONS.java.

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Definition at line 47 of file ICONS.java.

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Definition at line 48 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_BRUSHSIZE = PATH_ICONS + "brush_size.png"
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Definition at line 31 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_CREATEMASK = PATH_ICONS + "create_mask.png"
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Definition at line 26 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_CREATESELECTION = PATH_ICONS + "create_selection.png"
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Definition at line 27 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_INVERTMASK = PATH_ICONS + "invert_mask.png"
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Definition at line 29 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_INVERTSELECTION = PATH_ICONS + "invert_selection.png"
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Definition at line 28 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ACTION_SPECIFYSELECTION = PATH_ICONS + "specify_selection.png"
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Definition at line 30 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_ICONS = Filename.getXmippPath("resources/")
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Definition at line 18 of file ICONS.java.

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◆ PATH_MASK_LOCKED

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_MASK_LOCKED = PATH_ICONS + "locked.png"
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Definition at line 32 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_MASK_UNLOCKED = PATH_ICONS + "unlocked.png"
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Definition at line 33 of file ICONS.java.

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◆ PATH_TOOL_BRUSH

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_BRUSH = PATH_ICONS + "brush.png"
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Definition at line 25 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_ELLIPSE = PATH_ICONS + "ellipse.png"
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Definition at line 21 of file ICONS.java.

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_FREEHAND = PATH_ICONS + "freehand.png"
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Definition at line 24 of file ICONS.java.

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◆ PATH_TOOL_OVAL

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_OVAL = PATH_ICONS + "oval.png"
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Definition at line 22 of file ICONS.java.

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◆ PATH_TOOL_POLYGON

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_POLYGON = PATH_ICONS + "polygon.png"
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Definition at line 23 of file ICONS.java.

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◆ PATH_TOOL_RECTANGLE

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_RECTANGLE = PATH_ICONS + "rectangle.png"
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Definition at line 19 of file ICONS.java.

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◆ PATH_TOOL_ROUNDRECTANGLE

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final String xmipp.ij.plugins.maskstoolbar.ICONS.PATH_TOOL_ROUNDRECTANGLE = PATH_ICONS + "roundrectangle.png"
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Definition at line 20 of file ICONS.java.

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◆ TOOL_BRUSH

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ImageIcon xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_BRUSH
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Definition at line 40 of file ICONS.java.

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ImageIcon xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_ELLIPSE
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Definition at line 36 of file ICONS.java.

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◆ TOOL_FREEHAND

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ImageIcon xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_FREEHAND
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Definition at line 39 of file ICONS.java.

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ImageIcon xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_OVAL
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Definition at line 37 of file ICONS.java.

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Definition at line 38 of file ICONS.java.

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ImageIcon xmipp.ij.plugins.maskstoolbar.ICONS.TOOL_RECTANGLE
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Definition at line 34 of file ICONS.java.

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Definition at line 35 of file ICONS.java.

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- - diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS__coll__graph.dot b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS__coll__graph.dot deleted file mode 100644 index f0b51834..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.ij.plugins.maskstoolbar.ICONS" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node1 [label="xmipp.ij.plugins.maskstoolbar.\lICONS",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node2 -> Node1 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" TOOL_FREEHAND\nMASK_LOCKED\nACTION_CREATEMASK\nTOOL_OVAL\nTOOL_POLYGON\nTOOL_ELLIPSE\nTOOL_BRUSH\nACTION_INVERTSELECTION\nACTION_BRUSHSIZE\nACTION_INVERTMASK\n..." ,fontname="Helvetica"]; - Node2 [label="ImageIcon",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS__coll__graph.md5 b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS__coll__graph.md5 deleted file mode 100644 index cdb0abea..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1ICONS__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -a14ad66cdffdc8da2e70c761d7edcdaa \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1LABELS-members.html b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1LABELS-members.html deleted file mode 100644 index e366e703..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1LABELS-members.html +++ /dev/null @@ -1,100 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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ABOUT_TEXTxmipp.ij.plugins.maskstoolbar.LABELSstatic
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TOOLTIP_CREATEMASKxmipp.ij.plugins.maskstoolbar.LABELSstatic
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TOOLTIP_ELLIPSExmipp.ij.plugins.maskstoolbar.LABELSstatic
TOOLTIP_FREEHANDxmipp.ij.plugins.maskstoolbar.LABELSstatic
TOOLTIP_INVERTMASKxmipp.ij.plugins.maskstoolbar.LABELSstatic
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TOOLTIP_RECTANGLExmipp.ij.plugins.maskstoolbar.LABELSstatic
TOOLTIP_ROUNDRECTANGLExmipp.ij.plugins.maskstoolbar.LABELSstatic
TOOLTIP_SETBRUSHSIZExmipp.ij.plugins.maskstoolbar.LABELSstatic
TOOLTIP_SPECIFYSELECTIONxmipp.ij.plugins.maskstoolbar.LABELSstatic
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xmipp.ij.plugins.maskstoolbar.LABELS Class Reference
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static final String TITLE = "Masks Tool Bar"
 
static final String TOOLTIP_RECTANGLE = "Rectangle"
 
static final String TOOLTIP_ROUNDRECTANGLE = "Round Rectangle"
 
static final String TOOLTIP_ELLIPSE = "Ellipse"
 
static final String TOOLTIP_OVAL = "Oval"
 
static final String TOOLTIP_POLYGON = "Polygon"
 
static final String TOOLTIP_FREEHAND = "Freehand"
 
static final String TOOLTIP_BRUSH = "Brush"
 
static final String TOOLTIP_SETBRUSHSIZE = "Set Brush Size"
 
static final String TOOLTIP_CREATEMASK = "Create Mask"
 
static final String TOOLTIP_CREATESELECTION = "Create Selection"
 
static final String TOOLTIP_INVERTSELECTION = "Invert Selection"
 
static final String TOOLTIP_INVERTMASK = "Invert Mask"
 
static final String TOOLTIP_SPECIFYSELECTION = "Specify Selection"
 
static final String TOOLTIP_MASK_LOCKED = "Unlock Mask"
 
static final String TOOLTIP_MASK_UNLOCKED = "Lock Mask"
 
static final String ABOUT_TITLE = "About Xmipp Browser plugin..."
 
static final String ABOUT_TEXT
 
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Detailed Description

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Author
Juanjo Vega
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Definition at line 11 of file LABELS.java.

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Member Data Documentation

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◆ ABOUT_TEXT

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final String xmipp.ij.plugins.maskstoolbar.LABELS.ABOUT_TEXT
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-Initial value:
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"<html>"
+ "Masks Tool Bar for ImageJ"
+ "<hr>"
+ "Juanjo Vega.<br>"
+ "Biocomputing Unit.<br>"
+ "National Center for Biotechnology (CNB/CSIC).<br>"
+ "Madrid. May 2011."
+ "</html>"
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Definition at line 30 of file LABELS.java.

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◆ ABOUT_TITLE

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final String xmipp.ij.plugins.maskstoolbar.LABELS.ABOUT_TITLE = "About Xmipp Browser plugin..."
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Definition at line 29 of file LABELS.java.

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◆ TITLE

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TITLE = "Masks Tool Bar"
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Definition at line 13 of file LABELS.java.

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◆ TOOLTIP_BRUSH

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_BRUSH = "Brush"
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Definition at line 20 of file LABELS.java.

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◆ TOOLTIP_CREATEMASK

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_CREATEMASK = "Create Mask"
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Definition at line 22 of file LABELS.java.

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◆ TOOLTIP_CREATESELECTION

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_CREATESELECTION = "Create Selection"
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Definition at line 23 of file LABELS.java.

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◆ TOOLTIP_ELLIPSE

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_ELLIPSE = "Ellipse"
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Definition at line 16 of file LABELS.java.

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◆ TOOLTIP_FREEHAND

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_FREEHAND = "Freehand"
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Definition at line 19 of file LABELS.java.

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◆ TOOLTIP_INVERTMASK

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_INVERTMASK = "Invert Mask"
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Definition at line 25 of file LABELS.java.

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◆ TOOLTIP_INVERTSELECTION

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_INVERTSELECTION = "Invert Selection"
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Definition at line 24 of file LABELS.java.

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◆ TOOLTIP_MASK_LOCKED

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_MASK_LOCKED = "Unlock Mask"
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Definition at line 27 of file LABELS.java.

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◆ TOOLTIP_MASK_UNLOCKED

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_MASK_UNLOCKED = "Lock Mask"
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Definition at line 28 of file LABELS.java.

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◆ TOOLTIP_OVAL

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_OVAL = "Oval"
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Definition at line 17 of file LABELS.java.

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◆ TOOLTIP_POLYGON

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Definition at line 18 of file LABELS.java.

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◆ TOOLTIP_RECTANGLE

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_RECTANGLE = "Rectangle"
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Definition at line 14 of file LABELS.java.

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◆ TOOLTIP_ROUNDRECTANGLE

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_ROUNDRECTANGLE = "Round Rectangle"
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Definition at line 15 of file LABELS.java.

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◆ TOOLTIP_SETBRUSHSIZE

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_SETBRUSHSIZE = "Set Brush Size"
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Definition at line 21 of file LABELS.java.

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◆ TOOLTIP_SPECIFYSELECTION

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final String xmipp.ij.plugins.maskstoolbar.LABELS.TOOLTIP_SPECIFYSELECTION = "Specify Selection"
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Definition at line 26 of file LABELS.java.

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actionPerformed(ActionEvent ae)xmipp.ij.plugins.maskstoolbar.MasksToolBarinline
getInstance()xmipp.ij.plugins.maskstoolbar.MasksToolBarinlinestatic
MasksToolBar()xmipp.ij.plugins.maskstoolbar.MasksToolBarinline
windowClosed(WindowEvent e)xmipp.ij.plugins.maskstoolbar.MasksToolBarinline
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-Public Member Functions

 MasksToolBar ()
 
void actionPerformed (ActionEvent ae)
 
void windowClosed (WindowEvent e)
 
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-Static Public Member Functions

static MasksToolBar getInstance ()
 
-

Detailed Description

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Author
Juanjo Vega
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Definition at line 29 of file MasksToolBar.java.

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Constructor & Destructor Documentation

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◆ MasksToolBar()

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xmipp.ij.plugins.maskstoolbar.MasksToolBar.MasksToolBar ()
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Definition at line 57 of file MasksToolBar.java.

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57  {
58  super(LABELS.TITLE);
59 
60  setLayout(new GridLayout(2, 8));
61 
62  jtbRectangle.setIcon(ICONS.TOOL_RECTANGLE);
63  jtbRoundRectangle.setIcon(ICONS.TOOL_ROUNDRECTANGLE);
64  jtbEllipse.setIcon(ICONS.TOOL_ELLIPSE);
65  jtbOval.setIcon(ICONS.TOOL_OVAL);
66  jtbPolygon.setIcon(ICONS.TOOL_POLYGON);
67  jtbFreehand.setIcon(ICONS.TOOL_FREEHAND);
68  jtbBrush.setIcon(ICONS.TOOL_BRUSH);
69  jbSetBrushSize.setIcon(ICONS.ACTION_BRUSHSIZE);
70  jtbLockMask.setIcon(ICONS.MASK_UNLOCKED);
71  jbCreateMask.setIcon(ICONS.ACTION_CREATEMASK);
72  jbCreateSelection.setIcon(ICONS.ACTION_CREATESELECTION);
73  jbInvertSelection.setIcon(ICONS.ACTION_INVERTSELECTION);
74  jbInvertMask.setIcon(ICONS.ACTION_INVERTMASK);
75  jbSpecifySelection.setIcon(ICONS.ACTION_SPECIFYSELECTION);
76 
77  jtbRectangle.setToolTipText(LABELS.TOOLTIP_RECTANGLE);
78  jtbRoundRectangle.setToolTipText(LABELS.TOOLTIP_ROUNDRECTANGLE);
79  jtbEllipse.setToolTipText(LABELS.TOOLTIP_ELLIPSE);
80  jtbOval.setToolTipText(LABELS.TOOLTIP_OVAL);
81  jtbPolygon.setToolTipText(LABELS.TOOLTIP_POLYGON);
82  jtbFreehand.setToolTipText(LABELS.TOOLTIP_FREEHAND);
83  jtbBrush.setToolTipText(LABELS.TOOLTIP_BRUSH);
84  jbSetBrushSize.setToolTipText(LABELS.TOOLTIP_SETBRUSHSIZE);
85  jtbLockMask.setToolTipText(LABELS.TOOLTIP_MASK_UNLOCKED);
86  jbCreateMask.setToolTipText(LABELS.TOOLTIP_CREATEMASK);
87  jbCreateSelection.setToolTipText(LABELS.TOOLTIP_CREATESELECTION);
88  jbInvertSelection.setToolTipText(LABELS.TOOLTIP_INVERTSELECTION);
89  jbInvertMask.setToolTipText(LABELS.TOOLTIP_INVERTMASK);
90  jbSpecifySelection.setToolTipText(LABELS.TOOLTIP_SPECIFYSELECTION);
91 
92  add(jtbRectangle);
93  add(jtbRoundRectangle);
94  add(jtbEllipse);
95  add(jtbOval);
96  add(jtbPolygon);
97  add(jtbFreehand);
98  add(jtbBrush);
99  add(jbSetBrushSize);
100  add(jtbLockMask);
101  add(jbCreateMask);
102  add(jbCreateSelection);
103  add(jbInvertSelection);
104  add(jbInvertMask);
105  add(jbSpecifySelection);
106  add(Box.createVerticalGlue());
107 
108  jtbRectangle.addActionListener(this);
109  jtbRoundRectangle.addActionListener(this);
110  jtbEllipse.addActionListener(this);
111  jtbOval.addActionListener(this);
112  jtbPolygon.addActionListener(this);
113  jtbFreehand.addActionListener(this);
114  jtbBrush.addActionListener(this);
115  jbSetBrushSize.addActionListener(this);
116  jtbLockMask.addActionListener(this);
117  jbCreateMask.addActionListener(this);
118  jbCreateSelection.addActionListener(this);
119  jbInvertSelection.addActionListener(this);
120  jbInvertMask.addActionListener(this);
121  jbSpecifySelection.addActionListener(this);
122  jtbRectangle.setSelected(true);
123 
124  pack();
125  setResizable(false);
126  }
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Member Function Documentation

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◆ actionPerformed()

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void xmipp.ij.plugins.maskstoolbar.MasksToolBar.actionPerformed (ActionEvent ae)
- 		-inline
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Definition at line 241 of file MasksToolBar.java.

-
241  {
242  if (ae.getSource() == jtbRectangle) {
243  setTool("rectangle");
244  uselectOthers(jtbRectangle);
245  } else if (ae.getSource() == jtbRoundRectangle) {
246  setTool("roundrect");
247  uselectOthers(jtbRoundRectangle);
248  } else if (ae.getSource() == jtbEllipse) {
249  setTool("ellipse");
250  uselectOthers(jtbEllipse);
251  } else if (ae.getSource() == jtbOval) {
252  setTool("oval");
253  uselectOthers(jtbOval);
254  } else if (ae.getSource() == jtbPolygon) {
255  setTool("polygon");
256  uselectOthers(jtbPolygon);
257  } else if (ae.getSource() == jtbFreehand) {
258  setTool("freeroi");
259  uselectOthers(jtbFreehand);
260  } else if (ae.getSource() == jtbBrush) {
261  setTool("brush");
262  uselectOthers(jtbBrush);
263  } else if (ae.getSource() == jbSetBrushSize) {
264  showBrushDialog();
265  } else if (ae.getSource() == jtbLockMask) {
266  jtbLockMask.setIcon(jtbLockMask.isSelected() ? ICONS.MASK_LOCKED : ICONS.MASK_UNLOCKED);
267  jtbLockMask.setToolTipText(jtbLockMask.isSelected() ? LABELS.TOOLTIP_MASK_LOCKED : LABELS.TOOLTIP_MASK_UNLOCKED);
268  } else if (ae.getSource() == jbCreateMask) {
269  createMask();
270  } else if (ae.getSource() == jbCreateSelection) {
271  createSelection();
272  } else if (ae.getSource() == jbInvertSelection) {
273  invertSelection();
274  } else if (ae.getSource() == jbInvertMask) {
275  invertMask();
276  } else if (ae.getSource() == jbSpecifySelection) {
277  specifySelection();
278  }
279  }
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◆ getInstance()

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static MasksToolBar xmipp.ij.plugins.maskstoolbar.MasksToolBar.getInstance ()
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Definition at line 286 of file MasksToolBar.java.

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286  {
287  if (instance == null) {
288  createInstance();
289  }
290 
291  return instance;
292  }
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Definition at line 282 of file MasksToolBar.java.

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282  {
283  instance = null;
284  }
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run(String args)xmipp.ij.plugins.maskstoolbar.MasksToolBarPlugininline
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void run (String args)
 
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Detailed Description

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Definition at line 30 of file MasksToolBarPlugin.java.

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◆ run()

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void xmipp.ij.plugins.maskstoolbar.MasksToolBarPlugin.run (String args)
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Definition at line 33 of file MasksToolBarPlugin.java.

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33  {
34  MasksToolBar.getInstance().setVisible(true);
35  }
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- - diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__coll__graph.dot b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__coll__graph.dot deleted file mode 100644 index b5e269c2..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.ij.plugins.maskstoolbar.MasksToolBarPlugin" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.ij.plugins.maskstoolbar.\lMasksToolBarPlugin",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__coll__graph.md5 b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__coll__graph.md5 deleted file mode 100644 index 9a727f40..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -f38fdba15df4b20c0c7f294af4113c13 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__inherit__graph.dot b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__inherit__graph.dot deleted file mode 100644 index b12590e7..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.ij.plugins.maskstoolbar.MasksToolBarPlugin" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.ij.plugins.maskstoolbar.\lMasksToolBarPlugin",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugIn",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__inherit__graph.md5 b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__inherit__graph.md5 deleted file mode 100644 index adef080c..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBarPlugin__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -c922385e2b62f478198000bb701b3595 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__coll__graph.dot b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__coll__graph.dot deleted file mode 100644 index ba591ed6..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.ij.plugins.maskstoolbar.MasksToolBar" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="xmipp.ij.plugins.maskstoolbar.\lMasksToolBar",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="PlugInFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__coll__graph.md5 b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__coll__graph.md5 deleted file mode 100644 index e95e49ef..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ed1a0cad2016e0a7aef54629837cfaa1 \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__inherit__graph.dot b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__inherit__graph.dot deleted file mode 100644 index 5b8f5c5a..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.ij.plugins.maskstoolbar.MasksToolBar" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.ij.plugins.maskstoolbar.\lMasksToolBar",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="PlugInFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__inherit__graph.md5 b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__inherit__graph.md5 deleted file mode 100644 index 5ec3011b..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1MasksToolBar__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -9d1a627c52d9aedc5192629bb4ad420c \ No newline at end of file diff --git a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1Operations-members.html b/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1Operations-members.html deleted file mode 100644 index aaf3ef1e..00000000 --- a/html/classxmipp_1_1ij_1_1plugins_1_1maskstoolbar_1_1Operations-members.html +++ /dev/null @@ -1,83 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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binarize(ImagePlus ip)xmipp.ij.plugins.maskstoolbar.Operationsinlinestatic
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-Static Public Member Functions

static void binarize (ImagePlus ip)
 
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Juanjo Vega
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Definition at line 13 of file Operations.java.

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Member Function Documentation

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◆ binarize()

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static void xmipp.ij.plugins.maskstoolbar.Operations.binarize (ImagePlus ip)
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Definition at line 15 of file Operations.java.

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15  {
16  byte pixels[] = (byte[]) ip.getProcessor().getPixels();
17 
18  for (int i = 0; i < pixels.length; i++) {
19  if (pixels[i] > 0) {
20  pixels[i] = 1;
21  }
22  }
23 
24  ip.getProcessor().setPixels(pixels);
25  //ip.updateImage();
26  }
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BACKGROUND_NOISExmipp.jni.CTFDescriptionstatic
create()xmipp.jni.CTFDescriptionprotected
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CTFAverageProfiles(int samples)xmipp.jni.CTFDescriptioninline
CTFDescription()xmipp.jni.CTFDescriptioninline
CTFDescription(String filename)xmipp.jni.CTFDescriptioninline
CTFProfile(double angle, int samples)xmipp.jni.CTFDescriptioninline
destroy()xmipp.jni.CTFDescriptionprotected
downsamplingxmipp.jni.CTFDescription
ENVELOPExmipp.jni.CTFDescriptionstatic
finalize()xmipp.jni.CTFDescriptioninlineprotected
FMAXxmipp.jni.CTFDescription
profilesxmipp.jni.CTFDescription
PSDxmipp.jni.CTFDescriptionstatic
read(String filename)xmipp.jni.CTFDescriptioninline
read_(String filename)xmipp.jni.CTFDescription
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native void read_ (String filename) throws Exception
 
void read (String filename) throws Exception
 
void CTFProfile (double angle, int samples)
 
void CTFAverageProfiles (int samples)
 
 CTFDescription ()
 
 CTFDescription (String filename) throws Exception
 
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-Public Attributes

double [][] profiles
 
double FMAX
 
double downsampling
 
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static final int BACKGROUND_NOISE = 0
 
static final int ENVELOPE = 1
 
static final int PSD = 2
 
static final int CTF = 3
 
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-Protected Member Functions

native void create ()
 
synchronized native void destroy ()
 
void finalize () throws Throwable
 
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Definition at line 3 of file CTFDescription.java.

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62  {
63  create();
64  }
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Definition at line 66 of file CTFDescription.java.

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66  {
67  this();
68  read(filename);
69  }
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void read(String filename)
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Definition at line 56 of file CTFDescription.java.

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56  {
57  avgprofiles = CTFAverageProfile(FMAX, samples);
58  }
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Definition at line 50 of file CTFDescription.java.

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50  {
51  profiles = CTFProfile(angle, FMAX, samples);
52  }
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73  {
74  super.finalize();
75  destroy();
76  }
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Definition at line 33 of file CTFDescription.java.

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33  {
34  read_(filename);
35  MetaData md = new MetaData(filename);
36  if (md.containsLabel(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED))
37  downsampling = md.getValueDouble(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED, md.firstObject());
38  else
39  downsampling = 1.0;
40  md.destroy();
41 
42  FMAX = getFMAX()/downsampling;
43  }
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Definition at line 6 of file CTFDescription.java.

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Definition at line 9 of file CTFDescription.java.

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Definition at line 7 of file CTFDescription.java.

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CW_ADJUSTxmipp.jni.CastWriteModestatic
CW_CASTxmipp.jni.CastWriteModestatic
CW_CONVERTxmipp.jni.CastWriteModestatic
CW_LAST_LABELxmipp.jni.CastWriteModestatic
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-Static Public Attributes

static final int CW_CAST = 0
 
static final int CW_CONVERT = 1
 
static final int CW_ADJUST = 2
 
static final int CW_LAST_LABEL = 3
 
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Detailed Description

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Definition at line 3 of file CastWriteMode.java.

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◆ CW_ADJUST

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final int xmipp.jni.CastWriteMode.CW_ADJUST = 2
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Definition at line 6 of file CastWriteMode.java.

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Definition at line 5 of file CastWriteMode.java.

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Definition at line 7 of file CastWriteMode.java.

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applyChangesxmipp.jni.Classifierprotected
getParams()xmipp.jni.Classifierinline
getTrainingParticlesMinimum()xmipp.jni.Classifier
isApplyChanges()xmipp.jni.Classifierinline
needsTraining()xmipp.jni.Classifier
paramsxmipp.jni.Classifierprotected
setApplyChanges(boolean applyChanges)xmipp.jni.Classifierinline
setSize(int psize)xmipp.jni.Classifier
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abstract int getTrainingParticlesMinimum ()
 
abstract void setSize (int psize)
 
boolean isApplyChanges ()
 
void setApplyChanges (boolean applyChanges)
 
List< Classifier.Parameter > getParams ()
 
abstract boolean needsTraining ()
 
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List< Classifier.Parameter > params
 
boolean applyChanges
 
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Definition at line 5 of file Classifier.java.

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Definition at line 42 of file Classifier.java.

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44  return params;
45  }
xmipp.jni.Classifier.params
List< Classifier.Parameter > params
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Definition at line 19 of file Classifier.java.

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20  this.applyChanges = applyChanges;
21  }
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Definition at line 12 of file Classifier.java.

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◆ params

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List<Classifier.Parameter> xmipp.jni.Classifier.params
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Definition at line 7 of file Classifier.java.

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 Parameter (String name, String label, String help, String value)
 
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String name
 
String label
 
String help
 
String value
 
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Definition at line 25 of file Classifier.java.

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◆ Parameter()

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Definition at line 32 of file Classifier.java.

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33  {
34  this.name = name;
35  this.label = label;
36  this.help = help;
37  this.value = value;
38  }
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Definition at line 29 of file Classifier.java.

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Definition at line 30 of file Classifier.java.

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calculateDefocus(double minor, double major)xmipp.jni.EllipseCTFinline
EllipseCTF(long id, double Q0, double Cs, double downsampleFactor, double Ts, double kV, double mddefU, double mddefV, double defocusAngle, int D)xmipp.jni.EllipseCTFinline
getCTFMd()xmipp.jni.EllipseCTFinline
getD()xmipp.jni.EllipseCTFinline
getDefocusAngle()xmipp.jni.EllipseCTFinline
getDefocusU()xmipp.jni.EllipseCTFinline
getDefocusV()xmipp.jni.EllipseCTFinline
getDownsamplingFactor()xmipp.jni.EllipseCTFinline
getHighFreq()xmipp.jni.EllipseCTFinline
getId()xmipp.jni.EllipseCTFinline
getLowFreq()xmipp.jni.EllipseCTFinline
getQ0()xmipp.jni.EllipseCTFinline
getSamplingRate()xmipp.jni.EllipseCTFinline
getSphericalAberration()xmipp.jni.EllipseCTFinline
getVoltage()xmipp.jni.EllipseCTFinline
lambda(double Kv)xmipp.jni.EllipseCTFinlinestatic
setDefocus(double defU, double defV, double angle)xmipp.jni.EllipseCTFinline
setEllipseFitter(EllipseFitter ellipseFitter)xmipp.jni.EllipseCTFinline
setFreqRange(double lowFreq, double highFreq)xmipp.jni.EllipseCTFinline
toString()xmipp.jni.EllipseCTFinline
toString2()xmipp.jni.EllipseCTFinline
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void setEllipseFitter (EllipseFitter ellipseFitter)
 
double getDefocusAngle ()
 
 EllipseCTF (long id, double Q0, double Cs, double downsampleFactor, double Ts, double kV, double mddefU, double mddefV, double defocusAngle, int D)
 
long getId ()
 
double getDefocusU ()
 
double getDefocusV ()
 
void setFreqRange (double lowFreq, double highFreq)
 
double getLowFreq ()
 
double getHighFreq ()
 
double getQ0 ()
 
void calculateDefocus (double minor, double major)
 
double getSamplingRate ()
 
double getVoltage ()
 
double getSphericalAberration ()
 
String toString2 ()
 
String toString ()
 
int getD ()
 
MetaData getCTFMd ()
 
double getDownsamplingFactor ()
 
void setDefocus (double defU, double defV, double angle)
 
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static double lambda (double Kv)
 
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Definition at line 17 of file EllipseCTF.java.

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xmipp.jni.EllipseCTF.EllipseCTF (long id,
double Q0,
double Cs,
double downsampleFactor,
double Ts,
double kV,
double mddefU,
double mddefV,
double defocusAngle,
int D 
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Definition at line 36 of file EllipseCTF.java.

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37  {
38  this.id = id;
39  this.D = D;
40  this.Q0 = Q0;
41  this.Cs = Cs;
42  this.downsampleFactor = downsampleFactor;
43  this.Ts = Ts;
44  this.kV = kV;
45  this.lambda = EllipseCTF.lambda(kV);
46  this.mddefU = mddefU;
47  this.mddefV = mddefV;
48  this.defocusAngle = defocusAngle;
49  }
xmipp.jni.EllipseCTF.EllipseCTF
EllipseCTF(long id, double Q0, double Cs, double downsampleFactor, double Ts, double kV, double mddefU, double mddefV, double defocusAngle, int D)
Definition: EllipseCTF.java:36
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Definition at line 90 of file EllipseCTF.java.

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90  {
91  defocusU = defocus(minor, Q0, lambda, Cs, D, Ts * downsampleFactor);
92  defocusV = defocus(major, Q0, lambda, Cs, D, Ts * downsampleFactor);
93  }
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Definition at line 145 of file EllipseCTF.java.

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146  {
147  MetaData md = new MetaData();
148  md.setColumnFormat(true);
149  long id = md.addObject();
150  md.setValueDouble(MDLabel.MDL_CTF_Q0, Q0, id);
151  md.setValueDouble(MDLabel.MDL_CTF_CS, Cs, id);
152  md.setValueDouble(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED, downsampleFactor, id);
153  md.setValueDouble(MDLabel.MDL_SAMPLINGRATE, Ts,id);
154  md.setValueDouble(MDLabel.MDL_CTF_VOLTAGE, kV, id);
155  md.setValueDouble(MDLabel.MDL_CTF_DEFOCUSU, mddefU, id);
156  md.setValueDouble(MDLabel.MDL_CTF_DEFOCUSV, mddefV, id);
157  md.setValueDouble(MDLabel.MDL_CTF_DEFOCUS_ANGLE, defocusAngle, id);
158  //md.print();
159  return md;
160  }
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Definition at line 140 of file EllipseCTF.java.

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141  {
142  return D;
143  }
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Definition at line 32 of file EllipseCTF.java.

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32  {
33  return defocusAngle;
34  }
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Definition at line 63 of file EllipseCTF.java.

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63  {
64  return defocusU;
65  }
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Definition at line 67 of file EllipseCTF.java.

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68  return defocusV;
69  }
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Definition at line 162 of file EllipseCTF.java.

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162  {
163  return downsampleFactor;
164  }
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Definition at line 81 of file EllipseCTF.java.

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82  return highFreq;
83  }
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52  {
53  return id;
54  }
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Definition at line 77 of file EllipseCTF.java.

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77  {
78  return lowFreq;
79  }
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Definition at line 85 of file EllipseCTF.java.

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86  return Q0;
87  }
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Definition at line 106 of file EllipseCTF.java.

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106  {
107  return Ts;
108  }
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Definition at line 114 of file EllipseCTF.java.

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114  {
115  return Cs;
116  }
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Definition at line 110 of file EllipseCTF.java.

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111  return kV;
112  }
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Definition at line 56 of file EllipseCTF.java.

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56  {
57  double local_kV = Kv * 1.0e3;
58 
59  return 12.3 / Math.sqrt(local_kV * (1. + local_kV * 1e-6));
60  }
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void xmipp.jni.EllipseCTF.setDefocus (double defU,
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Definition at line 166 of file EllipseCTF.java.

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166  {
167  this.defocusU = defU;
168  this.defocusV = defV;
169  this.defocusAngle = angle;
170  }
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void xmipp.jni.EllipseCTF.setEllipseFitter (EllipseFitter ellipseFitter)
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Definition at line 27 of file EllipseCTF.java.

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27  {
28  this.ellipseFitter = ellipseFitter;
29  defocusAngle = ellipseFitter.angle;
30  }
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void xmipp.jni.EllipseCTF.setFreqRange (double lowFreq,
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Set the frequencies range to calculate CTF

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Definition at line 72 of file EllipseCTF.java.

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73  this.lowFreq = lowFreq;
74  this.highFreq = highFreq;
75  }
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Definition at line 134 of file EllipseCTF.java.

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135  {
136  String format = "%10.2f%10.2f%10.2f%10.2f%10.2f";
137  return String.format(Locale.ENGLISH, format, getDefocusU(), getDefocusV(), getDefocusAngle(), getLowFreq(), getHighFreq());
138  }
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double getDefocusAngle()
Definition: EllipseCTF.java:32
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Definition at line 119 of file EllipseCTF.java.

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119  {
120  return "---------------------------------------------------\n"
121  + "Q0: " + Q0 + "\n"
122  + "Cs: " + Cs + "\n"
123  + "D: " + D + "\n"
124  + "Ts: " + Ts + "\n"
125  + "Kv: " + kV + "\n"
126  + "lambda: " + lambda + "\n"
127  + "---------------------------------------------------\n"
128  + "defocusU: " + defocusU + " > (file: " + mddefU + ")\n"
129  + "defocusV: " + defocusV + " > (file: " + mddefV + ")\n"
130  + "---------------------------------------------------\n";
131  }
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- - diff --git a/html/classxmipp_1_1jni_1_1Filename-members.html b/html/classxmipp_1_1jni_1_1Filename-members.html deleted file mode 100644 index 1f4cf2eb..00000000 --- a/html/classxmipp_1_1jni_1_1Filename-members.html +++ /dev/null @@ -1,172 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.jni.Filename Member List
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This is the complete list of members for xmipp.jni.Filename, including all inherited members.

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compose(int slice, String path)xmipp.jni.Filenamestatic
compose(String prefix, String path)xmipp.jni.Filenameinlinestatic
exists(String path)xmipp.jni.Filenameinlinestatic
EXT_BOXxmipp.jni.Filenamestatic
EXT_CTFDATxmipp.jni.Filenamestatic
EXT_CTFPARAMxmipp.jni.Filenamestatic
EXT_DM3xmipp.jni.Filenamestatic
EXT_DM4xmipp.jni.Filenamestatic
EXT_DOCxmipp.jni.Filenamestatic
EXT_EMxmipp.jni.Filenamestatic
EXT_EMSxmipp.jni.Filenamestatic
EXT_ERRxmipp.jni.Filenamestatic
EXT_H5xmipp.jni.Filenamestatic
EXT_HDFxmipp.jni.Filenamestatic
EXT_HDF5xmipp.jni.Filenamestatic
EXT_HEDxmipp.jni.Filenamestatic
EXT_IMGxmipp.jni.Filenamestatic
EXT_INFxmipp.jni.Filenamestatic
EXT_JPGxmipp.jni.Filenamestatic
EXT_LOGxmipp.jni.Filenamestatic
EXT_MRCxmipp.jni.Filenamestatic
EXT_MRC2xmipp.jni.Filenamestatic
EXT_MRCRECxmipp.jni.Filenamestatic
EXT_MRCSxmipp.jni.Filenamestatic
EXT_MRCS2xmipp.jni.Filenamestatic
EXT_MRCSALIxmipp.jni.Filenamestatic
EXT_MRCSPREALIxmipp.jni.Filenamestatic
EXT_OUTxmipp.jni.Filenamestatic
EXT_PIFxmipp.jni.Filenamestatic
EXT_PNGxmipp.jni.Filenamestatic
EXT_POSxmipp.jni.Filenamestatic
EXT_PSDxmipp.jni.Filenamestatic
EXT_PYxmipp.jni.Filenamestatic
EXT_RAWxmipp.jni.Filenamestatic
EXT_SELxmipp.jni.Filenamestatic
EXT_SERxmipp.jni.Filenamestatic
EXT_SPExmipp.jni.Filenamestatic
EXT_SPIxmipp.jni.Filenamestatic
EXT_STKxmipp.jni.Filenamestatic
EXT_TIFxmipp.jni.Filenamestatic
EXT_TXTxmipp.jni.Filenamestatic
EXT_VOLxmipp.jni.Filenamestatic
EXT_XMDxmipp.jni.Filenamestatic
EXT_XMPxmipp.jni.Filenamestatic
findImagePath(String filename, String mdFilename, boolean shouldExist)xmipp.jni.Filenameinlinestatic
findProjectDir(String filename)xmipp.jni.Filenameinlinestatic
findProjectPath(String filename)xmipp.jni.Filenameinlinestatic
getBaseName(String path)xmipp.jni.Filenameinlinestatic
getClassBlockName(int ref)xmipp.jni.Filenameinlinestatic
getCurrentDir()xmipp.jni.Filenameinlinestatic
getFilename(String filename)xmipp.jni.Filenameinlinestatic
getNimage(String filename)xmipp.jni.Filenameinlinestatic
getPath(String baseDir, String fileName, int slice)xmipp.jni.Filenameinlinestatic
getPrefix(String filename)xmipp.jni.Filenameinlinestatic
getRelativePath(String absolutePath, String relativeTo)xmipp.jni.Filenameinlinestatic
getRelativePath(String path)xmipp.jni.Filenameinlinestatic
getSuffix(String filename)xmipp.jni.Filenameinlinestatic
getXmippPath()xmipp.jni.Filenamestatic
getXmippPath(String relpath)xmipp.jni.Filenameinlinestatic
hasPrefix(String filename)xmipp.jni.Filenameinlinestatic
hasStackExtension(String filename)xmipp.jni.Filenamestatic
hasSuffix(String filename)xmipp.jni.Filenameinlinestatic
hasVolumeExtension(String filename)xmipp.jni.Filenamestatic
humanReadableByteCount(long bytes)xmipp.jni.Filenameinlinestatic
isMetadata(String filename)xmipp.jni.Filenameinlinestatic
isMetadataExt(String filename)xmipp.jni.Filenameinlinestatic
isPSD(String filename)xmipp.jni.Filenameinlinestatic
isSingleImage(String filename)xmipp.jni.Filenameinlinestatic
isSingleImageExt(String filename)xmipp.jni.Filenameinlinestatic
isSpiderVolume(String filename)xmipp.jni.Filenameinlinestatic
isStack(String filename)xmipp.jni.Filenameinlinestatic
isStackExt(String filename)xmipp.jni.Filenameinlinestatic
isStackOrVolume(String filename)xmipp.jni.Filenameinlinestatic
isTextfile(String filename)xmipp.jni.Filenameinlinestatic
isVolume(String filename)xmipp.jni.Filenameinlinestatic
isVolumeExt(String filename)xmipp.jni.Filenameinlinestatic
isXmippSupported(String filename)xmipp.jni.Filenameinlinestatic
join(String... paths)xmipp.jni.Filenameinlinestatic
METADATASxmipp.jni.Filenamestatic
PROJECT_FILExmipp.jni.Filenamestatic
putExtension(String file, String ext)xmipp.jni.Filenameinlinestatic
removeExtension(String path)xmipp.jni.Filenameinlinestatic
removePrefix(String filename)xmipp.jni.Filenameinlinestatic
SEPARATORxmipp.jni.Filenamestatic
SINGLE_IMAGESxmipp.jni.Filenamestatic
SPIDERxmipp.jni.Filenamestatic
STACKSxmipp.jni.Filenamestatic
TEXTxmipp.jni.Filenamestatic
VOLUMESxmipp.jni.Filenamestatic
XMIPP_SUPPORTEDxmipp.jni.Filenamestatic
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-Static Public Member Functions | -Static Public Attributes | -List of all members
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xmipp.jni.Filename Class Reference
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-Static Public Member Functions

static boolean isPSD (String filename)
 
static boolean isSpiderVolume (String filename)
 
static native boolean hasStackExtension (String filename) throws Exception
 
static native boolean hasVolumeExtension (String filename) throws Exception
 
static native String compose (int slice, String path) throws Exception
 
static native String getXmippPath () throws Exception
 
static String getXmippPath (String relpath)
 
static boolean isSingleImage (String filename) throws Exception
 
static boolean isSingleImageExt (String filename)
 
static boolean isStackOrVolume (String filename)
 
static boolean isVolume (String filename)
 
static boolean isVolumeExt (String filename)
 
static boolean isStack (String filename)
 
static boolean isStackExt (String filename)
 
static boolean isMetadata (String filename)
 
static boolean isMetadataExt (String filename)
 
static boolean isTextfile (String filename)
 
static String findImagePath (String filename, String mdFilename, boolean shouldExist)
 
static boolean exists (String path)
 
static String findProjectPath (String filename)
 
static File findProjectDir (String filename)
 
static String getFilename (String filename)
 
static String getPath (String baseDir, String fileName, int slice) throws Exception
 
static long getNimage (String filename)
 
static String compose (String prefix, String path)
 
static boolean hasPrefix (String filename)
 
static boolean hasSuffix (String filename)
 
static String getPrefix (String filename)
 
static String getSuffix (String filename)
 
static String removePrefix (String filename)
 
static String getClassBlockName (int ref)
 
static String getCurrentDir ()
 
static String getRelativePath (String absolutePath, String relativeTo)
 
static String getRelativePath (String path)
 
static String getBaseName (String path)
 
static String removeExtension (String path)
 
static String join (String... paths)
 
static String humanReadableByteCount (long bytes)
 
static String putExtension (String file, String ext)
 
static boolean isXmippSupported (String filename)
 
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-Static Public Attributes

static final String PROJECT_FILE = ".project.sqlite"
 
static final String SEPARATOR = "@"
 
static final String EXT_SPI = ".spi"
 
static final String EXT_XMP = ".xmp"
 
static final String EXT_VOL = ".vol"
 
static final String EXT_STK = ".stk"
 
static final String EXT_MRC = ".mrc"
 
static final String EXT_MRC2 = ".map"
 
static final String EXT_MRCS = ".mrcs"
 
static final String EXT_MRCS2 = ".st"
 
static final String EXT_MRCREC = ".rec"
 
static final String EXT_MRCSALI = ".ali"
 
static final String EXT_MRCSPREALI = ".preali"
 
static final String EXT_IMG = ".img"
 
static final String EXT_HED = ".hed"
 
static final String EXT_SER = ".ser"
 
static final String EXT_DM3 = ".dm3"
 
static final String EXT_DM4 = ".dm4"
 
static final String EXT_EM = ".em"
 
static final String EXT_EMS = ".ems"
 
static final String EXT_PIF = ".pif"
 
static final String EXT_RAW = ".raw"
 
static final String EXT_INF = ".inf"
 
static final String EXT_SPE = ".spe"
 
static final String EXT_TIF = ".tif"
 
static final String EXT_JPG = ".jpg"
 
static final String EXT_PNG = ".png"
 
static final String EXT_PSD = ".psd"
 
static final String EXT_HDF = ".hdf"
 
static final String EXT_HDF5 = ".hdf5"
 
static final String EXT_H5 = ".h5"
 
static final String EXT_XMD = ".xmd"
 
static final String EXT_SEL = ".sel"
 
static final String EXT_DOC = ".doc"
 
static final String EXT_CTFPARAM = ".ctfparam"
 
static final String EXT_CTFDAT = ".ctfdat"
 
static final String EXT_POS = ".pos"
 
static final String EXT_LOG = ".log"
 
static final String EXT_OUT = ".out"
 
static final String EXT_ERR = ".err"
 
static final String EXT_PY = ".py"
 
static final String EXT_TXT = ".txt"
 
static final String EXT_BOX = ".box"
 
static final String [] SINGLE_IMAGES
 
static final String [] VOLUMES
 
static final String [] STACKS
 
static final String [] METADATAS
 
static final String [] SPIDER = new String[] { EXT_SPI, EXT_VOL }
 
static final String [] TEXT
 
static final String [] XMIPP_SUPPORTED
 
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Detailed Description

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Definition at line 5 of file Filename.java.

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Member Function Documentation

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◆ compose() [1/2]

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static native String xmipp.jni.Filename.compose (int slice,
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static String xmipp.jni.Filename.compose (String prefix,
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Definition at line 327 of file Filename.java.

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327  {
328  return prefix + SEPARATOR + path;
329  }
xmipp.jni.Filename.SEPARATOR
static final String SEPARATOR
Definition: Filename.java:8
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◆ exists()

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static boolean xmipp.jni.Filename.exists (String path)
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Return if the path exists removing the Xmipp special characters

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Definition at line 266 of file Filename.java.

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266  {
267  File f = new File(Filename.getFilename(path));
268  return f.exists();
269  }
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◆ findImagePath()

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static String xmipp.jni.Filename.findImagePath (String filename,
String mdFilename,
boolean shouldExist 
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This function will try to find where the images are located relative to the container metadata, the current dir or the project dir. The search will be in the following order: 1. From current dir (default behaivour if this function is not used) 2. Relative to metadata 3. Relative to the project root folder

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filenameimage filename (probably from a metadata)
mdFilenamemetadata filename, used to check if there are relative to there
shouldExist
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The path of the image if found, or null if not exists
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Definition at line 225 of file Filename.java.

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226  {
227  if(filename == null || filename.equals(""))
228  return null;
229  String path = Filename.getFilename(filename); // Remove special chars
230  String foundPath = null;
231  File f = new File(path);
232  // 1. Check if exists from current dir
233  if (f.exists()) {
234  foundPath = path;
235  } else if (mdFilename != null) {
236  // 2. Check if exists from mdFilename
237  f = new File(mdFilename);
238  if (!f.isDirectory())
239  f = f.getParentFile();
240  f = new File(f, path);
241  if (f.exists())
242  foundPath = f.getPath();
243  else {
244  // 3. Check if it is relative to project dir
245  File projectDir = findProjectDir(mdFilename);
246  if (projectDir != null) {
247  f = new File(projectDir, path);
248  if (f.exists())
249  foundPath = f.getPath();
250  }
251  }
252  }
253 
254  if (foundPath != null && hasPrefix(filename)) {
255  foundPath = compose(getPrefix(filename), foundPath);
256  }
257  if (foundPath != null && hasSuffix(filename)) {
258  foundPath += getSuffix(filename);
259  }
260  return foundPath;
261  }
xmipp.jni.Filename.hasPrefix
static boolean hasPrefix(String filename)
Definition: Filename.java:331
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xmipp.jni.Filename.getSuffix
static String getSuffix(String filename)
Definition: Filename.java:363
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xmipp.jni.Filename.hasSuffix
static boolean hasSuffix(String filename)
Definition: Filename.java:335
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xmipp.jni.Filename.compose
static native String compose(int slice, String path)
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xmipp.jni.Filename.getPrefix
static String getPrefix(String filename)
Definition: Filename.java:339
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xmipp.jni.Filename.findProjectDir
static File findProjectDir(String filename)
Definition: Filename.java:283
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static File xmipp.jni.Filename.findProjectDir (String filename)
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Find in the directory if the PROJECT_FILE is present, or in any of the parent directories

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Definition at line 283 of file Filename.java.

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283  {
284  filename = getFilename(filename);
285  File dir = new File(filename).getAbsoluteFile(); // Remove Xmipp special
286  // characters
287  if (!dir.isDirectory())
288  dir = dir.getParentFile();
289  while (dir != null) {
290  File f = new File(dir, PROJECT_FILE);
291  if (f.exists())
292  return dir;
293  dir = dir.getParentFile();
294  }
295 
296  return null;
297  }
xmipp.jni.Filename.PROJECT_FILE
static final String PROJECT_FILE
Definition: Filename.java:7
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xmipp.jni.Filename.getFilename
static String getFilename(String filename)
Definition: Filename.java:302
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static String xmipp.jni.Filename.findProjectPath (String filename)
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Find project path, see findProjectDir function

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Definition at line 272 of file Filename.java.

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272  {
273  File dir = findProjectDir(filename);
274  if (dir != null)
275  return dir.getPath();
276  return null;
277  }
xmipp.jni.Filename.findProjectDir
static File findProjectDir(String filename)
Definition: Filename.java:283
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◆ getBaseName()

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static String xmipp.jni.Filename.getBaseName (String path)
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Get the last part of the filename

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Definition at line 458 of file Filename.java.

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458  {
459  int index = path.lastIndexOf(File.separatorChar);
460  if (index != -1)
461  path = path.substring(index + 1, path.length());
462  return path;
463  }
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◆ getClassBlockName()

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static String xmipp.jni.Filename.getClassBlockName (int ref)
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Return the name of the block associated with class 'ref' in a results_classes.xmd metadata

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Definition at line 385 of file Filename.java.

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385  {
386  return String.format("class%06d_images", ref);
387  }
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static String xmipp.jni.Filename.getCurrentDir ()
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Return the current working directory

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Definition at line 390 of file Filename.java.

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390  {
391  return System.getProperty("user.dir");
392  }
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◆ getFilename()

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static String xmipp.jni.Filename.getFilename (String filename)
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Remove from the filename the Xmipp special characters

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Definition at line 302 of file Filename.java.

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302  {
303 
304  if (filename.contains(SEPARATOR))
305  filename = filename.split(SEPARATOR)[1];
306 
307  if (filename.contains(":"))
308  filename = filename.split(":")[0];
309  if (filename.contains("#"))
310  filename = filename.split("#")[0];
311 
312  return filename;
313  }
xmipp.jni.Filename.SEPARATOR
static final String SEPARATOR
Definition: Filename.java:8
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Definition at line 320 of file Filename.java.

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320  {
321  String prefix = getPrefix(filename);
322 
323  return prefix != null ? Long.valueOf(prefix).longValue()
324  : ImageGeneric.ALL_IMAGES;
325  }
xmipp.jni.Filename.getPrefix
static String getPrefix(String filename)
Definition: Filename.java:339
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static String xmipp.jni.Filename.getPath (String baseDir,
String fileName,
int slice 
) throws Exception
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Definition at line 315 of file Filename.java.

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316  {
317  return compose(slice, baseDir + File.separatorChar + fileName);
318  }
xmipp.jni.Filename.compose
static native String compose(int slice, String path)
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◆ getPrefix()

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static String xmipp.jni.Filename.getPrefix (String filename)
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Definition at line 339 of file Filename.java.

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339  {
340  if (hasPrefix(filename)) {
341  String prefix = "";
342  String str = filename.split(SEPARATOR)[0];
343  // if (!str.isEmpty()) {
344  // // str may have a string prefix before the number, so
345  // // grab the leftmost part
346  // int i = str.length() - 1;
347  // while (i >= 0) {
348  // if (str.charAt(i) == File.separatorChar) {
349  // break;
350  // }
351  // i--;
352  // }
353  //
354  // prefix = str.substring(i + 1, str.length());
355  // }
356  // return prefix;
357  return str;
358  }
359 
360  return null;
361  }
xmipp.jni.Filename.hasPrefix
static boolean hasPrefix(String filename)
Definition: Filename.java:331
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xmipp.jni.Filename.SEPARATOR
static final String SEPARATOR
Definition: Filename.java:8
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◆ getRelativePath() [1/2]

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static String xmipp.jni.Filename.getRelativePath (String absolutePath,
String relativeTo 
)
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Definition at line 403 of file Filename.java.

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403  {
404  StringBuilder relativePath = null;
405 
406  absolutePath = absolutePath.replaceAll("\\\\", "/");
407  relativeTo = relativeTo.replaceAll("\\\\", "/");
408 
409  if (absolutePath.equals(relativeTo) == true) {
410 
411  } else {
412  String[] absoluteDirectories = absolutePath.split("/");
413  String[] relativeDirectories = relativeTo.split("/");
414 
415  // Get the shortest of the two paths
416  int length = absoluteDirectories.length < relativeDirectories.length ? absoluteDirectories.length
417  : relativeDirectories.length;
418 
419  // Use to determine where in the loop we exited
420  int lastCommonRoot = -1;
421  int index;
422 
423  // Find common root
424  for (index = 0; index < length; index++) {
425  if (absoluteDirectories[index]
426  .equals(relativeDirectories[index])) {
427  lastCommonRoot = index;
428  } else {
429  break;
430  // If we didn't find a common prefix then throw
431  }
432  }
433  if (lastCommonRoot != -1) {
434  // Build up the relative path
435  relativePath = new StringBuilder();
436  // Add on the ..
437  for (index = lastCommonRoot + 1; index < absoluteDirectories.length; index++) {
438  if (absoluteDirectories[index].length() > 0) {
439  relativePath.append("../");
440  }
441  }
442  for (index = lastCommonRoot + 1; index < relativeDirectories.length - 1; index++) {
443  relativePath.append(relativeDirectories[index] + "/");
444  }
445  relativePath
446  .append(relativeDirectories[relativeDirectories.length - 1]);
447  }
448  }
449  return relativePath == null ? null : relativePath.toString();
450  }// function getRelativePath
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static String xmipp.jni.Filename.getRelativePath (String path)
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Overload using current working dir

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Definition at line 453 of file Filename.java.

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453  {
454  return getRelativePath(path, getCurrentDir());
455  }
xmipp.jni.Filename.getCurrentDir
static String getCurrentDir()
Definition: Filename.java:390
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xmipp.jni.Filename.getRelativePath
static String getRelativePath(String absolutePath, String relativeTo)
Definition: Filename.java:403
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◆ getSuffix()

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static String xmipp.jni.Filename.getSuffix (String filename)
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Definition at line 363 of file Filename.java.

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363  {
364  if (filename.contains(":")) {
365  return ":" + filename.split(":")[1];
366  } else if (filename.contains("#")) {
367  return "#" + filename.split("#")[1];
368  }
369 
370  return null;
371  }
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static String xmipp.jni.Filename.getXmippPath (String relpath)
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Definition at line 105 of file Filename.java.

-
105  {
106  try {
107  return getXmippPath() + File.separator + relpath;
108  } catch (Exception e) {
109  // TODO Auto-generated catch block
110  e.printStackTrace();
111  }
112  return null;
113  }
xmipp.jni.Filename.getXmippPath
static native String getXmippPath()
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◆ hasPrefix()

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static boolean xmipp.jni.Filename.hasPrefix (String filename)
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Definition at line 331 of file Filename.java.

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331  {
332  return filename.contains(SEPARATOR);
333  }
xmipp.jni.Filename.SEPARATOR
static final String SEPARATOR
Definition: Filename.java:8
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◆ hasStackExtension()

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static native boolean xmipp.jni.Filename.hasStackExtension (String filename) throws Exception
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◆ hasSuffix()

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static boolean xmipp.jni.Filename.hasSuffix (String filename)
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Definition at line 335 of file Filename.java.

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335  {
336  return filename.contains(":") || filename.contains("#");
337  }
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◆ hasVolumeExtension()

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static native boolean xmipp.jni.Filename.hasVolumeExtension (String filename) throws Exception
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◆ humanReadableByteCount()

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static String xmipp.jni.Filename.humanReadableByteCount (long bytes)
- 		-inlinestatic
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Definition at line 483 of file Filename.java.

-
483  {
484  int unit = 1024;
485  if (bytes < unit)
486  return bytes + " B";
487  int exp = (int) (Math.log(bytes) / Math.log(unit));
488  String pre = "KMGTPE".charAt(exp - 1) + "i";
489  return String.format("%.1f %sB", bytes / Math.pow(unit, exp), pre);
490  }
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◆ isMetadata()

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static boolean xmipp.jni.Filename.isMetadata (String filename)
- 		-inlinestatic
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Definition at line 165 of file Filename.java.

-
165  {
166  try {
167  if (filename != null)
168  return isMetaDataFile(filename);
169  } catch (Exception e) {
170  e.printStackTrace();
171  }
172  return false;
173  }// function isMetadata
-
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◆ isMetadataExt()

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static boolean xmipp.jni.Filename.isMetadataExt (String filename)
- 		-inlinestatic
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- -

Definition at line 175 of file Filename.java.

-
175  {
176  return filename != null && isFileType(filename, METADATAS);
177  }
xmipp.jni.Filename.METADATAS
static final String [] METADATAS
Definition: Filename.java:70
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◆ isPSD()

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static boolean xmipp.jni.Filename.isPSD (String filename)
- 		-inlinestatic
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- -

Definition at line 82 of file Filename.java.

-
82  {
83  return filename != null && filename.endsWith(EXT_PSD);
84  }
xmipp.jni.Filename.EXT_PSD
static final String EXT_PSD
Definition: Filename.java:35
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◆ isSingleImage()

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static boolean xmipp.jni.Filename.isSingleImage (String filename) throws Exception
- 		-inlinestatic
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Definition at line 115 of file Filename.java.

-
115  {
116  try {
117  if(isXmippSupported(filename))
118  return (new ImageGeneric(filename)).isSingleImage();
119  else
120  return isFileType(filename, SINGLE_IMAGES);
121  } catch (Exception ex) {
122  return filename != null && isFileType(filename, SINGLE_IMAGES);
123  }
124  }
xmipp.jni.Filename.SINGLE_IMAGES
static final String [] SINGLE_IMAGES
Definition: Filename.java:60
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xmipp.jni.Filename.isXmippSupported
static boolean isXmippSupported(String filename)
Definition: Filename.java:502
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◆ isSingleImageExt()

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static boolean xmipp.jni.Filename.isSingleImageExt (String filename)
- 		-inlinestatic
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Definition at line 126 of file Filename.java.

-
126  {
127  return filename != null && isFileType(filename, SINGLE_IMAGES);
128  }
xmipp.jni.Filename.SINGLE_IMAGES
static final String [] SINGLE_IMAGES
Definition: Filename.java:60
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◆ isSpiderVolume()

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static boolean xmipp.jni.Filename.isSpiderVolume (String filename)
- 		-inlinestatic
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- -

Definition at line 86 of file Filename.java.

-
86  {
87  return filename != null && isFileType(filename, SPIDER);
88  }
xmipp.jni.Filename.SPIDER
static final String [] SPIDER
Definition: Filename.java:73
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◆ isStack()

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static boolean xmipp.jni.Filename.isStack (String filename)
- 		-inlinestatic
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- -

Definition at line 150 of file Filename.java.

-
150  {
151  try {
152  if(isXmippSupported(filename))
153  return (new ImageGeneric(filename)).isStack();
154  else
155  return isFileType(filename, STACKS);
156  } catch (Exception ex) {
157  return filename != null && isFileType(filename, STACKS);
158  }
159  }
xmipp.jni.Filename.isXmippSupported
static boolean isXmippSupported(String filename)
Definition: Filename.java:502
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xmipp.jni.Filename.STACKS
static final String [] STACKS
Definition: Filename.java:67
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◆ isStackExt()

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static boolean xmipp.jni.Filename.isStackExt (String filename)
- 		-inlinestatic
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- -

Definition at line 161 of file Filename.java.

-
161  {
162  return filename != null && isFileType(filename, STACKS);
163  }
xmipp.jni.Filename.STACKS
static final String [] STACKS
Definition: Filename.java:67
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◆ isStackOrVolume()

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static boolean xmipp.jni.Filename.isStackOrVolume (String filename)
- 		-inlinestatic
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Definition at line 130 of file Filename.java.

-
130  {
131  return isStack(filename) || isVolume(filename);
132  }
xmipp.jni.Filename.isVolume
static boolean isVolume(String filename)
Definition: Filename.java:134
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xmipp.jni.Filename.isStack
static boolean isStack(String filename)
Definition: Filename.java:150
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◆ isTextfile()

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static boolean xmipp.jni.Filename.isTextfile (String filename)
- 		-inlinestatic
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Definition at line 179 of file Filename.java.

-
179  {
180  return isFileType(filename, TEXT) || isFileType(filename, METADATAS)
181  || isMetadata(filename);
182  }
xmipp.jni.Filename.TEXT
static final String [] TEXT
Definition: Filename.java:75
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xmipp.jni.Filename.METADATAS
static final String [] METADATAS
Definition: Filename.java:70
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xmipp.jni.Filename.isMetadata
static boolean isMetadata(String filename)
Definition: Filename.java:165
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◆ isVolume()

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static boolean xmipp.jni.Filename.isVolume (String filename)
- 		-inlinestatic
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- -

Definition at line 134 of file Filename.java.

-
134  {
135 
136  try {
137  if(isXmippSupported(filename))
138  return (new ImageGeneric(filename)).isVolume();
139  else
140  return isFileType(filename, VOLUMES);
141  } catch (Exception ex) {
142  return isFileType(filename, VOLUMES);
143  }
144  }
xmipp.jni.Filename.isXmippSupported
static boolean isXmippSupported(String filename)
Definition: Filename.java:502
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xmipp.jni.Filename.VOLUMES
static final String [] VOLUMES
Definition: Filename.java:64
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◆ isVolumeExt()

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static boolean xmipp.jni.Filename.isVolumeExt (String filename)
- 		-inlinestatic
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Definition at line 146 of file Filename.java.

-
146  {
147  return filename != null && isFileType(filename, VOLUMES);
148  }
xmipp.jni.Filename.VOLUMES
static final String [] VOLUMES
Definition: Filename.java:64
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◆ isXmippSupported()

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static boolean xmipp.jni.Filename.isXmippSupported (String filename)
- 		-inlinestatic
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- -

Definition at line 502 of file Filename.java.

-
502  {
503  return isFileType(filename, XMIPP_SUPPORTED);
504  }
xmipp.jni.Filename.XMIPP_SUPPORTED
static final String [] XMIPP_SUPPORTED
Definition: Filename.java:78
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◆ join()

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static String xmipp.jni.Filename.join (String... paths)
- 		-inlinestatic
-
-

Join a set of paths

- -

Definition at line 473 of file Filename.java.

-
473  {
474  String joined = paths[0];
475  for (int i = 1; i < paths.length; ++i) {
476  if (!joined.endsWith(File.separator))
477  joined += File.separator;
478  joined += paths[i];
479  }
480  return joined;
481  }
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◆ putExtension()

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static String xmipp.jni.Filename.putExtension (String file,
String ext 
)
- 		-inlinestatic
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- -

Definition at line 492 of file Filename.java.

-
493  {
494  int sepindex = file.lastIndexOf(".");//-1 if separator does not exists
495  if(sepindex == -1)
496  return file + "." + ext;
497  String part1 = file.substring(0, sepindex);
498  return part1 + "." + ext;
499 
500  }
-
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◆ removeExtension()

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static String xmipp.jni.Filename.removeExtension (String path)
- 		-inlinestatic
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- -

Definition at line 465 of file Filename.java.

-
465  {
466  int index = path.lastIndexOf(".");
467  if (index != -1)
468  path = path.substring(0, index);
469  return path;
470  }
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◆ removePrefix()

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static String xmipp.jni.Filename.removePrefix (String filename)
- 		-inlinestatic
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Definition at line 373 of file Filename.java.

-
373  {
374  String prefix = getPrefix(filename);
375  if (prefix == null)
376  return filename;
377  else
378  return filename.split(SEPARATOR)[1];
379  }
xmipp.jni.Filename.getPrefix
static String getPrefix(String filename)
Definition: Filename.java:339
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xmipp.jni.Filename.SEPARATOR
static final String SEPARATOR
Definition: Filename.java:8
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Member Data Documentation

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◆ EXT_BOX

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final String xmipp.jni.Filename.EXT_BOX = ".box"
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Definition at line 52 of file Filename.java.

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◆ EXT_CTFDAT

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final String xmipp.jni.Filename.EXT_CTFDAT = ".ctfdat"
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Definition at line 45 of file Filename.java.

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◆ EXT_CTFPARAM

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final String xmipp.jni.Filename.EXT_CTFPARAM = ".ctfparam"
- 		-static
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Definition at line 44 of file Filename.java.

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◆ EXT_DM3

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final String xmipp.jni.Filename.EXT_DM3 = ".dm3"
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Definition at line 24 of file Filename.java.

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◆ EXT_DM4

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final String xmipp.jni.Filename.EXT_DM4 = ".dm4"
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Definition at line 25 of file Filename.java.

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◆ EXT_DOC

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final String xmipp.jni.Filename.EXT_DOC = ".doc"
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Definition at line 43 of file Filename.java.

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◆ EXT_EM

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final String xmipp.jni.Filename.EXT_EM = ".em"
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Definition at line 26 of file Filename.java.

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◆ EXT_EMS

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final String xmipp.jni.Filename.EXT_EMS = ".ems"
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Definition at line 27 of file Filename.java.

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◆ EXT_ERR

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final String xmipp.jni.Filename.EXT_ERR = ".err"
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Definition at line 49 of file Filename.java.

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◆ EXT_H5

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final String xmipp.jni.Filename.EXT_H5 = ".h5"
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Definition at line 38 of file Filename.java.

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◆ EXT_HDF

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final String xmipp.jni.Filename.EXT_HDF = ".hdf"
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Definition at line 36 of file Filename.java.

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◆ EXT_HDF5

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final String xmipp.jni.Filename.EXT_HDF5 = ".hdf5"
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Definition at line 37 of file Filename.java.

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◆ EXT_HED

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final String xmipp.jni.Filename.EXT_HED = ".hed"
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Definition at line 22 of file Filename.java.

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◆ EXT_IMG

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final String xmipp.jni.Filename.EXT_IMG = ".img"
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Definition at line 21 of file Filename.java.

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◆ EXT_INF

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final String xmipp.jni.Filename.EXT_INF = ".inf"
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Definition at line 30 of file Filename.java.

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◆ EXT_JPG

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final String xmipp.jni.Filename.EXT_JPG = ".jpg"
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Definition at line 33 of file Filename.java.

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◆ EXT_LOG

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final String xmipp.jni.Filename.EXT_LOG = ".log"
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Definition at line 47 of file Filename.java.

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◆ EXT_MRC

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final String xmipp.jni.Filename.EXT_MRC = ".mrc"
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Definition at line 14 of file Filename.java.

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◆ EXT_MRC2

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final String xmipp.jni.Filename.EXT_MRC2 = ".map"
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Definition at line 15 of file Filename.java.

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◆ EXT_MRCREC

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final String xmipp.jni.Filename.EXT_MRCREC = ".rec"
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Definition at line 18 of file Filename.java.

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◆ EXT_MRCS

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final String xmipp.jni.Filename.EXT_MRCS = ".mrcs"
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Definition at line 16 of file Filename.java.

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◆ EXT_MRCS2

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final String xmipp.jni.Filename.EXT_MRCS2 = ".st"
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Definition at line 17 of file Filename.java.

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◆ EXT_MRCSALI

- -
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final String xmipp.jni.Filename.EXT_MRCSALI = ".ali"
- 		-static
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Definition at line 19 of file Filename.java.

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◆ EXT_MRCSPREALI

- -
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final String xmipp.jni.Filename.EXT_MRCSPREALI = ".preali"
- 		-static
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Definition at line 20 of file Filename.java.

- -
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◆ EXT_OUT

- -
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final String xmipp.jni.Filename.EXT_OUT = ".out"
- 		-static
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Definition at line 48 of file Filename.java.

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final String xmipp.jni.Filename.EXT_PIF = ".pif"
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Definition at line 28 of file Filename.java.

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final String xmipp.jni.Filename.EXT_PNG = ".png"
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Definition at line 34 of file Filename.java.

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final String xmipp.jni.Filename.EXT_POS = ".pos"
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Definition at line 46 of file Filename.java.

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final String xmipp.jni.Filename.EXT_PSD = ".psd"
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Definition at line 35 of file Filename.java.

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Definition at line 50 of file Filename.java.

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final String xmipp.jni.Filename.EXT_RAW = ".raw"
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Definition at line 29 of file Filename.java.

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final String xmipp.jni.Filename.EXT_SEL = ".sel"
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Definition at line 42 of file Filename.java.

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Definition at line 23 of file Filename.java.

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Definition at line 31 of file Filename.java.

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Definition at line 10 of file Filename.java.

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Definition at line 32 of file Filename.java.

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Definition at line 51 of file Filename.java.

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Definition at line 12 of file Filename.java.

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Definition at line 41 of file Filename.java.

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final String xmipp.jni.Filename.EXT_XMP = ".xmp"
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Definition at line 11 of file Filename.java.

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final String [] xmipp.jni.Filename.METADATAS
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Definition at line 70 of file Filename.java.

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Definition at line 7 of file Filename.java.

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Definition at line 8 of file Filename.java.

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final String [] xmipp.jni.Filename.SINGLE_IMAGES
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= new String[] { EXT_XMP,
EXT_IMG, EXT_HED, EXT_PSD, EXT_SER, EXT_DM3, EXT_EM, EXT_PIF,
EXT_RAW, EXT_INF, EXT_SPE, EXT_SPI, EXT_TIF, EXT_MRC, EXT_MRC2, EXT_PNG, EXT_JPG }
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Definition at line 60 of file Filename.java.

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final String [] xmipp.jni.Filename.SPIDER = new String[] { EXT_SPI, EXT_VOL }
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Definition at line 73 of file Filename.java.

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final String [] xmipp.jni.Filename.STACKS
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= new String[] { EXT_MRCS, EXT_MRCS2, EXT_MRCSALI, EXT_MRCSPREALI,
EXT_STK, EXT_PIF, EXT_EMS, EXT_DM4}
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Definition at line 67 of file Filename.java.

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final String [] xmipp.jni.Filename.TEXT
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Definition at line 75 of file Filename.java.

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final String [] xmipp.jni.Filename.VOLUMES
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Definition at line 64 of file Filename.java.

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final String [] xmipp.jni.Filename.XMIPP_SUPPORTED
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= new String[]{EXT_RAW, EXT_SPI, EXT_XMP, EXT_VOL, EXT_STK, EXT_MRC, EXT_MRC2, EXT_MRCS2, EXT_MRCS,
EXT_MRCSALI, EXT_MRCSPREALI, EXT_MRCREC,
EXT_HED, EXT_IMG, EXT_INF, EXT_RAW, EXT_TIF, EXT_DM3, EXT_DM4, EXT_SER, EXT_SPE, EXT_EM, EXT_EMS, EXT_PIF, EXT_HDF, EXT_HDF5, EXT_H5, EXT_PSD}
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Definition at line 78 of file Filename.java.

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- - diff --git a/html/classxmipp_1_1jni_1_1ImageGeneric-members.html b/html/classxmipp_1_1jni_1_1ImageGeneric-members.html deleted file mode 100644 index b04d7944..00000000 --- a/html/classxmipp_1_1jni_1_1ImageGeneric-members.html +++ /dev/null @@ -1,182 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.jni.ImageGeneric Member List
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This is the complete list of members for xmipp.jni.ImageGeneric, including all inherited members.

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alignImage(ImageGeneric img)xmipp.jni.ImageGeneric
ALL_IMAGESxmipp.jni.ImageGenericstatic
ALL_SLICESxmipp.jni.ImageGenericstatic
applyAlignment(ImageGeneric img, int index, double rot, double tilt, double psi)xmipp.jni.ImageGeneric
applyGeo(double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap, double scaleFactor)xmipp.jni.ImageGeneric
applyGeo(double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap)xmipp.jni.ImageGenericinline
applyGeoMatrix(String matrixString, boolean wrap)xmipp.jni.ImageGenericinline
applyGeoMatrix(String matrixString, double scaleFactor, boolean wrap)xmipp.jni.ImageGeneric
bestShift(ImageGeneric img)xmipp.jni.ImageGeneric
Boolxmipp.jni.ImageGenericstatic
ComplexDoublexmipp.jni.ImageGenericstatic
ComplexFloatxmipp.jni.ImageGenericstatic
ComplexIntxmipp.jni.ImageGenericstatic
ComplexShortxmipp.jni.ImageGenericstatic
convert2Datatype(int dataType)xmipp.jni.ImageGeneric
convertPSD(boolean useLogarithm)xmipp.jni.ImageGeneric
Defaultxmipp.jni.ImageGenericstatic
destroy()xmipp.jni.ImageGeneric
Doublexmipp.jni.ImageGenericstatic
equal(ImageGeneric img, double accuracy)xmipp.jni.ImageGeneric
exists(String imagepath)xmipp.jni.ImageGenericinlinestatic
finalize()xmipp.jni.ImageGenericinlineprotected
FIRST_IMAGExmipp.jni.ImageGenericstatic
FIRST_SLICExmipp.jni.ImageGenericstatic
Floatxmipp.jni.ImageGenericstatic
generateImageWithTwoCTFs(MetaData md1, MetaData md2, int xdim)xmipp.jni.ImageGeneric
generatePSDCTF(MetaData md)xmipp.jni.ImageGeneric
getArrayByte(long select_image, int slice)xmipp.jni.ImageGeneric
getArrayFloat(long select_image, int slice)xmipp.jni.ImageGeneric
getArrayShort(long select_image, int slice)xmipp.jni.ImageGeneric
getDataType()xmipp.jni.ImageGeneric
getFilename()xmipp.jni.ImageGenericinline
getNDim()xmipp.jni.ImageGeneric
getPreview(ImageGeneric imgOut, int xdim, int ydim, int select_slice, long select_image)xmipp.jni.ImageGeneric
getRadialAvg(ImageGeneric radialimg)xmipp.jni.ImageGeneric
getReslice(ImageGeneric imgOut, int view)xmipp.jni.ImageGeneric
getStatistics()xmipp.jni.ImageGeneric
getUseLogarithm()xmipp.jni.ImageGenericinline
getXDim()xmipp.jni.ImageGeneric
getYDim()xmipp.jni.ImageGeneric
getZDim()xmipp.jni.ImageGeneric
ImageGeneric()xmipp.jni.ImageGenericinline
ImageGeneric(int datatype)xmipp.jni.ImageGenericinline
ImageGeneric(String filename)xmipp.jni.ImageGenericinline
Intxmipp.jni.ImageGenericstatic
isPSD()xmipp.jni.ImageGenericinline
isSingleImage()xmipp.jni.ImageGenericinline
isStack()xmipp.jni.ImageGenericinline
isStackOrVolume()xmipp.jni.ImageGenericinline
isVolume()xmipp.jni.ImageGenericinline
LastEntryxmipp.jni.ImageGenericstatic
Longxmipp.jni.ImageGenericstatic
mapFile2Write(int xDim, int yDim, int zDim, String filename, long nimage)xmipp.jni.ImageGeneric
MID_SLICExmipp.jni.ImageGenericstatic
printShape()xmipp.jni.ImageGeneric
read(int slice)xmipp.jni.ImageGenericinline
read(int width, int height, int slice)xmipp.jni.ImageGenericinline
read(int slice, long image)xmipp.jni.ImageGenericinline
read(long image)xmipp.jni.ImageGenericinline
read(int width, int height, long image)xmipp.jni.ImageGenericinline
read(int width, int height, int slice, long image)xmipp.jni.ImageGenericinline
read(String filename, boolean map)xmipp.jni.ImageGenericinline
read(String filename, int width, int height)xmipp.jni.ImageGenericinline
read(int width, int height)xmipp.jni.ImageGenericinline
readApplyGeo(String filename, MetaData metadata, long id)xmipp.jni.ImageGenericinline
readApplyGeo(String filename, MetaData metadata, long id, boolean wrap)xmipp.jni.ImageGenericinline
readApplyGeo(String filename, MetaData metadata, long id, int w, int h)xmipp.jni.ImageGenericinline
readApplyGeo(String filename, MetaData metadata, long id, int w, int h, boolean wrap)xmipp.jni.ImageGenericinline
readApplyGeo(MetaData metadata, long id, int w, int h)xmipp.jni.ImageGenericinline
readApplyGeo(MetaData metadata, long id, int w, int h, boolean wrap)xmipp.jni.ImageGenericinline
removeAlignment(ImageGeneric img, int index, double rot, double tilt, double psi)xmipp.jni.ImageGeneric
resize(int w, int h)xmipp.jni.ImageGenericinline
resize(int w, int h, int d)xmipp.jni.ImageGenericinline
resize(int h, int w, int d, long n)xmipp.jni.ImageGeneric
reslice(int view)xmipp.jni.ImageGeneric
SCharxmipp.jni.ImageGenericstatic
setArrayByte(byte data[], long select_image, int slice)xmipp.jni.ImageGeneric
setArrayFloat(float data[], long select_image, int slice)xmipp.jni.ImageGeneric
setArrayShort(short data[], long select_image, int slice)xmipp.jni.ImageGeneric
setDataType(int dataType)xmipp.jni.ImageGeneric
setFilename(String filename)xmipp.jni.ImageGenericinline
setUseLogarithm(boolean useLogarithm)xmipp.jni.ImageGenericinline
setXmippOrigin()xmipp.jni.ImageGeneric
Shortxmipp.jni.ImageGenericstatic
smooth(ImageGeneric imgResult)xmipp.jni.ImageGeneric
subtract(ImageGeneric imgSubtrahend, ImageGeneric imgResult)xmipp.jni.ImageGeneric
UCharxmipp.jni.ImageGenericstatic
UHalfBytexmipp.jni.ImageGenericstatic
UIntxmipp.jni.ImageGenericstatic
ULongxmipp.jni.ImageGenericstatic
Unknown_Typexmipp.jni.ImageGenericstatic
UShortxmipp.jni.ImageGenericstatic
VIEWSxmipp.jni.ImageGenericstatic
write(String filename)xmipp.jni.ImageGeneric
X_NEGxmipp.jni.ImageGenericstatic
X_POSxmipp.jni.ImageGenericstatic
Y_NEGxmipp.jni.ImageGenericstatic
Y_POSxmipp.jni.ImageGenericstatic
Z_NEGxmipp.jni.ImageGenericstatic
Z_POSxmipp.jni.ImageGenericstatic
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-Public Member Functions | -Static Public Member Functions | -Static Public Attributes | -Protected Member Functions | -List of all members
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xmipp.jni.ImageGeneric Class Reference
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-Public Member Functions

synchronized native void destroy ()
 
 ImageGeneric () throws Exception
 
 ImageGeneric (int datatype) throws Exception
 
 ImageGeneric (String filename) throws Exception
 
void setFilename (String filename) throws Exception
 
void resize (int w, int h) throws Exception
 
void resize (int w, int h, int d) throws Exception
 
native void resize (int h, int w, int d, long n) throws Exception
 
String getFilename ()
 
native int getXDim () throws Exception
 
native int getYDim () throws Exception
 
native int getZDim () throws Exception
 
native long getNDim () throws Exception
 
native int getDataType () throws Exception
 
boolean getUseLogarithm ()
 
void setUseLogarithm (boolean useLogarithm)
 
void read (int slice) throws Exception
 
void read (int width, int height, int slice) throws Exception
 
void read (int slice, long image) throws Exception
 
void read (long image) throws Exception
 
void read (int width, int height, long image) throws Exception
 
void read (int width, int height, int slice, long image) throws Exception
 
void read (String filename, boolean map) throws Exception
 
void read (String filename, int width, int height) throws Exception
 
void read (int width, int height) throws Exception
 
void readApplyGeo (String filename, MetaData metadata, long id) throws Exception
 
void readApplyGeo (String filename, MetaData metadata, long id, boolean wrap) throws Exception
 
void readApplyGeo (String filename, MetaData metadata, long id, int w, int h) throws Exception
 
void readApplyGeo (String filename, MetaData metadata, long id, int w, int h, boolean wrap) throws Exception
 
void readApplyGeo (MetaData metadata, long id, int w, int h) throws Exception
 
void readApplyGeo (MetaData metadata, long id, int w, int h, boolean wrap) throws Exception
 
native byte [] getArrayByte (long select_image, int slice) throws Exception
 
native short [] getArrayShort (long select_image, int slice) throws Exception
 
native float [] getArrayFloat (long select_image, int slice) throws Exception
 
native void setArrayByte (byte data[], long select_image, int slice) throws Exception
 
native void setArrayShort (short data[], long select_image, int slice) throws Exception
 
native void setArrayFloat (float data[], long select_image, int slice) throws Exception
 
final native void setDataType (int dataType) throws Exception
 
final native void convert2Datatype (int dataType) throws Exception
 
native void mapFile2Write (int xDim, int yDim, int zDim, String filename, long nimage) throws Exception
 
native void write (String filename) throws Exception
 
native void printShape () throws Exception
 
native double [] getStatistics () throws Exception
 
native void setXmippOrigin () throws Exception
 
native void convertPSD (boolean useLogarithm) throws Exception
 
native void generatePSDCTF (MetaData md) throws Exception
 
native void generateImageWithTwoCTFs (MetaData md1, MetaData md2, int xdim) throws Exception
 
native void getReslice (ImageGeneric imgOut, int view) throws Exception
 
native void reslice (int view) throws Exception
 
native void getPreview (ImageGeneric imgOut, int xdim, int ydim, int select_slice, long select_image) throws Exception
 
synchronized native double [] alignImage (ImageGeneric img) throws Exception
 
synchronized native void getRadialAvg (ImageGeneric radialimg) throws Exception
 
native void applyAlignment (ImageGeneric img, int index, double rot, double tilt, double psi) throws Exception
 
native void removeAlignment (ImageGeneric img, int index, double rot, double tilt, double psi) throws Exception
 
native Particle bestShift (ImageGeneric img) throws Exception
 
native boolean equal (ImageGeneric img, double accuracy) throws Exception
 
native void subtract (ImageGeneric imgSubtrahend, ImageGeneric imgResult) throws Exception
 
native void smooth (ImageGeneric imgResult) throws Exception
 
boolean isPSD ()
 
boolean isStack () throws Exception
 
boolean isVolume () throws Exception
 
boolean isStackOrVolume () throws Exception
 
boolean isSingleImage () throws Exception
 
native void applyGeo (double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap, double scaleFactor)
 
void applyGeo (double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap)
 
void applyGeoMatrix (String matrixString, boolean wrap)
 
native void applyGeoMatrix (String matrixString, double scaleFactor, boolean wrap)
 
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-Static Public Member Functions

static boolean exists (String imagepath)
 
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-Static Public Attributes

static final long FIRST_IMAGE = 1
 
static final int FIRST_SLICE = 1
 
static final long ALL_IMAGES = 0
 
static final int ALL_SLICES = 0
 
static final int MID_SLICE = -1
 
static final int Default = -1
 
static final int Unknown_Type = 0
 
static final int UChar = 1
 
static final int SChar = 2
 
static final int UShort = 3
 
static final int Short = 4
 
static final int UInt = 5
 
static final int Int = 6
 
static final int ULong = 7
 
static final int Long = 8
 
static final int Float = 9
 
static final int Double = 10
 
static final int ComplexShort = 11
 
static final int ComplexInt = 12
 
static final int ComplexFloat = 13
 
static final int ComplexDouble = 14
 
static final int Bool = 15
 
static final int UHalfByte = 16
 
static final int LastEntry = 17
 
static final int Z_NEG = 0
 
static final int Z_POS = 1
 
static final int Y_NEG = 2
 
static final int Y_POS = 3
 
static final int X_NEG = 4
 
static final int X_POS = 5
 
static final int VIEWS [] = {Z_NEG, Y_NEG, X_NEG, Y_POS, X_POS }
 
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-Protected Member Functions

void finalize () throws Throwable
 
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Detailed Description

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Definition at line 5 of file ImageGeneric.java.

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Constructor & Destructor Documentation

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◆ ImageGeneric() [1/3]

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Definition at line 68 of file ImageGeneric.java.

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Definition at line 72 of file ImageGeneric.java.

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73  this();
74 
75  setDataType(datatype);
76  }
xmipp.jni.ImageGeneric.setDataType
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Definition at line 78 of file ImageGeneric.java.

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78  {
79  this();
80  setFilename(filename);
81 
82  }
xmipp.jni.ImageGeneric.setFilename
void setFilename(String filename)
Definition: ImageGeneric.java:85
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◆ alignImage()

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synchronized native double [] xmipp.jni.ImageGeneric.alignImage (ImageGeneric img) throws Exception
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◆ applyAlignment()

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native void xmipp.jni.ImageGeneric.applyAlignment (ImageGeneric img,
int index,
double rot,
double tilt,
double psi 
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native void xmipp.jni.ImageGeneric.applyGeo (double shiftX,
double shiftY,
double anglepsi,
boolean flip,
boolean wrap,
double scaleFactor 
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void xmipp.jni.ImageGeneric.applyGeo (double shiftX,
double shiftY,
double anglepsi,
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Definition at line 318 of file ImageGeneric.java.

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319  {
320  applyGeo(shiftX, shiftY, anglepsi, flip, wrap, 1.);
321  }
xmipp.jni.ImageGeneric.applyGeo
native void applyGeo(double shiftX, double shiftY, double anglepsi, boolean flip, boolean wrap, double scaleFactor)
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void xmipp.jni.ImageGeneric.applyGeoMatrix (String matrixString,
boolean wrap 
)
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Same as previous function, but reading the geometry information from the transformation matrix. The matrix will be passed to the binding in its string representation read from the sqlite file.

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Definition at line 328 of file ImageGeneric.java.

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329  {
330  applyGeoMatrix(matrixString, 1, wrap);
331  }
xmipp.jni.ImageGeneric.applyGeoMatrix
void applyGeoMatrix(String matrixString, boolean wrap)
Definition: ImageGeneric.java:328
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native void xmipp.jni.ImageGeneric.applyGeoMatrix (String matrixString,
double scaleFactor,
boolean wrap 
)
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◆ bestShift()

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native Particle xmipp.jni.ImageGeneric.bestShift (ImageGeneric img) throws Exception
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◆ convert2Datatype()

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final native void xmipp.jni.ImageGeneric.convert2Datatype (int dataType) throws Exception
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◆ convertPSD()

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native void xmipp.jni.ImageGeneric.convertPSD (boolean useLogarithm) throws Exception
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◆ destroy()

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◆ equal()

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native boolean xmipp.jni.ImageGeneric.equal (ImageGeneric img,
double accuracy 
) throws Exception
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◆ exists()

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static boolean xmipp.jni.ImageGeneric.exists (String imagepath)
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Definition at line 291 of file ImageGeneric.java.

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292  {
293  if(imagepath == null || imagepath.isEmpty())
294  return false;
295  String prefix = Filename.getPrefix(imagepath);
296  if(prefix == null)
297  return new File(imagepath).exists();
298  try
299  {
300 
301  int index = Integer.parseInt(prefix);
302  String file = Filename.removePrefix(imagepath);
303  ImageGeneric ig = new ImageGeneric(file);
304  ig.readHeader(file);
305  if(index < 0 || index > ig.getNDim())
306  return false;
307  return true;
308 
309  }
310  catch (Exception e)
311  {
312  return false;
313  }
314  }
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◆ finalize()

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void xmipp.jni.ImageGeneric.finalize () throws Throwable
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Definition at line 286 of file ImageGeneric.java.

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286  {
287  super.finalize();
288  destroy();
289  }
xmipp.jni.ImageGeneric.destroy
synchronized native void destroy()
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◆ generateImageWithTwoCTFs()

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native void xmipp.jni.ImageGeneric.generateImageWithTwoCTFs (MetaData md1,
MetaData md2,
int xdim 
) throws Exception
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◆ generatePSDCTF()

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native void xmipp.jni.ImageGeneric.generatePSDCTF (MetaData md) throws Exception
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◆ getArrayByte()

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native byte [] xmipp.jni.ImageGeneric.getArrayByte (long select_image,
int slice 
) throws Exception
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◆ getArrayFloat()

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native float [] xmipp.jni.ImageGeneric.getArrayFloat (long select_image,
int slice 
) throws Exception
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◆ getArrayShort()

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native short [] xmipp.jni.ImageGeneric.getArrayShort (long select_image,
int slice 
) throws Exception
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◆ getDataType()

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native int xmipp.jni.ImageGeneric.getDataType () throws Exception
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◆ getFilename()

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String xmipp.jni.ImageGeneric.getFilename ()
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Definition at line 100 of file ImageGeneric.java.

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100  {
101  return filename;
102  }
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◆ getNDim()

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native long xmipp.jni.ImageGeneric.getNDim () throws Exception
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◆ getPreview()

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native void xmipp.jni.ImageGeneric.getPreview (ImageGeneric imgOut,
int xdim,
int ydim,
int select_slice,
long select_image 
) throws Exception
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◆ getRadialAvg()

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synchronized native void xmipp.jni.ImageGeneric.getRadialAvg (ImageGeneric radialimg) throws Exception
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◆ getReslice()

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native void xmipp.jni.ImageGeneric.getReslice (ImageGeneric imgOut,
int view 
) throws Exception
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◆ getStatistics()

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native double [] xmipp.jni.ImageGeneric.getStatistics () throws Exception
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◆ getUseLogarithm()

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boolean xmipp.jni.ImageGeneric.getUseLogarithm ()
- 		-inline
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Definition at line 114 of file ImageGeneric.java.

-
114  {
115  return useLogarithm;
116  }
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◆ getXDim()

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native int xmipp.jni.ImageGeneric.getXDim () throws Exception
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◆ getYDim()

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native int xmipp.jni.ImageGeneric.getYDim () throws Exception
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◆ getZDim()

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native int xmipp.jni.ImageGeneric.getZDim () throws Exception
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◆ isPSD()

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boolean xmipp.jni.ImageGeneric.isPSD ()
- 		-inline
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Definition at line 263 of file ImageGeneric.java.

-
263  {
264  return Filename.isPSD(filename);
265  }
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◆ isSingleImage()

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boolean xmipp.jni.ImageGeneric.isSingleImage () throws Exception
- 		-inline
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Definition at line 279 of file ImageGeneric.java.

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279  {
280  return !isStackOrVolume();
281  }
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◆ isStack()

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boolean xmipp.jni.ImageGeneric.isStack () throws Exception
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Definition at line 267 of file ImageGeneric.java.

-
267  {
268  return getNDim() > 1;
269  }
xmipp.jni.ImageGeneric.getNDim
native long getNDim()
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◆ isStackOrVolume()

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boolean xmipp.jni.ImageGeneric.isStackOrVolume () throws Exception
- 		-inline
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Definition at line 275 of file ImageGeneric.java.

-
275  {
276  return isStack() || isVolume();
277  }
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◆ isVolume()

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boolean xmipp.jni.ImageGeneric.isVolume () throws Exception
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Definition at line 271 of file ImageGeneric.java.

-
271  {
272  return getZDim() > 1;
273  }
xmipp.jni.ImageGeneric.getZDim
native int getZDim()
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◆ mapFile2Write()

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native void xmipp.jni.ImageGeneric.mapFile2Write (int xDim,
int yDim,
int zDim,
String filename,
long nimage 
) throws Exception
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◆ printShape()

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native void xmipp.jni.ImageGeneric.printShape () throws Exception
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◆ read() [1/9]

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void xmipp.jni.ImageGeneric.read (int slice) throws Exception
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Definition at line 126 of file ImageGeneric.java.

-
126  {
127  read(slice, FIRST_IMAGE);
128  }
xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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◆ read() [2/9]

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void xmipp.jni.ImageGeneric.read (int width,
int height,
int slice 
) throws Exception
- 		-inline
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Definition at line 130 of file ImageGeneric.java.

-
130  {
131  read(width, height, slice, FIRST_IMAGE);
132  }
xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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◆ read() [3/9]

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void xmipp.jni.ImageGeneric.read (int slice,
long image 
) throws Exception
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Definition at line 134 of file ImageGeneric.java.

-
134  {
135  read(getXDim(), getYDim(), slice, image);
136  }
xmipp.jni.ImageGeneric.getYDim
native int getYDim()
-
xmipp.jni.ImageGeneric.getXDim
native int getXDim()
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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◆ read() [4/9]

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void xmipp.jni.ImageGeneric.read (long image) throws Exception
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Definition at line 138 of file ImageGeneric.java.

-
138  {
139  read(ALL_SLICES, image);
140  }
xmipp.jni.ImageGeneric.ALL_SLICES
static final int ALL_SLICES
Definition: ImageGeneric.java:11
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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◆ read() [5/9]

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void xmipp.jni.ImageGeneric.read (int width,
int height,
long image 
) throws Exception
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Definition at line 142 of file ImageGeneric.java.

-
142  {
143  read(width, height, ALL_SLICES, image);
144  }
xmipp.jni.ImageGeneric.ALL_SLICES
static final int ALL_SLICES
Definition: ImageGeneric.java:11
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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◆ read() [6/9]

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void xmipp.jni.ImageGeneric.read (int width,
int height,
int slice,
long image 
) throws Exception
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Definition at line 146 of file ImageGeneric.java.

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146  {
147  read(filename, width, height, slice, image, true);
148  // At this moment we don't know why
149 // read(Filename.getFilename(filename), width, height, slice, image, true);
150  }
xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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◆ read() [7/9]

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void xmipp.jni.ImageGeneric.read (String filename,
boolean map 
) throws Exception
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Definition at line 152 of file ImageGeneric.java.

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152  {
153  setFilename(filename);
154  read(filename, getXDim(), getYDim(), MID_SLICE, ALL_IMAGES, map);//image in filename will be used
155  }
xmipp.jni.ImageGeneric.getYDim
native int getYDim()
-
xmipp.jni.ImageGeneric.getXDim
native int getXDim()
-
xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.ImageGeneric.ALL_IMAGES
static final long ALL_IMAGES
Definition: ImageGeneric.java:10
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xmipp.jni.ImageGeneric.setFilename
void setFilename(String filename)
Definition: ImageGeneric.java:85
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xmipp.jni.ImageGeneric.MID_SLICE
static final int MID_SLICE
Definition: ImageGeneric.java:12
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◆ read() [8/9]

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void xmipp.jni.ImageGeneric.read (String filename,
int width,
int height 
) throws Exception
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Definition at line 157 of file ImageGeneric.java.

-
157  {
158  this.filename = filename;
159  read(filename, width, height, MID_SLICE, ALL_IMAGES, true);//image in filename will be used
160  }
xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.ImageGeneric.ALL_IMAGES
static final long ALL_IMAGES
Definition: ImageGeneric.java:10
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static final int MID_SLICE
Definition: ImageGeneric.java:12
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void xmipp.jni.ImageGeneric.read (int width,
int height 
) throws Exception
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Definition at line 162 of file ImageGeneric.java.

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162  {
163  read(filename, width, height, MID_SLICE, ALL_IMAGES, true);//image in filename will be used
164  }
xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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xmipp.jni.ImageGeneric.ALL_IMAGES
static final long ALL_IMAGES
Definition: ImageGeneric.java:10
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xmipp.jni.ImageGeneric.MID_SLICE
static final int MID_SLICE
Definition: ImageGeneric.java:12
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◆ readApplyGeo() [1/6]

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void xmipp.jni.ImageGeneric.readApplyGeo (String filename,
MetaData metadata,
long id 
) throws Exception
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Definition at line 168 of file ImageGeneric.java.

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168  {
169  readApplyGeo(filename, metadata, id, true);
170  }
xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(String filename, MetaData metadata, long id)
Definition: ImageGeneric.java:168
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void xmipp.jni.ImageGeneric.readApplyGeo (String filename,
MetaData metadata,
long id,
boolean wrap 
) throws Exception
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Definition at line 172 of file ImageGeneric.java.

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172  {
173  //ImageGeneric image = new ImageGeneric(filename);
174  readHeader(filename);
175  readApplyGeo(filename, metadata, id, getXDim(), getYDim(), wrap);
176  }
xmipp.jni.ImageGeneric.readApplyGeo
void readApplyGeo(String filename, MetaData metadata, long id)
Definition: ImageGeneric.java:168
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xmipp.jni.ImageGeneric.getYDim
native int getYDim()
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◆ readApplyGeo() [3/6]

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void xmipp.jni.ImageGeneric.readApplyGeo (String filename,
MetaData metadata,
long id,
int w,
int h 
) throws Exception
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Definition at line 178 of file ImageGeneric.java.

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178  {
179  this.filename = filename;
180  readApplyGeo_(filename, metadata, id, w, h, true);
181  }
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void xmipp.jni.ImageGeneric.readApplyGeo (String filename,
MetaData metadata,
long id,
int w,
int h,
boolean wrap 
) throws Exception
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Definition at line 183 of file ImageGeneric.java.

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183  {
184  this.filename = filename;
185  readApplyGeo_(filename, metadata, id, w, h, wrap);
186  }
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void xmipp.jni.ImageGeneric.readApplyGeo (MetaData metadata,
long id,
int w,
int h 
) throws Exception
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Definition at line 188 of file ImageGeneric.java.

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188  {
189  readApplyGeo_(filename, metadata, id, w, h, true);
190  }
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void xmipp.jni.ImageGeneric.readApplyGeo (MetaData metadata,
long id,
int w,
int h,
boolean wrap 
) throws Exception
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Definition at line 192 of file ImageGeneric.java.

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192  {
193  readApplyGeo_(filename, metadata, id, w, h, wrap);
194  }
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◆ removeAlignment()

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native void xmipp.jni.ImageGeneric.removeAlignment (ImageGeneric img,
int index,
double rot,
double tilt,
double psi 
) throws Exception
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◆ resize() [1/3]

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void xmipp.jni.ImageGeneric.resize (int w,
int h 
) throws Exception
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Definition at line 90 of file ImageGeneric.java.

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90  {
91  resize(w, h, 1);
92  }
xmipp.jni.ImageGeneric.resize
void resize(int w, int h)
Definition: ImageGeneric.java:90
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void xmipp.jni.ImageGeneric.resize (int w,
int h,
int d 
) throws Exception
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Definition at line 94 of file ImageGeneric.java.

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94  {
95  resize(w, h, d, 1);
96  }
xmipp.jni.ImageGeneric.resize
void resize(int w, int h)
Definition: ImageGeneric.java:90
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◆ resize() [3/3]

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native void xmipp.jni.ImageGeneric.resize (int h,
int w,
int d,
long n 
) throws Exception
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◆ reslice()

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native void xmipp.jni.ImageGeneric.reslice (int view) throws Exception
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◆ setArrayByte()

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native void xmipp.jni.ImageGeneric.setArrayByte (byte data[],
long select_image,
int slice 
) throws Exception
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◆ setArrayFloat()

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native void xmipp.jni.ImageGeneric.setArrayFloat (float data[],
long select_image,
int slice 
) throws Exception
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◆ setArrayShort()

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native void xmipp.jni.ImageGeneric.setArrayShort (short data[],
long select_image,
int slice 
) throws Exception
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◆ setDataType()

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final native void xmipp.jni.ImageGeneric.setDataType (int dataType) throws Exception
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◆ setFilename()

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void xmipp.jni.ImageGeneric.setFilename (String filename) throws Exception
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-

Set a new filename and reload the header

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Definition at line 85 of file ImageGeneric.java.

-
85  {
86  this.filename = filename;
87  readHeader(filename);//Filename.getFilename(filename));
88  }
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◆ setUseLogarithm()

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void xmipp.jni.ImageGeneric.setUseLogarithm (boolean useLogarithm)
- 		-inline
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Definition at line 118 of file ImageGeneric.java.

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118  {
119  this.useLogarithm = useLogarithm;
120  }
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final long xmipp.jni.ImageGeneric.ALL_IMAGES = 0
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Definition at line 10 of file ImageGeneric.java.

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Definition at line 11 of file ImageGeneric.java.

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Definition at line 30 of file ImageGeneric.java.

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Definition at line 29 of file ImageGeneric.java.

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Definition at line 28 of file ImageGeneric.java.

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Definition at line 27 of file ImageGeneric.java.

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Definition at line 26 of file ImageGeneric.java.

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Definition at line 14 of file ImageGeneric.java.

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Definition at line 25 of file ImageGeneric.java.

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Definition at line 8 of file ImageGeneric.java.

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Definition at line 9 of file ImageGeneric.java.

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Definition at line 24 of file ImageGeneric.java.

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Definition at line 21 of file ImageGeneric.java.

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Definition at line 32 of file ImageGeneric.java.

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Definition at line 23 of file ImageGeneric.java.

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Definition at line 12 of file ImageGeneric.java.

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Definition at line 17 of file ImageGeneric.java.

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Definition at line 19 of file ImageGeneric.java.

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Definition at line 16 of file ImageGeneric.java.

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final int xmipp.jni.ImageGeneric.UHalfByte = 16
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Definition at line 31 of file ImageGeneric.java.

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final int xmipp.jni.ImageGeneric.UInt = 5
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Definition at line 20 of file ImageGeneric.java.

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final int xmipp.jni.ImageGeneric.ULong = 7
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Definition at line 22 of file ImageGeneric.java.

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◆ Unknown_Type

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final int xmipp.jni.ImageGeneric.Unknown_Type = 0
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Definition at line 15 of file ImageGeneric.java.

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final int xmipp.jni.ImageGeneric.UShort = 3
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Definition at line 18 of file ImageGeneric.java.

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◆ VIEWS

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final int xmipp.jni.ImageGeneric.VIEWS[] = {Z_NEG, Y_NEG, X_NEG, Y_POS, X_POS }
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Definition at line 42 of file ImageGeneric.java.

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◆ X_NEG

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final int xmipp.jni.ImageGeneric.X_NEG = 4
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Definition at line 39 of file ImageGeneric.java.

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final int xmipp.jni.ImageGeneric.X_POS = 5
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Definition at line 40 of file ImageGeneric.java.

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◆ Y_NEG

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final int xmipp.jni.ImageGeneric.Y_NEG = 2
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Definition at line 37 of file ImageGeneric.java.

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final int xmipp.jni.ImageGeneric.Y_POS = 3
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Definition at line 38 of file ImageGeneric.java.

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final int xmipp.jni.ImageGeneric.Z_NEG = 0
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Definition at line 35 of file ImageGeneric.java.

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◆ Z_POS

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final int xmipp.jni.ImageGeneric.Z_POS = 1
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Definition at line 36 of file ImageGeneric.java.

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xmipp.jni.ImageWriteMode Member List
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This is the complete list of members for xmipp.jni.ImageWriteMode, including all inherited members.

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WRITE_APPENDxmipp.jni.ImageWriteModestatic
WRITE_LAST_LABELxmipp.jni.ImageWriteModestatic
WRITE_OVERWRITExmipp.jni.ImageWriteModestatic
WRITE_READONLYxmipp.jni.ImageWriteModestatic
WRITE_REPLACExmipp.jni.ImageWriteModestatic
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xmipp.jni.ImageWriteMode Class Reference
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-Static Public Attributes

static final int WRITE_READONLY = 0
 
static final int WRITE_OVERWRITE = 1
 
static final int WRITE_REPLACE = 2
 
static final int WRITE_APPEND = 3
 
static final int WRITE_LAST_LABEL = 4
 
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Detailed Description

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Definition at line 3 of file ImageWriteMode.java.

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Member Data Documentation

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◆ WRITE_APPEND

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final int xmipp.jni.ImageWriteMode.WRITE_APPEND = 3
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Definition at line 7 of file ImageWriteMode.java.

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◆ WRITE_LAST_LABEL

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final int xmipp.jni.ImageWriteMode.WRITE_LAST_LABEL = 4
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Definition at line 8 of file ImageWriteMode.java.

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◆ WRITE_OVERWRITE

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final int xmipp.jni.ImageWriteMode.WRITE_OVERWRITE = 1
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Definition at line 5 of file ImageWriteMode.java.

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◆ WRITE_READONLY

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final int xmipp.jni.ImageWriteMode.WRITE_READONLY = 0
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Definition at line 4 of file ImageWriteMode.java.

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◆ WRITE_REPLACE

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final int xmipp.jni.ImageWriteMode.WRITE_REPLACE = 2
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Definition at line 6 of file ImageWriteMode.java.

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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1jni_1_1LinearAlgebra-members.html b/html/classxmipp_1_1jni_1_1LinearAlgebra-members.html deleted file mode 100644 index 215bd751..00000000 --- a/html/classxmipp_1_1jni_1_1LinearAlgebra-members.html +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.jni.LinearAlgebra Member List
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This is the complete list of members for xmipp.jni.LinearAlgebra, including all inherited members.

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clear()xmipp.jni.LinearAlgebra
finalize()xmipp.jni.LinearAlgebrainlineprotected
LinearAlgebra()xmipp.jni.LinearAlgebrainline
solveLinearSystem()xmipp.jni.LinearAlgebra
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xmipp.jni.LinearAlgebra Class Reference
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-Public Member Functions

native void solveLinearSystem ()
 
native void clear ()
 
 LinearAlgebra ()
 
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-Protected Member Functions

void finalize () throws Throwable
 
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Detailed Description

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Definition at line 3 of file LinearAlgebra.java.

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Constructor & Destructor Documentation

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◆ LinearAlgebra()

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xmipp.jni.LinearAlgebra.LinearAlgebra ()
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Definition at line 29 of file LinearAlgebra.java.

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30  {
31  create();
32  }
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◆ clear()

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native void xmipp.jni.LinearAlgebra.clear ()
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◆ finalize()

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void xmipp.jni.LinearAlgebra.finalize () throws Throwable
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Definition at line 36 of file LinearAlgebra.java.

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37  {
38  super.finalize();
39  destroy();
40  }
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◆ solveLinearSystem()

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native void xmipp.jni.LinearAlgebra.solveLinearSystem ()
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xmipp.jni.MDLabel Member List
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This is the complete list of members for xmipp.jni.MDLabel, including all inherited members.

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MDL_ANGLE_DIFFxmipp.jni.MDLabelstatic
MDL_ANGLE_DIFF0xmipp.jni.MDLabelstatic
MDL_ANGLE_DIFF2xmipp.jni.MDLabelstatic
MDL_ANGLE_PSIxmipp.jni.MDLabelstatic
MDL_ANGLE_PSI2xmipp.jni.MDLabelstatic
MDL_ANGLE_PSI3xmipp.jni.MDLabelstatic
MDL_ANGLE_PSI_DIFFxmipp.jni.MDLabelstatic
MDL_ANGLE_ROTxmipp.jni.MDLabelstatic
MDL_ANGLE_ROT2xmipp.jni.MDLabelstatic
MDL_ANGLE_ROT3xmipp.jni.MDLabelstatic
MDL_ANGLE_ROT_DIFFxmipp.jni.MDLabelstatic
MDL_ANGLE_TEMPERATURExmipp.jni.MDLabelstatic
MDL_ANGLE_TILTxmipp.jni.MDLabelstatic
MDL_ANGLE_TILT2xmipp.jni.MDLabelstatic
MDL_ANGLE_TILT3xmipp.jni.MDLabelstatic
MDL_ANGLE_TILT_DIFFxmipp.jni.MDLabelstatic
MDL_ANGLE_Yxmipp.jni.MDLabelstatic
MDL_ANGLE_Y2xmipp.jni.MDLabelstatic
MDL_APPLY_SHIFTxmipp.jni.MDLabelstatic
MDL_ASSIGNED_DIR_REF_CCxmipp.jni.MDLabelstatic
MDL_AVGxmipp.jni.MDLabelstatic
MDL_AVG_CHANGES_CLASSESxmipp.jni.MDLabelstatic
MDL_AVG_CHANGES_OFFSETSxmipp.jni.MDLabelstatic
MDL_AVG_CHANGES_ORIENTATIONSxmipp.jni.MDLabelstatic
MDL_AVGPMAXxmipp.jni.MDLabelstatic
MDL_BFACTORxmipp.jni.MDLabelstatic
MDL_BGMEANxmipp.jni.MDLabelstatic
MDL_BLOCK_NUMBERxmipp.jni.MDLabelstatic
MDL_CL2D_CHANGESxmipp.jni.MDLabelstatic
MDL_CL2D_SIMILARITYxmipp.jni.MDLabelstatic
MDL_CLASS_COUNTxmipp.jni.MDLabelstatic
MDL_CLASS_INTERSECTION_RELATIVE_SIZE_PVALUExmipp.jni.MDLabelstatic
MDL_CLASS_INTERSECTION_SIZE_PVALUExmipp.jni.MDLabelstatic
MDL_CLASS_PERCENTAGExmipp.jni.MDLabelstatic
MDL_CLASSIFICATION_DATAxmipp.jni.MDLabelstatic
MDL_CLASSIFICATION_DATA_SIZExmipp.jni.MDLabelstatic
MDL_CLASSIFICATION_DPR_05xmipp.jni.MDLabelstatic
MDL_CLASSIFICATION_FRC_05xmipp.jni.MDLabelstatic
MDL_CLASSIFICATION_INTRACLASS_DISTANCExmipp.jni.MDLabelstatic
MDL_COLORxmipp.jni.MDLabelstatic
MDL_COMMENTxmipp.jni.MDLabelstatic
MDL_CONTINUOUS_FLIPxmipp.jni.MDLabelstatic
MDL_CONTINUOUS_GRAY_Axmipp.jni.MDLabelstatic
MDL_CONTINUOUS_GRAY_Bxmipp.jni.MDLabelstatic
MDL_CONTINUOUS_SCALE_ANGLExmipp.jni.MDLabelstatic
MDL_CONTINUOUS_SCALE_Xxmipp.jni.MDLabelstatic
MDL_CONTINUOUS_SCALE_Yxmipp.jni.MDLabelstatic
MDL_CONTINUOUS_Xxmipp.jni.MDLabelstatic
MDL_CONTINUOUS_Yxmipp.jni.MDLabelstatic
MDL_COORD_CONSENSUS_SCORExmipp.jni.MDLabelstatic
MDL_CORR_DENOISED_NOISYxmipp.jni.MDLabelstatic
MDL_CORR_DENOISED_PROJECTIONxmipp.jni.MDLabelstatic
MDL_CORRELATION_IDXxmipp.jni.MDLabelstatic
MDL_CORRELATION_MASKxmipp.jni.MDLabelstatic
MDL_CORRELATION_WEIGHTxmipp.jni.MDLabelstatic
MDL_COSTxmipp.jni.MDLabelstatic
MDL_COST_PERCENTILExmipp.jni.MDLabelstatic
MDL_COUNTxmipp.jni.MDLabelstatic
MDL_COUNT2xmipp.jni.MDLabelstatic
MDL_CRYSTAL_CELLXxmipp.jni.MDLabelstatic
MDL_CRYSTAL_CELLYxmipp.jni.MDLabelstatic
MDL_CRYSTAL_DISAPPEAR_THRExmipp.jni.MDLabelstatic
MDL_CRYSTAL_LATTICE_Axmipp.jni.MDLabelstatic
MDL_CRYSTAL_LATTICE_Bxmipp.jni.MDLabelstatic
MDL_CRYSTAL_NOISE_SHIFTxmipp.jni.MDLabelstatic
MDL_CRYSTAL_ORTHO_PRJxmipp.jni.MDLabelstatic
MDL_CRYSTAL_PROJxmipp.jni.MDLabelstatic
MDL_CRYSTAL_SHFILExmipp.jni.MDLabelstatic
MDL_CRYSTAL_SHIFTXxmipp.jni.MDLabelstatic
MDL_CRYSTAL_SHIFTYxmipp.jni.MDLabelstatic
MDL_CRYSTAL_SHIFTZxmipp.jni.MDLabelstatic
MDL_CTF_BG_BASELINExmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN2_ANGLExmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN2_CUxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN2_CVxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN2_Kxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN2_SIGMAUxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN2_SIGMAVxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN_ANGLExmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN_CUxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN_CVxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN_Kxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN_SIGMAUxmipp.jni.MDLabelstatic
MDL_CTF_BG_GAUSSIAN_SIGMAVxmipp.jni.MDLabelstatic
MDL_CTF_BG_R1xmipp.jni.MDLabelstatic
MDL_CTF_BG_R2xmipp.jni.MDLabelstatic
MDL_CTF_BG_R3xmipp.jni.MDLabelstatic
MDL_CTF_BG_SQRT_ANGLExmipp.jni.MDLabelstatic
MDL_CTF_BG_SQRT_Kxmipp.jni.MDLabelstatic
MDL_CTF_BG_SQRT_Uxmipp.jni.MDLabelstatic
MDL_CTF_BG_SQRT_Vxmipp.jni.MDLabelstatic
MDL_CTF_CAxmipp.jni.MDLabelstatic
MDL_CTF_CONVERGENCE_CONExmipp.jni.MDLabelstatic
MDL_CTF_CORRECTEDxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_DAMPINGxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_DIFF_RATIOxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_RATIOxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_FIRSTZEROAVGxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_FIRSTZERODISAGREEMENTxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_FIRSTZERORATIOxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_FITTINGCORR13xmipp.jni.MDLabelstatic
MDL_CTF_CRIT_FITTINGSCORExmipp.jni.MDLabelstatic
MDL_CTF_CRIT_ICENESSxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_MAXFREQxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_NONASTIGMATICVALIDITYxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_NORMALITYxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_PSDCORRELATION90xmipp.jni.MDLabelstatic
MDL_CTF_CRIT_PSDPCA1VARIANCExmipp.jni.MDLabelstatic
MDL_CTF_CRIT_PSDPCARUNSTESTxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_PSDRADIALINTEGRALxmipp.jni.MDLabelstatic
MDL_CTF_CRIT_PSDVARIANCExmipp.jni.MDLabelstatic
MDL_CTF_CSxmipp.jni.MDLabelstatic
MDL_CTF_DATA_PHASE_FLIPPEDxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_ANGLExmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_CHANGExmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_COEFSxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_PLANEUAxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_PLANEUBxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_PLANEUCxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_PLANEVAxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_PLANEVBxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_PLANEVCxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_R2xmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUS_RESIDUALxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUSAxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUSUxmipp.jni.MDLabelstatic
MDL_CTF_DEFOCUSVxmipp.jni.MDLabelstatic
MDL_CTF_DIMENSIONSxmipp.jni.MDLabelstatic
MDL_CTF_DOWNSAMPLE_PERFORMEDxmipp.jni.MDLabelstatic
MDL_CTF_ENERGY_LOSSxmipp.jni.MDLabelstatic
MDL_CTF_ENV_R0xmipp.jni.MDLabelstatic
MDL_CTF_ENV_R1xmipp.jni.MDLabelstatic
MDL_CTF_ENV_R2xmipp.jni.MDLabelstatic
MDL_CTF_ENVELOPExmipp.jni.MDLabelstatic
MDL_CTF_ENVELOPE_PLOTxmipp.jni.MDLabelstatic
MDL_CTF_GROUPxmipp.jni.MDLabelstatic
MDL_CTF_INPUTPARAMSxmipp.jni.MDLabelstatic
MDL_CTF_Kxmipp.jni.MDLabelstatic
MDL_CTF_LAMBDAxmipp.jni.MDLabelstatic
MDL_CTF_LENS_STABILITYxmipp.jni.MDLabelstatic
MDL_CTF_LONGITUDINAL_DISPLACEMENTxmipp.jni.MDLabelstatic
MDL_CTF_MODELxmipp.jni.MDLabelstatic
MDL_CTF_MODEL2xmipp.jni.MDLabelstatic
MDL_CTF_PHASE_SHIFTxmipp.jni.MDLabelstatic
MDL_CTF_Q0xmipp.jni.MDLabelstatic
MDL_CTF_SAMPLING_RATExmipp.jni.MDLabelstatic
MDL_CTF_SAMPLING_RATE_Zxmipp.jni.MDLabelstatic
MDL_CTF_TRANSVERSAL_DISPLACEMENTxmipp.jni.MDLabelstatic
MDL_CTF_VOLTAGExmipp.jni.MDLabelstatic
MDL_CTF_VPP_RADIUSxmipp.jni.MDLabelstatic
MDL_CTF_X0xmipp.jni.MDLabelstatic
MDL_CTF_XFxmipp.jni.MDLabelstatic
MDL_CTF_XRAY_LENS_TYPExmipp.jni.MDLabelstatic
MDL_CTF_XRAY_OUTER_ZONE_WIDTHxmipp.jni.MDLabelstatic
MDL_CTF_XRAY_ZONES_NUMBERxmipp.jni.MDLabelstatic
MDL_CTF_Y0xmipp.jni.MDLabelstatic
MDL_CTF_YFxmipp.jni.MDLabelstatic
MDL_CUMULATIVE_SSNRxmipp.jni.MDLabelstatic
MDL_DATATYPExmipp.jni.MDLabelstatic
MDL_DATExmipp.jni.MDLabelstatic
MDL_DEFGROUPxmipp.jni.MDLabelstatic
MDL_DIMENSIONS_2Dxmipp.jni.MDLabelstatic
MDL_DIMENSIONS_3Dxmipp.jni.MDLabelstatic
MDL_DIMREDxmipp.jni.MDLabelstatic
MDL_DIRECTIONxmipp.jni.MDLabelstatic
MDL_DM3_IDTAGxmipp.jni.MDLabelstatic
MDL_DM3_NODEIDxmipp.jni.MDLabelstatic
MDL_DM3_NUMBER_TYPExmipp.jni.MDLabelstatic
MDL_DM3_PARENTIDxmipp.jni.MDLabelstatic
MDL_DM3_SIZExmipp.jni.MDLabelstatic
MDL_DM3_TAGCLASSxmipp.jni.MDLabelstatic
MDL_DM3_TAGNAMExmipp.jni.MDLabelstatic
MDL_DM3_VALUExmipp.jni.MDLabelstatic
MDL_DOSExmipp.jni.MDLabelstatic
MDL_ENABLEDxmipp.jni.MDLabelstatic
MDL_FIRST_LABELxmipp.jni.MDLabelstatic
MDL_FLIPxmipp.jni.MDLabelstatic
MDL_FOMxmipp.jni.MDLabelstatic
MDL_FRAME_IDxmipp.jni.MDLabelstatic
MDL_GATHER_IDxmipp.jni.MDLabelstatic
MDL_GOOD_REGION_SCORExmipp.jni.MDLabelstatic
MDL_GRAPH_CCxmipp.jni.MDLabelstatic
MDL_GRAPH_CC_PREVIOUSxmipp.jni.MDLabelstatic
MDL_GRAPH_DISTANCE2MAXxmipp.jni.MDLabelstatic
MDL_GRAPH_DISTANCE2MAX_PREVIOUSxmipp.jni.MDLabelstatic
MDL_HALF1xmipp.jni.MDLabelstatic
MDL_HALF2xmipp.jni.MDLabelstatic
MDL_IDXxmipp.jni.MDLabelstatic
MDL_IMAGExmipp.jni.MDLabelstatic
MDL_IMAGE1xmipp.jni.MDLabelstatic
MDL_IMAGE2xmipp.jni.MDLabelstatic
MDL_IMAGE3xmipp.jni.MDLabelstatic
MDL_IMAGE4xmipp.jni.MDLabelstatic
MDL_IMAGE5xmipp.jni.MDLabelstatic
MDL_IMAGE_COVARIANCExmipp.jni.MDLabelstatic
MDL_IMAGE_IDXxmipp.jni.MDLabelstatic
MDL_IMAGE_ORIGINALxmipp.jni.MDLabelstatic
MDL_IMAGE_REFxmipp.jni.MDLabelstatic
MDL_IMAGE_RESIDUALxmipp.jni.MDLabelstatic
MDL_IMAGE_TILTEDxmipp.jni.MDLabelstatic
MDL_IMEDxmipp.jni.MDLabelstatic
MDL_IMGMDxmipp.jni.MDLabelstatic
MDL_INTSCALExmipp.jni.MDLabelstatic
MDL_ITEM_IDxmipp.jni.MDLabelstatic
MDL_ITERxmipp.jni.MDLabelstatic
MDL_KERDENSOM_FUNCTIONALxmipp.jni.MDLabelstatic
MDL_KERDENSOM_REGULARIZATIONxmipp.jni.MDLabelstatic
MDL_KERDENSOM_SIGMAxmipp.jni.MDLabelstatic
MDL_KEYWORDSxmipp.jni.MDLabelstatic
MDL_KMEANS2D_CENTROIDxmipp.jni.MDLabelstatic
MDL_KSTESTxmipp.jni.MDLabelstatic
MDL_LAST_LABELxmipp.jni.MDLabelstatic
MDL_LLxmipp.jni.MDLabelstatic
MDL_LOCAL_ALIGNMENT_COEFFS_Xxmipp.jni.MDLabelstatic
MDL_LOCAL_ALIGNMENT_COEFFS_Yxmipp.jni.MDLabelstatic
MDL_LOCAL_ALIGNMENT_CONF_2_5_PERCxmipp.jni.MDLabelstatic
MDL_LOCAL_ALIGNMENT_CONF_97_5_PERCxmipp.jni.MDLabelstatic
MDL_LOCAL_ALIGNMENT_CONTROL_POINTSxmipp.jni.MDLabelstatic
MDL_LOCAL_ALIGNMENT_PATCHESxmipp.jni.MDLabelstatic
MDL_MACRO_CMDxmipp.jni.MDLabelstatic
MDL_MACRO_CMD_ARGSxmipp.jni.MDLabelstatic
MDL_MAGNIFICATIONxmipp.jni.MDLabelstatic
MDL_MAPTOPOLOGYxmipp.jni.MDLabelstatic
MDL_MASKxmipp.jni.MDLabelstatic
MDL_MAXxmipp.jni.MDLabelstatic
MDL_MAXCCxmipp.jni.MDLabelstatic
MDL_MAXCC_PERCENTILExmipp.jni.MDLabelstatic
MDL_MAXCC_PREVIOUSxmipp.jni.MDLabelstatic
MDL_MICROGRAPHxmipp.jni.MDLabelstatic
MDL_MICROGRAPH_IDxmipp.jni.MDLabelstatic
MDL_MICROGRAPH_MOVIExmipp.jni.MDLabelstatic
MDL_MICROGRAPH_MOVIE_IDxmipp.jni.MDLabelstatic
MDL_MICROGRAPH_ORIGINALxmipp.jni.MDLabelstatic
MDL_MICROGRAPH_PARTICLESxmipp.jni.MDLabelstatic
MDL_MICROGRAPH_TILTEDxmipp.jni.MDLabelstatic
MDL_MICROGRAPH_TILTED_ORIGINALxmipp.jni.MDLabelstatic
MDL_MINxmipp.jni.MDLabelstatic
MDL_MIRRORFRACxmipp.jni.MDLabelstatic
MDL_MISSINGREGION_NRxmipp.jni.MDLabelstatic
MDL_MISSINGREGION_THX0xmipp.jni.MDLabelstatic
MDL_MISSINGREGION_THXFxmipp.jni.MDLabelstatic
MDL_MISSINGREGION_THY0xmipp.jni.MDLabelstatic
MDL_MISSINGREGION_THYFxmipp.jni.MDLabelstatic
MDL_MISSINGREGION_TYPExmipp.jni.MDLabelstatic
MDL_MLF_CTFxmipp.jni.MDLabelstatic
MDL_MLF_NOISExmipp.jni.MDLabelstatic
MDL_MLF_SIGNALxmipp.jni.MDLabelstatic
MDL_MLF_WIENERxmipp.jni.MDLabelstatic
MDL_MODELFRACxmipp.jni.MDLabelstatic
MDL_NEIGHBORxmipp.jni.MDLabelstatic
MDL_NEIGHBORHOOD_RADIUSxmipp.jni.MDLabelstatic
MDL_NEIGHBORSxmipp.jni.MDLabelstatic
MDL_NMAxmipp.jni.MDLabelstatic
MDL_NMA_ATOMSHIFTxmipp.jni.MDLabelstatic
MDL_NMA_COLLECTIVITYxmipp.jni.MDLabelstatic
MDL_NMA_EIGENVALxmipp.jni.MDLabelstatic
MDL_NMA_ENERGYxmipp.jni.MDLabelstatic
MDL_NMA_MAXRANGExmipp.jni.MDLabelstatic
MDL_NMA_MINRANGExmipp.jni.MDLabelstatic
MDL_NMA_MODEFILExmipp.jni.MDLabelstatic
MDL_NMA_SCORExmipp.jni.MDLabelstatic
MDL_NOISE_ANGLESxmipp.jni.MDLabelstatic
MDL_NOISE_COORDxmipp.jni.MDLabelstatic
MDL_NOISE_PARTICLE_COORDxmipp.jni.MDLabelstatic
MDL_NOISE_PIXEL_LEVELxmipp.jni.MDLabelstatic
MDL_OBJIDxmipp.jni.MDLabelstatic
MDL_OPTICALFLOW_MEANXxmipp.jni.MDLabelstatic
MDL_OPTICALFLOW_MEANYxmipp.jni.MDLabelstatic
MDL_OPTICALFLOW_STDXxmipp.jni.MDLabelstatic
MDL_OPTICALFLOW_STDYxmipp.jni.MDLabelstatic
MDL_ORDERxmipp.jni.MDLabelstatic
MDL_ORIGIN_Xxmipp.jni.MDLabelstatic
MDL_ORIGIN_Yxmipp.jni.MDLabelstatic
MDL_ORIGIN_Zxmipp.jni.MDLabelstatic
MDL_PARTICLE_IDxmipp.jni.MDLabelstatic
MDL_PHANTOM_BGDENSITYxmipp.jni.MDLabelstatic
MDL_PHANTOM_FEATURE_CENTERxmipp.jni.MDLabelstatic
MDL_PHANTOM_FEATURE_DENSITYxmipp.jni.MDLabelstatic
MDL_PHANTOM_FEATURE_OPERATIONxmipp.jni.MDLabelstatic
MDL_PHANTOM_FEATURE_SPECIFICxmipp.jni.MDLabelstatic
MDL_PHANTOM_FEATURE_TYPExmipp.jni.MDLabelstatic
MDL_PHANTOM_SCALExmipp.jni.MDLabelstatic
MDL_PICKING_AUTOPARTICLES_SIZExmipp.jni.MDLabelstatic
MDL_PICKING_AUTOPICKPERCENTxmipp.jni.MDLabelstatic
MDL_PICKING_MANUALPARTICLES_SIZExmipp.jni.MDLabelstatic
MDL_PICKING_MICROGRAPH_STATExmipp.jni.MDLabelstatic
MDL_PICKING_PARTICLE_SIZExmipp.jni.MDLabelstatic
MDL_PICKING_STATExmipp.jni.MDLabelstatic
MDL_PICKING_TEMPLATESxmipp.jni.MDLabelstatic
MDL_PMAXxmipp.jni.MDLabelstatic
MDL_POINTSASYMETRICUNITxmipp.jni.MDLabelstatic
MDL_PRJ_ANGFILExmipp.jni.MDLabelstatic
MDL_PRJ_DIMENSIONSxmipp.jni.MDLabelstatic
MDL_PRJ_PSI_NOISExmipp.jni.MDLabelstatic
MDL_PRJ_PSI_RANDSTRxmipp.jni.MDLabelstatic
MDL_PRJ_PSI_RANGExmipp.jni.MDLabelstatic
MDL_PRJ_ROT_NOISExmipp.jni.MDLabelstatic
MDL_PRJ_ROT_RANDSTRxmipp.jni.MDLabelstatic
MDL_PRJ_ROT_RANGExmipp.jni.MDLabelstatic
MDL_PRJ_TILT_NOISExmipp.jni.MDLabelstatic
MDL_PRJ_TILT_RANDSTRxmipp.jni.MDLabelstatic
MDL_PRJ_TILT_RANGExmipp.jni.MDLabelstatic
MDL_PRJ_VOLxmipp.jni.MDLabelstatic
MDL_PROGRAMxmipp.jni.MDLabelstatic
MDL_PSDxmipp.jni.MDLabelstatic
MDL_PSD_ENHANCEDxmipp.jni.MDLabelstatic
MDL_RANDOMSEEDxmipp.jni.MDLabelstatic
MDL_REFxmipp.jni.MDLabelstatic
MDL_REF2xmipp.jni.MDLabelstatic
MDL_REF3Dxmipp.jni.MDLabelstatic
MDL_REFMDxmipp.jni.MDLabelstatic
MDL_RESIDUExmipp.jni.MDLabelstatic
MDL_RESOLUTION_ANISOTROPYxmipp.jni.MDLabelstatic
MDL_RESOLUTION_DPRxmipp.jni.MDLabelstatic
MDL_RESOLUTION_ERRORL2xmipp.jni.MDLabelstatic
MDL_RESOLUTION_FRCxmipp.jni.MDLabelstatic
MDL_RESOLUTION_FRCRANDOMNOISExmipp.jni.MDLabelstatic
MDL_RESOLUTION_FREQxmipp.jni.MDLabelstatic
MDL_RESOLUTION_FREQ2xmipp.jni.MDLabelstatic
MDL_RESOLUTION_FREQREALxmipp.jni.MDLabelstatic
MDL_RESOLUTION_FSOxmipp.jni.MDLabelstatic
MDL_RESOLUTION_LOCAL_RESIDUExmipp.jni.MDLabelstatic
MDL_RESOLUTION_LOG_STRUCTURE_FACTORxmipp.jni.MDLabelstatic
MDL_RESOLUTION_RFACTORxmipp.jni.MDLabelstatic
MDL_RESOLUTION_SSNRxmipp.jni.MDLabelstatic
MDL_RESOLUTION_STRUCTURE_FACTORxmipp.jni.MDLabelstatic
MDL_SAMPLINGRATExmipp.jni.MDLabelstatic
MDL_SAMPLINGRATE_ORIGINALxmipp.jni.MDLabelstatic
MDL_SAMPLINGRATE_Xxmipp.jni.MDLabelstatic
MDL_SAMPLINGRATE_Yxmipp.jni.MDLabelstatic
MDL_SAMPLINGRATE_Zxmipp.jni.MDLabelstatic
MDL_SCALExmipp.jni.MDLabelstatic
MDL_SCORE_BY_ALIGNABILITYxmipp.jni.MDLabelstatic
MDL_SCORE_BY_ALIGNABILITY_ACCURACYxmipp.jni.MDLabelstatic
MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXPxmipp.jni.MDLabelstatic
MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REFxmipp.jni.MDLabelstatic
MDL_SCORE_BY_ALIGNABILITY_NOISExmipp.jni.MDLabelstatic
MDL_SCORE_BY_ALIGNABILITY_PRECISIONxmipp.jni.MDLabelstatic
MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXPxmipp.jni.MDLabelstatic
MDL_SCORE_BY_ALIGNABILITY_PRECISION_REFxmipp.jni.MDLabelstatic
MDL_SCORE_BY_EMPTINESSxmipp.jni.MDLabelstatic
MDL_SCORE_BY_ENTROPYxmipp.jni.MDLabelstatic
MDL_SCORE_BY_GINIxmipp.jni.MDLabelstatic
MDL_SCORE_BY_GRANULOxmipp.jni.MDLabelstatic
MDL_SCORE_BY_HISTDISTxmipp.jni.MDLabelstatic
MDL_SCORE_BY_LBPxmipp.jni.MDLabelstatic
MDL_SCORE_BY_MIRRORxmipp.jni.MDLabelstatic
MDL_SCORE_BY_PCA_RESIDUALxmipp.jni.MDLabelstatic
MDL_SCORE_BY_PCA_RESIDUAL_EXPxmipp.jni.MDLabelstatic
MDL_SCORE_BY_PCA_RESIDUAL_PROJxmipp.jni.MDLabelstatic
MDL_SCORE_BY_RAMPxmipp.jni.MDLabelstatic
MDL_SCORE_BY_SCREENINGxmipp.jni.MDLabelstatic
MDL_SCORE_BY_VARxmipp.jni.MDLabelstatic
MDL_SCORE_BY_VARIANCExmipp.jni.MDLabelstatic
MDL_SCORE_BY_ZERNIKExmipp.jni.MDLabelstatic
MDL_SCORE_BY_ZSCORExmipp.jni.MDLabelstatic
MDL_SELFILExmipp.jni.MDLabelstatic
MDL_SERIExmipp.jni.MDLabelstatic
MDL_SHIFT_DIFFxmipp.jni.MDLabelstatic
MDL_SHIFT_DIFF0xmipp.jni.MDLabelstatic
MDL_SHIFT_DIFF2xmipp.jni.MDLabelstatic
MDL_SHIFT_Xxmipp.jni.MDLabelstatic
MDL_SHIFT_X2xmipp.jni.MDLabelstatic
MDL_SHIFT_X3xmipp.jni.MDLabelstatic
MDL_SHIFT_X_DIFFxmipp.jni.MDLabelstatic
MDL_SHIFT_Yxmipp.jni.MDLabelstatic
MDL_SHIFT_Y2xmipp.jni.MDLabelstatic
MDL_SHIFT_Y3xmipp.jni.MDLabelstatic
MDL_SHIFT_Y_DIFFxmipp.jni.MDLabelstatic
MDL_SHIFT_Zxmipp.jni.MDLabelstatic
MDL_SHIFT_Z2xmipp.jni.MDLabelstatic
MDL_SHIFT_Z3xmipp.jni.MDLabelstatic
MDL_SIGMANOISExmipp.jni.MDLabelstatic
MDL_SIGMAOFFSETxmipp.jni.MDLabelstatic
MDL_SIGNALCHANGExmipp.jni.MDLabelstatic
MDL_SPH_COEFFICIENTSxmipp.jni.MDLabelstatic
MDL_SPH_DEFORMATIONxmipp.jni.MDLabelstatic
MDL_SPH_TSNE_COEFF1Dxmipp.jni.MDLabelstatic
MDL_SPH_TSNE_COEFF2Dxmipp.jni.MDLabelstatic
MDL_STAR_COMMENTxmipp.jni.MDLabelstatic
MDL_STDDEVxmipp.jni.MDLabelstatic
MDL_SUBTRACTION_BETA0xmipp.jni.MDLabelstatic
MDL_SUBTRACTION_BETA1xmipp.jni.MDLabelstatic
MDL_SUBTRACTION_R2xmipp.jni.MDLabelstatic
MDL_SUMxmipp.jni.MDLabelstatic
MDL_SUMWEIGHTxmipp.jni.MDLabelstatic
MDL_SYMNOxmipp.jni.MDLabelstatic
MDL_TEST_SIZExmipp.jni.MDLabelstatic
MDL_TILT_ANALYSIS_MAXxmipp.jni.MDLabelstatic
MDL_TILT_ANALYSIS_MEANxmipp.jni.MDLabelstatic
MDL_TILT_ANALYSIS_MINxmipp.jni.MDLabelstatic
MDL_TILT_ANALYSIS_PSDsxmipp.jni.MDLabelstatic
MDL_TILT_ANALYSIS_STDxmipp.jni.MDLabelstatic
MDL_TIMExmipp.jni.MDLabelstatic
MDL_TOMOGRAM_VOLUMExmipp.jni.MDLabelstatic
MDL_TOMOGRAMMDxmipp.jni.MDLabelstatic
MDL_TRANSFORM_MATRIXxmipp.jni.MDLabelstatic
MDL_TSIDxmipp.jni.MDLabelstatic
MDL_UNDEFINEDxmipp.jni.MDLabelstatic
MDL_USERxmipp.jni.MDLabelstatic
MDL_VOLUME_SCORE1xmipp.jni.MDLabelstatic
MDL_VOLUME_SCORE2xmipp.jni.MDLabelstatic
MDL_VOLUME_SCORE3xmipp.jni.MDLabelstatic
MDL_VOLUME_SCORE4xmipp.jni.MDLabelstatic
MDL_VOLUME_SCORE_MEANxmipp.jni.MDLabelstatic
MDL_VOLUME_SCORE_MINxmipp.jni.MDLabelstatic
MDL_VOLUME_SCORE_SUMxmipp.jni.MDLabelstatic
MDL_VOLUME_SCORE_SUM_THxmipp.jni.MDLabelstatic
MDL_WEIGHTxmipp.jni.MDLabelstatic
MDL_WEIGHT_ACCURACY_ALIGNABILITYxmipp.jni.MDLabelstatic
MDL_WEIGHT_ALIGNABILITYxmipp.jni.MDLabelstatic
MDL_WEIGHT_CONTINUOUS2xmipp.jni.MDLabelstatic
MDL_WEIGHT_JUMPERxmipp.jni.MDLabelstatic
MDL_WEIGHT_JUMPER0xmipp.jni.MDLabelstatic
MDL_WEIGHT_JUMPER2xmipp.jni.MDLabelstatic
MDL_WEIGHT_Pxmipp.jni.MDLabelstatic
MDL_WEIGHT_PHASECORRxmipp.jni.MDLabelstatic
MDL_WEIGHT_PRECISION_ALIGNABILITYxmipp.jni.MDLabelstatic
MDL_WEIGHT_PRECISION_MIRRORxmipp.jni.MDLabelstatic
MDL_WEIGHT_REALCORRxmipp.jni.MDLabelstatic
MDL_WEIGHT_SIGNIFICANTxmipp.jni.MDLabelstatic
MDL_WEIGHT_SSNRxmipp.jni.MDLabelstatic
MDL_WROBUSTxmipp.jni.MDLabelstatic
MDL_Xxmipp.jni.MDLabelstatic
MDL_XCOORxmipp.jni.MDLabelstatic
MDL_XCOOR_TILTxmipp.jni.MDLabelstatic
MDL_XSIZExmipp.jni.MDLabelstatic
MDL_Yxmipp.jni.MDLabelstatic
MDL_YCOORxmipp.jni.MDLabelstatic
MDL_YCOOR_TILTxmipp.jni.MDLabelstatic
MDL_YSIZExmipp.jni.MDLabelstatic
MDL_Zxmipp.jni.MDLabelstatic
MDL_ZCOORxmipp.jni.MDLabelstatic
MDL_ZSCORExmipp.jni.MDLabelstatic
MDL_ZSCORE_DEEPLEARNING1xmipp.jni.MDLabelstatic
MDL_ZSCORE_HISTOGRAMxmipp.jni.MDLabelstatic
MDL_ZSCORE_RESCOVxmipp.jni.MDLabelstatic
MDL_ZSCORE_RESMEANxmipp.jni.MDLabelstatic
MDL_ZSCORE_RESVARxmipp.jni.MDLabelstatic
MDL_ZSCORE_SHAPE1xmipp.jni.MDLabelstatic
MDL_ZSCORE_SHAPE2xmipp.jni.MDLabelstatic
MDL_ZSCORE_SNR1xmipp.jni.MDLabelstatic
MDL_ZSCORE_SNR2xmipp.jni.MDLabelstatic
MDL_ZSIZExmipp.jni.MDLabelstatic
RLN_AREA_IDxmipp.jni.MDLabelstatic
RLN_AREA_NAMExmipp.jni.MDLabelstatic
RLN_COMMENTxmipp.jni.MDLabelstatic
RLN_CTF_BFACTORxmipp.jni.MDLabelstatic
RLN_CTF_CAxmipp.jni.MDLabelstatic
RLN_CTF_CONVERGENCE_CONExmipp.jni.MDLabelstatic
RLN_CTF_CSxmipp.jni.MDLabelstatic
RLN_CTF_DEFOCUS_ANGLExmipp.jni.MDLabelstatic
RLN_CTF_DEFOCUSUxmipp.jni.MDLabelstatic
RLN_CTF_DEFOCUSVxmipp.jni.MDLabelstatic
RLN_CTF_DETECTOR_PIXEL_SIZExmipp.jni.MDLabelstatic
RLN_CTF_ENERGY_LOSSxmipp.jni.MDLabelstatic
RLN_CTF_FOMxmipp.jni.MDLabelstatic
RLN_CTF_IMAGExmipp.jni.MDLabelstatic
RLN_CTF_Kxmipp.jni.MDLabelstatic
RLN_CTF_LENS_STABILITYxmipp.jni.MDLabelstatic
RLN_CTF_LONGITUDINAL_DISPLACEMENTxmipp.jni.MDLabelstatic
RLN_CTF_MAGNIFICATIONxmipp.jni.MDLabelstatic
RLN_CTF_MAXRESxmipp.jni.MDLabelstatic
RLN_CTF_PHASESHIFTxmipp.jni.MDLabelstatic
RLN_CTF_Q0xmipp.jni.MDLabelstatic
RLN_CTF_SAMPLING_RATExmipp.jni.MDLabelstatic
RLN_CTF_SCALEFACTORxmipp.jni.MDLabelstatic
RLN_CTF_TRANSVERSAL_DISPLACEMENTxmipp.jni.MDLabelstatic
RLN_CTF_VALIDATIONSCORExmipp.jni.MDLabelstatic
RLN_CTF_VALUExmipp.jni.MDLabelstatic
RLN_CTF_VOLTAGExmipp.jni.MDLabelstatic
RLN_IMAGE_BEAMTILT_GROUPxmipp.jni.MDLabelstatic
RLN_IMAGE_BEAMTILT_Xxmipp.jni.MDLabelstatic
RLN_IMAGE_BEAMTILT_Yxmipp.jni.MDLabelstatic
RLN_IMAGE_COORD_Xxmipp.jni.MDLabelstatic
RLN_IMAGE_COORD_Yxmipp.jni.MDLabelstatic
RLN_IMAGE_COORD_Zxmipp.jni.MDLabelstatic
RLN_IMAGE_DATATYPExmipp.jni.MDLabelstatic
RLN_IMAGE_DIMENSIONALITYxmipp.jni.MDLabelstatic
RLN_IMAGE_ENABLEDxmipp.jni.MDLabelstatic
RLN_IMAGE_FRAME_NRxmipp.jni.MDLabelstatic
RLN_IMAGE_IDxmipp.jni.MDLabelstatic
RLN_IMAGE_MAGNIFICATION_CORRECTIONxmipp.jni.MDLabelstatic
RLN_IMAGE_NAMExmipp.jni.MDLabelstatic
RLN_IMAGE_NORM_CORRECTIONxmipp.jni.MDLabelstatic
RLN_IMAGE_ORI_NAMExmipp.jni.MDLabelstatic
RLN_IMAGE_RECONSTRUCT_NAMExmipp.jni.MDLabelstatic
RLN_IMAGE_SAMPLINGRATExmipp.jni.MDLabelstatic
RLN_IMAGE_SAMPLINGRATE_Xxmipp.jni.MDLabelstatic
RLN_IMAGE_SAMPLINGRATE_Yxmipp.jni.MDLabelstatic
RLN_IMAGE_SAMPLINGRATE_Zxmipp.jni.MDLabelstatic
RLN_IMAGE_SIZExmipp.jni.MDLabelstatic
RLN_IMAGE_SIZEXxmipp.jni.MDLabelstatic
RLN_IMAGE_SIZEYxmipp.jni.MDLabelstatic
RLN_IMAGE_SIZEZxmipp.jni.MDLabelstatic
RLN_IMAGE_STATS_AVGxmipp.jni.MDLabelstatic
RLN_IMAGE_STATS_KURTxmipp.jni.MDLabelstatic
RLN_IMAGE_STATS_MAXxmipp.jni.MDLabelstatic
RLN_IMAGE_STATS_MINxmipp.jni.MDLabelstatic
RLN_IMAGE_STATS_SKEWxmipp.jni.MDLabelstatic
RLN_IMAGE_STATS_STDDEVxmipp.jni.MDLabelstatic
RLN_IMAGE_WEIGHTxmipp.jni.MDLabelstatic
RLN_MASK_NAMExmipp.jni.MDLabelstatic
RLN_MATRIX_1_1xmipp.jni.MDLabelstatic
RLN_MATRIX_1_2xmipp.jni.MDLabelstatic
RLN_MATRIX_1_3xmipp.jni.MDLabelstatic
RLN_MATRIX_2_1xmipp.jni.MDLabelstatic
RLN_MATRIX_2_2xmipp.jni.MDLabelstatic
RLN_MATRIX_2_3xmipp.jni.MDLabelstatic
RLN_MATRIX_3_1xmipp.jni.MDLabelstatic
RLN_MATRIX_3_2xmipp.jni.MDLabelstatic
RLN_MATRIX_3_3xmipp.jni.MDLabelstatic
RLN_MICROGRAPH_IDxmipp.jni.MDLabelstatic
RLN_MICROGRAPH_MOVIE_NAMExmipp.jni.MDLabelstatic
RLN_MICROGRAPH_NAMExmipp.jni.MDLabelstatic
RLN_MICROGRAPH_NAME_WODOSExmipp.jni.MDLabelstatic
RLN_MICROGRAPH_TILT_ANGLExmipp.jni.MDLabelstatic
RLN_MICROGRAPH_TILT_AXIS_DIRECTIONxmipp.jni.MDLabelstatic
RLN_MICROGRAPH_TILT_AXIS_OUTOFPLANExmipp.jni.MDLabelstatic
RLN_MLMODEL_ACCURACY_ROTxmipp.jni.MDLabelstatic
RLN_MLMODEL_ACCURACY_TRANSxmipp.jni.MDLabelstatic
RLN_MLMODEL_AVE_PMAXxmipp.jni.MDLabelstatic
RLN_MLMODEL_CURRENT_RESOLUTIONxmipp.jni.MDLabelstatic
RLN_MLMODEL_CURRENT_SIZExmipp.jni.MDLabelstatic
RLN_MLMODEL_DATA_VS_PRIOR_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_DIFF2_HALVES_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_DIMENSIONALITYxmipp.jni.MDLabelstatic
RLN_MLMODEL_DIMENSIONALITY_DATAxmipp.jni.MDLabelstatic
RLN_MLMODEL_ESTIM_RESOL_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_FOURIER_COVERAGE_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_FOURIER_COVERAGE_TOTAL_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_FSC_HALVES_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_GROUP_NAMExmipp.jni.MDLabelstatic
RLN_MLMODEL_GROUP_NOxmipp.jni.MDLabelstatic
RLN_MLMODEL_GROUP_NR_PARTICLESxmipp.jni.MDLabelstatic
RLN_MLMODEL_GROUP_SCALE_CORRECTIONxmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_NR_ASUxmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_RISExmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_RISE_INITIAL_STEPxmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_RISE_MAXxmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_RISE_MINxmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_TWISTxmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_TWIST_INITIAL_STEPxmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_TWIST_MAXxmipp.jni.MDLabelstatic
RLN_MLMODEL_HELICAL_TWIST_MINxmipp.jni.MDLabelstatic
RLN_MLMODEL_INTERPOLATORxmipp.jni.MDLabelstatic
RLN_MLMODEL_IS_HELIXxmipp.jni.MDLabelstatic
RLN_MLMODEL_LLxmipp.jni.MDLabelstatic
RLN_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATIONxmipp.jni.MDLabelstatic
RLN_MLMODEL_NORM_CORRECTION_AVGxmipp.jni.MDLabelstatic
RLN_MLMODEL_NR_BODIESxmipp.jni.MDLabelstatic
RLN_MLMODEL_NR_CLASSESxmipp.jni.MDLabelstatic
RLN_MLMODEL_NR_GROUPSxmipp.jni.MDLabelstatic
RLN_MLMODEL_ORIENTABILITY_CONTRIBUTIONxmipp.jni.MDLabelstatic
RLN_MLMODEL_ORIGINAL_SIZExmipp.jni.MDLabelstatic
RLN_MLMODEL_PADDING_FACTORxmipp.jni.MDLabelstatic
RLN_MLMODEL_PDF_CLASSxmipp.jni.MDLabelstatic
RLN_MLMODEL_PDF_ORIENTxmipp.jni.MDLabelstatic
RLN_MLMODEL_PIXEL_SIZExmipp.jni.MDLabelstatic
RLN_MLMODEL_POWER_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_PRIOR_MODExmipp.jni.MDLabelstatic
RLN_MLMODEL_PRIOR_OFFX_CLASSxmipp.jni.MDLabelstatic
RLN_MLMODEL_PRIOR_OFFY_CLASSxmipp.jni.MDLabelstatic
RLN_MLMODEL_REF_IMAGExmipp.jni.MDLabelstatic
RLN_MLMODEL_SGD_GRADIENT_IMAGExmipp.jni.MDLabelstatic
RLN_MLMODEL_SIGMA2_NOISExmipp.jni.MDLabelstatic
RLN_MLMODEL_SIGMA2_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_SIGMA_OFFSETxmipp.jni.MDLabelstatic
RLN_MLMODEL_SIGMA_PSIxmipp.jni.MDLabelstatic
RLN_MLMODEL_SIGMA_ROTxmipp.jni.MDLabelstatic
RLN_MLMODEL_SIGMA_TILTxmipp.jni.MDLabelstatic
RLN_MLMODEL_SSNR_REFxmipp.jni.MDLabelstatic
RLN_MLMODEL_TAU2_FUDGE_FACTORxmipp.jni.MDLabelstatic
RLN_MLMODEL_TAU2_REFxmipp.jni.MDLabelstatic
RLN_OPTIMISER_ACCURACY_ROTxmipp.jni.MDLabelstatic
RLN_OPTIMISER_ACCURACY_TRANSxmipp.jni.MDLabelstatic
RLN_OPTIMISER_ADAPTIVE_FRACTIONxmipp.jni.MDLabelstatic
RLN_OPTIMISER_ADAPTIVE_OVERSAMPLINGxmipp.jni.MDLabelstatic
RLN_OPTIMISER_AUTO_LOCAL_HP_ORDERxmipp.jni.MDLabelstatic
RLN_OPTIMISER_AVAILABLE_MEMORYxmipp.jni.MDLabelstatic
RLN_OPTIMISER_BEST_RESOL_THUS_FARxmipp.jni.MDLabelstatic
RLN_OPTIMISER_CHANGES_OPTIMAL_CLASSESxmipp.jni.MDLabelstatic
RLN_OPTIMISER_CHANGES_OPTIMAL_OFFSETSxmipp.jni.MDLabelstatic
RLN_OPTIMISER_CHANGES_OPTIMAL_ORIENTSxmipp.jni.MDLabelstatic
RLN_OPTIMISER_COARSE_SIZExmipp.jni.MDLabelstatic
RLN_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPEDxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DATA_ARE_CTF_PREMULTIPLIEDxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DATA_STARFILExmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_AUTO_REFINExmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_CORRECT_CTFxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_CORRECT_MAGNIFICATIONxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_CORRECT_NORMxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_CORRECT_SCALExmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_HELICAL_REFINExmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_MAPxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_ONLY_FLIP_CTF_PHASESxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_REALIGN_MOVIESxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_SGDxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_SKIP_ALIGNxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_SKIP_ROTATExmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_SOLVENT_FLATTENxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_SPLIT_RANDOM_HALVESxmipp.jni.MDLabelstatic
RLN_OPTIMISER_DO_ZERO_MASKxmipp.jni.MDLabelstatic
RLN_OPTIMISER_FIX_SIGMA_NOISExmipp.jni.MDLabelstatic
RLN_OPTIMISER_FIX_SIGMA_OFFSETxmipp.jni.MDLabelstatic
RLN_OPTIMISER_FIX_TAUxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HAS_CONVERGEDxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HAS_HIGH_FSC_AT_LIMITxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGOxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HELICAL_KEEP_TILT_PRIOR_FIXEDxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HELICAL_RISE_INITIALxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HELICAL_SIGMA_DISTANCExmipp.jni.MDLabelstatic
RLN_OPTIMISER_HELICAL_SYMMETRY_LOCAL_REFINEMENTxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HELICAL_TUBE_INNER_DIAMETERxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HELICAL_TUBE_OUTER_DIAMETERxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HELICAL_TWIST_INITIALxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HELICAL_Z_PERCENTAGExmipp.jni.MDLabelstatic
RLN_OPTIMISER_HIGHRES_LIMIT_EXPxmipp.jni.MDLabelstatic
RLN_OPTIMISER_HIGHRES_LIMIT_SGDxmipp.jni.MDLabelstatic
RLN_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAKxmipp.jni.MDLabelstatic
RLN_OPTIMISER_IGNORE_HELICAL_SYMMETRYxmipp.jni.MDLabelstatic
RLN_OPTIMISER_INCR_SIZExmipp.jni.MDLabelstatic
RLN_OPTIMISER_ITERATION_NOxmipp.jni.MDLabelstatic
RLN_OPTIMISER_LOCAL_SYMMETRY_FILENAMExmipp.jni.MDLabelstatic
RLN_OPTIMISER_LOWRES_JOIN_RANDOM_HALVESxmipp.jni.MDLabelstatic
RLN_OPTIMISER_MAGNIFICATION_RANGExmipp.jni.MDLabelstatic
RLN_OPTIMISER_MAGNIFICATION_STEPxmipp.jni.MDLabelstatic
RLN_OPTIMISER_MAX_COARSE_SIZExmipp.jni.MDLabelstatic
RLN_OPTIMISER_MAX_NR_POOLxmipp.jni.MDLabelstatic
RLN_OPTIMISER_MODEL_STARFILExmipp.jni.MDLabelstatic
RLN_OPTIMISER_MODEL_STARFILE2xmipp.jni.MDLabelstatic
RLN_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGESxmipp.jni.MDLabelstatic
RLN_OPTIMISER_NR_ITER_WO_RESOL_GAINxmipp.jni.MDLabelstatic
RLN_OPTIMISER_NR_ITERATIONSxmipp.jni.MDLabelstatic
RLN_OPTIMISER_OUTPUT_ROOTNAMExmipp.jni.MDLabelstatic
RLN_OPTIMISER_PARTICLE_DIAMETERxmipp.jni.MDLabelstatic
RLN_OPTIMISER_RADIUS_MASK_3D_MAPxmipp.jni.MDLabelstatic
RLN_OPTIMISER_RADIUS_MASK_EXP_PARTICLESxmipp.jni.MDLabelstatic
RLN_OPTIMISER_RANDOM_SEEDxmipp.jni.MDLabelstatic
RLN_OPTIMISER_REFS_ARE_CTF_CORRECTEDxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SAMPLING_STARFILExmipp.jni.MDLabelstatic
RLN_OPTIMISER_SGD_MAX_SUBSETSxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SGD_MUxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SGD_SIGMA2FUDGE_HALFLIFExmipp.jni.MDLabelstatic
RLN_OPTIMISER_SGD_SIGMA2FUDGE_INIxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SGD_STEPSIZExmipp.jni.MDLabelstatic
RLN_OPTIMISER_SGD_SUBSET_SIZExmipp.jni.MDLabelstatic
RLN_OPTIMISER_SGD_SUBSET_STARTxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SGD_WRITE_EVERY_SUBSETxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSESxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETSxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTSxmipp.jni.MDLabelstatic
RLN_OPTIMISER_SOLVENT_MASK2_NAMExmipp.jni.MDLabelstatic
RLN_OPTIMISER_SOLVENT_MASK_NAMExmipp.jni.MDLabelstatic
RLN_OPTIMISER_TAU_SPECTRUM_NAMExmipp.jni.MDLabelstatic
RLN_OPTIMISER_USE_TOO_COARSE_SAMPLINGxmipp.jni.MDLabelstatic
RLN_OPTIMISER_WIDTH_MASK_EDGExmipp.jni.MDLabelstatic
RLN_ORIENT_FLIPxmipp.jni.MDLabelstatic
RLN_ORIENT_IDxmipp.jni.MDLabelstatic
RLN_ORIENT_ORIGIN_Xxmipp.jni.MDLabelstatic
RLN_ORIENT_ORIGIN_X_PRIORxmipp.jni.MDLabelstatic
RLN_ORIENT_ORIGIN_Yxmipp.jni.MDLabelstatic
RLN_ORIENT_ORIGIN_Y_PRIORxmipp.jni.MDLabelstatic
RLN_ORIENT_ORIGIN_Zxmipp.jni.MDLabelstatic
RLN_ORIENT_ORIGIN_Z_PRIORxmipp.jni.MDLabelstatic
RLN_ORIENT_PSIxmipp.jni.MDLabelstatic
RLN_ORIENT_PSI_PRIORxmipp.jni.MDLabelstatic
RLN_ORIENT_PSI_PRIOR_FLIP_RATIOxmipp.jni.MDLabelstatic
RLN_ORIENT_ROTxmipp.jni.MDLabelstatic
RLN_ORIENT_ROT_PRIORxmipp.jni.MDLabelstatic
RLN_ORIENT_TILTxmipp.jni.MDLabelstatic
RLN_ORIENT_TILT_PRIORxmipp.jni.MDLabelstatic
RLN_PARTICLE_AUTOPICK_FOMxmipp.jni.MDLabelstatic
RLN_PARTICLE_CLASSxmipp.jni.MDLabelstatic
RLN_PARTICLE_DLLxmipp.jni.MDLabelstatic
RLN_PARTICLE_FOMxmipp.jni.MDLabelstatic
RLN_PARTICLE_HELICAL_TRACK_LENGTHxmipp.jni.MDLabelstatic
RLN_PARTICLE_HELICAL_TUBE_IDxmipp.jni.MDLabelstatic
RLN_PARTICLE_HELICAL_TUBE_PITCHxmipp.jni.MDLabelstatic
RLN_PARTICLE_IDxmipp.jni.MDLabelstatic
RLN_PARTICLE_KL_DIVERGENCExmipp.jni.MDLabelstatic
RLN_PARTICLE_MOVIE_RUNNING_AVGxmipp.jni.MDLabelstatic
RLN_PARTICLE_NAMExmipp.jni.MDLabelstatic
RLN_PARTICLE_NR_FRAMESxmipp.jni.MDLabelstatic
RLN_PARTICLE_NR_FRAMES_AVGxmipp.jni.MDLabelstatic
RLN_PARTICLE_NR_SIGNIFICANT_SAMPLESxmipp.jni.MDLabelstatic
RLN_PARTICLE_ORI_NAMExmipp.jni.MDLabelstatic
RLN_PARTICLE_PMAXxmipp.jni.MDLabelstatic
RLN_PARTICLE_RANDOM_SUBSETxmipp.jni.MDLabelstatic
RLN_PERFRAME_CUMULATIVE_WEIGHTxmipp.jni.MDLabelstatic
RLN_PERFRAME_RELATIVE_WEIGHTxmipp.jni.MDLabelstatic
RLN_PIPELINE_EDGE_FROMxmipp.jni.MDLabelstatic
RLN_PIPELINE_EDGE_PROCESSxmipp.jni.MDLabelstatic
RLN_PIPELINE_EDGE_TOxmipp.jni.MDLabelstatic
RLN_PIPELINE_JOB_COUNTERxmipp.jni.MDLabelstatic
RLN_PIPELINE_NODE_NAMExmipp.jni.MDLabelstatic
RLN_PIPELINE_NODE_TYPExmipp.jni.MDLabelstatic
RLN_PIPELINE_PROCESS_ALIASxmipp.jni.MDLabelstatic
RLN_PIPELINE_PROCESS_NAMExmipp.jni.MDLabelstatic
RLN_PIPELINE_PROCESS_STATUSxmipp.jni.MDLabelstatic
RLN_PIPELINE_PROCESS_TYPExmipp.jni.MDLabelstatic
RLN_POSTPROCESS_AMPLCORR_MASKEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_AMPLCORR_UNMASKEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_BFACTORxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_DPR_MASKEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_DPR_UNMASKEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_FINAL_RESOLUTIONxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_FSC_GENERALxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_FSC_MASKEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_FSC_RANDOM_MASKEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_FSC_TRUExmipp.jni.MDLabelstatic
RLN_POSTPROCESS_FSC_UNMASKEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_FIT_CORRELATIONxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_FIT_INTERCEPTxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_FIT_SLOPExmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_RESOL_SQUAREDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_VALUE_INxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_VALUE_INTERCEPTxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_VALUE_INVMTFxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_VALUE_SHARPENEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_GUINIER_VALUE_WEIGHTEDxmipp.jni.MDLabelstatic
RLN_POSTPROCESS_MTF_VALUExmipp.jni.MDLabelstatic
RLN_RESOLUTIONxmipp.jni.MDLabelstatic
RLN_RESOLUTION_ANGSTROMxmipp.jni.MDLabelstatic
RLN_RESOLUTION_INVPIXELxmipp.jni.MDLabelstatic
RLN_SAMPLING_HEALPIX_ORDERxmipp.jni.MDLabelstatic
RLN_SAMPLING_HELICAL_OFFSET_STEPxmipp.jni.MDLabelstatic
RLN_SAMPLING_IS_3Dxmipp.jni.MDLabelstatic
RLN_SAMPLING_IS_3D_TRANSxmipp.jni.MDLabelstatic
RLN_SAMPLING_LIMIT_TILTxmipp.jni.MDLabelstatic
RLN_SAMPLING_OFFSET_RANGExmipp.jni.MDLabelstatic
RLN_SAMPLING_OFFSET_STEPxmipp.jni.MDLabelstatic
RLN_SAMPLING_PERTURBxmipp.jni.MDLabelstatic
RLN_SAMPLING_PERTURBATION_FACTORxmipp.jni.MDLabelstatic
RLN_SAMPLING_PRIOR_MODExmipp.jni.MDLabelstatic
RLN_SAMPLING_PSI_STEPxmipp.jni.MDLabelstatic
RLN_SAMPLING_SIGMA_PSIxmipp.jni.MDLabelstatic
RLN_SAMPLING_SIGMA_ROTxmipp.jni.MDLabelstatic
RLN_SAMPLING_SIGMA_TILTxmipp.jni.MDLabelstatic
RLN_SAMPLING_SYMMETRYxmipp.jni.MDLabelstatic
RLN_SELECT_PARTICLES_ZSCORExmipp.jni.MDLabelstatic
RLN_SELECTEDxmipp.jni.MDLabelstatic
RLN_SORTED_IDXxmipp.jni.MDLabelstatic
RLN_SPECTRAL_IDXxmipp.jni.MDLabelstatic
RLN_STARFILE_MOVIE_PARTICLESxmipp.jni.MDLabelstatic
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Xmipp -  v20.07 -
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-Static Public Attributes | -List of all members
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xmipp.jni.MDLabel Class Reference
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-Static Public Attributes

static final int MDL_UNDEFINED = -1
 
static final int MDL_FIRST_LABEL = 0
 
static final int MDL_OBJID = MDL_FIRST_LABEL
 < The label MDL_OBJID is special and should not be used More...
 
static final int MDL_GATHER_ID = 1
 < object id (int), NOTE: This label is special and shouldn't be used More...
 
static final int MDL_ANGLE_PSI = 2
 Special label to be used when gathering MDs in MpiMetadataPrograms. More...
 
static final int MDL_ANGLE_PSI2 = 3
 < Psi angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_PSI3 = 4
 < Psi angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_PSI_DIFF = 5
 < Psi angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_ROT = 6
 < difference between psi angles (double,degrees) More...
 
static final int MDL_ANGLE_ROT2 = 7
 < Rotation angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_ROT3 = 8
 < Rotation angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_ROT_DIFF = 9
 < Rotation angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_TILT = 10
 < difference between rot angles (double,degrees) More...
 
static final int MDL_ANGLE_TILT2 = 11
 < Tilting angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_TILT3 = 12
 < Tilting angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_TILT_DIFF = 13
 < Tilting angle of an image (double,degrees) More...
 
static final int MDL_ANGLE_DIFF0 = 14
 < difference between tilt angles (double,degrees) More...
 
static final int MDL_ANGLE_DIFF = 15
 < difference between two angles (double,degrees) More...
 
static final int MDL_ANGLE_DIFF2 = 16
 < difference between two angles (double,degrees) More...
 
static final int MDL_ANGLE_Y = 17
 < difference between two angles (double,degrees) More...
 
static final int MDL_ANGLE_Y2 = 18
 < Angle between y-axis and tilt-axis (double, degrees) for untilted micrographs More...
 
static final int MDL_ANGLE_TEMPERATURE = 19
 < Angle between y-axis and tilt-axis (double, degrees) for tilted micrographs More...
 
static final int MDL_APPLY_SHIFT = 20
 < Angular temperature (double,degrees) More...
 
static final int MDL_AVG = 21
 <Apply shift when project the volume , More...
 
static final int MDL_AVG_CHANGES_ORIENTATIONS = 22
 < average value (double) More...
 
static final int MDL_AVG_CHANGES_OFFSETS = 23
 Average change in angular orientation (double degrees) More...
 
static final int MDL_AVG_CHANGES_CLASSES = 24
 Average change in offset (double pixels) More...
 
static final int MDL_AVGPMAX = 25
 Average change in class assignment(double dimensionaless) More...
 
static final int MDL_BFACTOR = 26
 < Average (per class) of the maximum value of normalized probability function) (double) More...
 
static final int MDL_BGMEAN = 27
 <Bfactor of a map, or even a local bfactor More...
 
static final int MDL_BLOCK_NUMBER = 28
 < Mean background value for an image More...
 
static final int MDL_CL2D_CHANGES = 29
 < Current block number (for incremental EM) More...
 
static final int MDL_CL2D_SIMILARITY = 30
 < Number of changes between iterations More...
 
static final int MDL_CLASS_COUNT = 31
 < Average cross-correlation for the image (double) More...
 
static final int MDL_CLASS_PERCENTAGE = 32
 < Number of images assigned to the same class as this image More...
 
static final int MDL_CLASSIFICATION_DATA = 33
 < Percentage of images assigned to the same class as this image More...
 
static final int MDL_CLASSIFICATION_DATA_SIZE = 34
 < Data vector for classification (vector double) More...
 
static final int MDL_CLASSIFICATION_DPR_05 = 35
 < Size of data vectors for classification (int) More...
 
static final int MDL_CLASSIFICATION_INTRACLASS_DISTANCE = 36
 < Differential Phase Residual evaluated at FRC=0.5 More...
 
static final int MDL_CLASSIFICATION_FRC_05 = 37
 < Average intraclass distance (double) More...
 
static final int MDL_COMMENT = 38
 < Digital frequency at which the FRC drops below 0.5 (double) More...
 
static final int MDL_COORD_CONSENSUS_SCORE = 39
 < Serve to make annotations on the metadata row More...
 
static final int MDL_COST = 40
 < Store a score for the coords. consensus (it will change the behavoir of the viewer) More...
 
static final int MDL_COST_PERCENTILE = 41
 < Cost for the image (double) More...
 
static final int MDL_COUNT = 42
 < Cost percentile for the image (double) More...
 
static final int MDL_COUNT2 = 43
 < Number of elements of a type (int) [this is a genereic type do not use to transfer information to another program] More...
 
static final int MDL_CORR_DENOISED_PROJECTION = 44
 < Number of elements of a type (int) [this is a genereic type do not use to transfer information to another program] More...
 
static final int MDL_CORR_DENOISED_NOISY = 45
 <Correlation between the denoised image and the projection proposed More...
 
static final int MDL_CLASS_INTERSECTION_SIZE_PVALUE = 46
 <Correlation between the denoised image and the noisy version More...
 
static final int MDL_CLASS_INTERSECTION_RELATIVE_SIZE_PVALUE = 47
 < P-value (1-percentile) of the class size compared to a random distribution (double in [0, 1]) More...
 
static final int MDL_CRYSTAL_CELLX = 48
 < P-value (1-percentile) of the relative class size (size/max(original_classes)) compared to a random distribution (double in [0, 1]) More...
 
static final int MDL_CRYSTAL_CELLY = 49
 < Cell location for crystals More...
 
static final int MDL_CRYSTAL_LATTICE_A = 50
 < Cell location for crystals More...
 
static final int MDL_CRYSTAL_LATTICE_B = 51
 < Lattice vector for projection (vector double) More...
 
static final int MDL_CRYSTAL_DISAPPEAR_THRE = 52
 < Lattice vector for projection (vector double) More...
 
static final int MDL_CRYSTAL_SHFILE = 53
 < Disappearing threshold (double) More...
 
static final int MDL_CRYSTAL_ORTHO_PRJ = 54
 < Shift file for crystal projection More...
 
static final int MDL_CRYSTAL_PROJ = 55
 <Orthogonal projection or not (bool) More...
 
static final int MDL_CRYSTAL_SHIFTX = 56
 < Have a crystal projection (bool) More...
 
static final int MDL_CRYSTAL_SHIFTY = 57
 < Shift for the image in the X axis (double) for crystals More...
 
static final int MDL_CRYSTAL_SHIFTZ = 58
 < Shift for the image in the Y axis (double) for crystals More...
 
static final int MDL_CRYSTAL_NOISE_SHIFT = 59
 < Shift for the image in the Z axis (double) for crystals More...
 
static final int MDL_CONTINUOUS_X = 60
 < noise if center of unit cell (vector double) More...
 
static final int MDL_CONTINUOUS_Y = 61
 < X shift of continuous assignment More...
 
static final int MDL_CONTINUOUS_FLIP = 62
 < Y shift of continuous assignment More...
 
static final int MDL_CONTINUOUS_GRAY_A = 63
 < Flip of continuous assignment More...
 
static final int MDL_CONTINUOUS_GRAY_B = 64
 < a value of continuous assignment More...
 
static final int MDL_CONTINUOUS_SCALE_ANGLE = 65
 < b value of continuous assignment More...
 
static final int MDL_CONTINUOUS_SCALE_X = 66
 < scale angle of continuous assignment More...
 
static final int MDL_CONTINUOUS_SCALE_Y = 67
 < scale x of continuous assignment More...
 
static final int MDL_CORRELATION_IDX = 68
 < scale y of continuous assignment More...
 
static final int MDL_CORRELATION_MASK = 69
 < correlation value between a particle and its assigned projection More...
 
static final int MDL_CORRELATION_WEIGHT = 70
 < masked correlation value between a particle and its assigned projection inside the region with pixel values higher than the standard deviation More...
 
static final int MDL_CTF_DATA_PHASE_FLIPPED = 71
 < weighted correlation value between a particle and its assigned projection taking into the difference between both images More...
 
static final int MDL_CTF_CORRECTED = 72
 
static final int MDL_CTF_INPUTPARAMS = 73
 
static final int MDL_CTF_MODEL = 74
 < Parameters file for the CTF Model (std::string) More...
 
static final int MDL_CTF_MODEL2 = 75
 < Name for the CTF Model (std::string) More...
 
static final int MDL_CTF_SAMPLING_RATE = 76
 < Name for another CTF model (std::string) More...
 
static final int MDL_CTF_SAMPLING_RATE_Z = 77
 < Sampling rate More...
 
static final int MDL_CTF_VOLTAGE = 78
 < Sampling rate in Z direction More...
 
static final int MDL_CTF_DEFOCUSA = 79
 < Microscope voltage (kV) More...
 
static final int MDL_CTF_DEFOCUSU = 80
 < average defocus (Angtroms) More...
 
static final int MDL_CTF_DEFOCUSV = 81
 < Defocus U (Angstroms) More...
 
static final int MDL_CTF_DEFOCUS_CHANGE = 82
 < Defocus V (Angstroms) More...
 
static final int MDL_CTF_DEFOCUS_R2 = 83
 < Defocus change with respect to previous defoucs (Angstroms) More...
 
static final int MDL_CTF_DEFOCUS_COEFS = 84
 < Defocus coefficient of determination More...
 
static final int MDL_CTF_DEFOCUS_RESIDUAL = 85
 < Coefficients of the defocus adjustment plane More...
 
static final int MDL_CTF_X0 = 86
 < Difference between the observed defocus value and the estimated defocus value More...
 
static final int MDL_CTF_Y0 = 87
 < The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates More...
 
static final int MDL_CTF_XF = 88
 < The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates More...
 
static final int MDL_CTF_YF = 89
 < The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates More...
 
static final int MDL_CTF_DEFOCUS_PLANEUA = 90
 < The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates More...
 
static final int MDL_CTF_DEFOCUS_PLANEUB = 91
 < Defocus = A*x+B*y+C More...
 
static final int MDL_CTF_DEFOCUS_PLANEUC = 92
 < Defocus = A*x+B*y+C More...
 
static final int MDL_CTF_DEFOCUS_PLANEVA = 93
 < Defocus = A*x+B*y+C More...
 
static final int MDL_CTF_DEFOCUS_PLANEVB = 94
 < Defocus = A*x+B*y+C More...
 
static final int MDL_CTF_DEFOCUS_PLANEVC = 95
 < Defocus = A*x+B*y+C More...
 
static final int MDL_CTF_DEFOCUS_ANGLE = 96
 < Defocus = A*x+B*y+C More...
 
static final int MDL_CTF_CS = 97
 < Defocus angle (degrees) More...
 
static final int MDL_CTF_CA = 98
 < Spherical aberration More...
 
static final int MDL_CTF_GROUP = 99
 < Chromatic aberration More...
 
static final int MDL_CTF_ENERGY_LOSS = 100
 < group images by defocus More...
 
static final int MDL_CTF_ENVELOPE = 101
 < Energy loss More...
 
static final int MDL_CTF_ENVELOPE_PLOT = 102
 
static final int MDL_CTF_LENS_STABILITY = 103
 
static final int MDL_CTF_CONVERGENCE_CONE = 104
 < Lens stability More...
 
static final int MDL_CTF_LONGITUDINAL_DISPLACEMENT = 105
 < Convergence cone More...
 
static final int MDL_CTF_TRANSVERSAL_DISPLACEMENT = 106
 < Longitudinal displacement More...
 
static final int MDL_CTF_Q0 = 107
 < Transversal displacemente More...
 
static final int MDL_CTF_K = 108
 < Inelastic absorption More...
 
static final int MDL_CTF_ENV_R0 = 109
 < CTF gain More...
 
static final int MDL_CTF_ENV_R1 = 110
 < CTF Envelope polynomial parameter More...
 
static final int MDL_CTF_ENV_R2 = 111
 < CTF Envelope polynomial parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN_K = 112
 < CTF Envelope polynomial parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN_SIGMAU = 113
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN_SIGMAV = 114
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN_CU = 115
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN_CV = 116
 <CTF_ CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN_ANGLE = 117
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_SQRT_K = 118
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_SQRT_U = 119
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_SQRT_V = 120
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_SQRT_ANGLE = 121
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_BASELINE = 122
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN2_K = 123
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN2_SIGMAU = 124
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN2_SIGMAV = 125
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN2_CU = 126
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN2_CV = 127
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_GAUSSIAN2_ANGLE = 128
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_R1 = 129
 < CTF Background parameter More...
 
static final int MDL_CTF_BG_R2 = 130
 < CTF Background polynomial parameter More...
 
static final int MDL_CTF_BG_R3 = 131
 < CTF Background polynomial parameter More...
 
static final int MDL_CTF_CRIT_NONASTIGMATICVALIDITY = 132
 < CTF Background polynomial parameter More...
 
static final int MDL_CTF_CRIT_PSDCORRELATION90 = 133
 < Maximum frequency (in Angstroms) at which non-astigmatic CTF correction is valid More...
 
static final int MDL_CTF_CRIT_FIRSTZERORATIO = 134
 < PSD correlation at 90 degrees More...
 
static final int MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_RATIO = 135
 < First zero ratio More...
 
static final int MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_DIFF_RATIO = 136
 < Ratio sigma(firstMinimum)/sigma(firstZero) More...
 
static final int MDL_CTF_CRIT_FIRSTZEROAVG = 137
 < Ratio sigma(firstMinimum-firstZero)/sigma(firstZero) More...
 
static final int MDL_CTF_CRIT_FIRSTZERODISAGREEMENT = 138
 < First zero average (in Angstroms) More...
 
static final int MDL_CTF_CRIT_MAXFREQ = 139
 < First zero disagreement with second model (in Angstroms) More...
 
static final int MDL_CTF_CRIT_DAMPING = 140
 < Maximum frequency at which the envelope drops below 0.1 (in Angstroms) More...
 
static final int MDL_CTF_CRIT_PSDRADIALINTEGRAL = 141
 < Minimum damping at border More...
 
static final int MDL_CTF_CRIT_FITTINGSCORE = 142
 < Integral of the radial PSD More...
 
static final int MDL_CTF_CRIT_FITTINGCORR13 = 143
 < Score of the fitting More...
 
static final int MDL_CTF_CRIT_PSDVARIANCE = 144
 < Correlation between the 1st and 3rd ring of the CTF More...
 
static final int MDL_CTF_CRIT_PSDPCA1VARIANCE = 145
 < PSD variance More...
 
static final int MDL_CTF_CRIT_PSDPCARUNSTEST = 146
 < Variance in the first principal component of the PSDs More...
 
static final int MDL_CTF_CRIT_NORMALITY = 147
 < Runs test on the projection of the PSD on the first principal component More...
 
static final int MDL_CTF_CRIT_ICENESS = 148
 < Normality test between histogram of micrography and gaussian distribution More...
 
static final int MDL_CTF_DOWNSAMPLE_PERFORMED = 149
 < Iceness of the micrograph More...
 
static final int MDL_CTF_DIMENSIONS = 150
 < Downsampling performed to estimate the CTF More...
 
static final int MDL_CTF_LAMBDA = 151
 
static final int MDL_CTF_XRAY_LENS_TYPE = 152
 Wavelength (nm) More...
 
static final int MDL_CTF_XRAY_OUTER_ZONE_WIDTH = 153
 Algorithm used to generate Xray PSF. More...
 
static final int MDL_CTF_XRAY_ZONES_NUMBER = 154
 Outermost zone width of the X-ray Fresnel lens (nm) More...
 
static final int MDL_CTF_PHASE_SHIFT = 155
 
static final int MDL_CTF_VPP_RADIUS = 156
 
static final int MDL_CUMULATIVE_SSNR = 157
 
static final int MDL_DATATYPE = 158
 <Cumulative SSNR (double) More...
 
static final int MDL_DEFGROUP = 159
 < if read from file original image datatype, this is an struct defined in image More...
 
static final int MDL_DIMRED = 160
 < Defocus group More...
 
static final int MDL_DIRECTION = 161
 < Projection onto a reduced manifold (vector double) More...
 
static final int MDL_DM3_IDTAG = 162
 < Direction in 3D More...
 
static final int MDL_DM3_NODEID = 163
 
static final int MDL_DM3_NUMBER_TYPE = 164
 
static final int MDL_DM3_PARENTID = 165
 
static final int MDL_DM3_TAGCLASS = 166
 
static final int MDL_DM3_TAGNAME = 167
 
static final int MDL_DM3_SIZE = 168
 
static final int MDL_DM3_VALUE = 169
 
static final int MDL_DOSE = 170
 
static final int MDL_ENABLED = 171
 < Dose e/A^2 (double) More...
 
static final int MDL_DATE = 172
 < Is this image enabled? (int [-1 or 1]) More...
 
static final int MDL_TIME = 173
 
static final int MDL_FLIP = 174
 
static final int MDL_FOM = 175
 < Flip the image? (bool) More...
 
static final int MDL_FRAME_ID = 176
 < Figure of Merit in 0-1 range (double) More...
 
static final int MDL_GRAPH_DISTANCE2MAX = 177
 < Unique id of frame inside a Movie More...
 
static final int MDL_GRAPH_DISTANCE2MAX_PREVIOUS = 178
 < Distance to graph filtered max More...
 
static final int MDL_GRAPH_CC = 179
 < when previous assignment validation More...
 
static final int MDL_GRAPH_CC_PREVIOUS = 180
 < Correlation between assigned direction and graph filtered maximum More...
 
static final int MDL_HALF1 = 181
 < when previous assignment validation More...
 
static final int MDL_HALF2 = 182
 < Half map/image 1 file name (string) More...
 
static final int MDL_IDX = 183
 < Half map/image file name (string) More...
 
static final int MDL_IMAGE = 184
 < Index within a list (size_t) More...
 
static final int MDL_IMAGE_COVARIANCE = 185
 < Name of an image (std::string) More...
 
static final int MDL_IMAGE_IDX = 186
 < Name of the covariance imagee associated to this image More...
 
static final int MDL_IMAGE_ORIGINAL = 187
 < Index of an image within a list (size_t) More...
 
static final int MDL_IMAGE_REF = 188
 < Name of an image from which MDL_IMAGE is coming from More...
 
static final int MDL_IMAGE_RESIDUAL = 189
 < Name of of the class image from which MDL_IMAGE is coming from More...
 
static final int MDL_IMAGE_TILTED = 190
 < Name of a residual image associated to this image More...
 
static final int MDL_IMED = 191
 < Name of the tilted images associated to MDL_IMAGE More...
 
static final int MDL_IMGMD = 192
 < imed value between a particle and its assigned projection More...
 
static final int MDL_IMAGE1 = 193
 < Name of Metadata file for all images (string) More...
 
static final int MDL_IMAGE2 = 194
 < Image associated to this object (std::string) More...
 
static final int MDL_IMAGE3 = 195
 < Image associated to this object (std::string) More...
 
static final int MDL_IMAGE4 = 196
 < Image associated to this object (std::string) More...
 
static final int MDL_IMAGE5 = 197
 < Image associated to this object (std::string) More...
 
static final int MDL_INTSCALE = 198
 < Image associated to this object (std::string) More...
 
static final int MDL_ITEM_ID = 199
 < Intensity scale for an image More...
 
static final int MDL_ITER = 200
 < Unique identifier for items inside a list or set (std::size_t) More...
 
static final int MDL_KERDENSOM_FUNCTIONAL = 201
 < Current iteration number (int) More...
 
static final int MDL_KERDENSOM_REGULARIZATION = 202
 < Functional value (double) More...
 
static final int MDL_KERDENSOM_SIGMA = 203
 < Regularization value (double) More...
 
static final int MDL_KEYWORDS = 204
 < Sigma value (double) More...
 
static final int MDL_KMEANS2D_CENTROID = 205
 < Keywords associated to this line, should be a single string block (do not use spaces as separators) More...
 
static final int MDL_KSTEST = 206
 < Centroid of a cluster for the KMEANS2D classification More...
 
static final int MDL_LL = 207
 <KS-test statistics More...
 
static final int MDL_LOCAL_ALIGNMENT_PATCHES = 208
 < contribution of an image to log-likelihood value More...
 
static final int MDL_LOCAL_ALIGNMENT_COEFFS_X = 209
 < Two values representing number of patches used for local alignment (X, Y) More...
 
static final int MDL_LOCAL_ALIGNMENT_COEFFS_Y = 210
 < BSpline coefficient in X dim More...
 
static final int MDL_LOCAL_ALIGNMENT_CONF_2_5_PERC = 211
 < BSpline coefficient in Y dim More...
 
static final int MDL_LOCAL_ALIGNMENT_CONF_97_5_PERC = 212
 < A shift amount at confidence level of 2.5% More...
 
static final int MDL_LOCAL_ALIGNMENT_CONTROL_POINTS = 213
 < A shift amount at confidence level of 95.5% More...
 
static final int MDL_MAGNIFICATION = 214
 < Three values representing number of control points used for local alignment (X, Y, N) More...
 
static final int MDL_MAPTOPOLOGY = 215
 Magnification of microscope. More...
 
static final int MDL_MASK = 216
 < Map topology (KerDenSOM, ...) More...
 
static final int MDL_MAXCC = 217
 < Name of a mask associated to image More...
 
static final int MDL_MAXCC_PERCENTILE = 218
 < Maximum cross-correlation for the image (double) More...
 
static final int MDL_MAX = 219
 < Percentile of the maximum cross-correlation for the image (double) More...
 
static final int MDL_MAXCC_PREVIOUS = 220
 < Maximum value (double) More...
 
static final int MDL_MICROGRAPH = 221
 < Correlation from previous alignment More...
 
static final int MDL_MICROGRAPH_ID = 222
 < Name of a micrograph (std::string) More...
 
static final int MDL_MICROGRAPH_MOVIE = 223
 < Micrograph unique id for reference (MDL_ITEM_ID should be used for Micrographs list) More...
 
static final int MDL_MICROGRAPH_MOVIE_ID = 224
 < Name of a movie (std::string) More...
 
static final int MDL_MICROGRAPH_PARTICLES = 225
 < Unique identifier of a movie. More...
 
static final int MDL_MICROGRAPH_ORIGINAL = 226
 < Name of a position file (std::string) More...
 
static final int MDL_MICROGRAPH_TILTED = 227
 < Name of the original micrograph, MDL_MICROGRAPH is probably a downsampled version of this one (std::string) More...
 
static final int MDL_MICROGRAPH_TILTED_ORIGINAL = 228
 < Name of the corresponding tilted micrograph (std::string) More...
 
static final int MDL_MIN = 229
 < Name of the corresponding original, tilted micrograph (std::string) More...
 
static final int MDL_MIRRORFRAC = 230
 < Minimum value (double) More...
 
static final int MDL_MISSINGREGION_NR = 231
 < Mirror fraction for a Maximum Likelihood model More...
 
static final int MDL_MISSINGREGION_TYPE = 232
 < Number of missing region in subtomogram More...
 
static final int MDL_MISSINGREGION_THY0 = 233
 < Type of missing region in subtomogram More...
 
static final int MDL_MISSINGREGION_THYF = 234
 < Initial tilt angle in Y for missing region in subtomogram More...
 
static final int MDL_MISSINGREGION_THX0 = 235
 < Final tilt angle in Y for missing region in subtomogram More...
 
static final int MDL_MISSINGREGION_THXF = 236
 < Initial tilt angle in X for missing region in subtomogram More...
 
static final int MDL_MLF_CTF = 237
 < Final tilt angle in X for missing region in subtomogram More...
 
static final int MDL_MLF_WIENER = 238
 < MLF CTF estimated value (double) More...
 
static final int MDL_MLF_SIGNAL = 239
 < MLF Wiener filter (double) More...
 
static final int MDL_MLF_NOISE = 240
 < MLF signal (double) More...
 
static final int MDL_MODELFRAC = 241
 < MLF Wiener filter (double) More...
 
static final int MDL_NEIGHBORS = 242
 < Model fraction (alpha_k) for a Maximum Likelihood model More...
 
static final int MDL_NEIGHBOR = 243
 < Vector of indexes to points some "neighbors" More...
 
static final int MDL_NEIGHBORHOOD_RADIUS = 244
 < Particular neighbor (pointed myNEIGHBORS) More...
 
static final int MDL_NMA = 245
 < Radius of the neighborhood (radians) More...
 
static final int MDL_NMA_COLLECTIVITY = 246
 < Normal mode displacements (vector double) More...
 
static final int MDL_NMA_ATOMSHIFT = 247
 < NMA Collectivity of a given mode More...
 
static final int MDL_NMA_ENERGY = 248
 < NMA Atom shift in Angstroms More...
 
static final int MDL_NMA_MINRANGE = 249
 < NMA energy contained in the NMA displacement vector More...
 
static final int MDL_NMA_MAXRANGE = 250
 < Minimum value observed for a given NMA mode More...
 
static final int MDL_NMA_MODEFILE = 251
 < Maximum value observed for a given NMA mode More...
 
static final int MDL_NMA_SCORE = 252
 < File with an NMA mode More...
 
static final int MDL_NMA_EIGENVAL = 253
 < NMA Score of a given mode More...
 
static final int MDL_NOISE_ANGLES = 254
 < NMA Eigenvalue of a given mode More...
 
static final int MDL_NOISE_PARTICLE_COORD = 255
 < Noise description for projected angles More...
 
static final int MDL_NOISE_COORD = 256
 < Noise description for particle's center coordenates (when projecting) More...
 
static final int MDL_NOISE_PIXEL_LEVEL = 257
 
static final int MDL_ORDER = 258
 < Noise description for pixels' gray level (when projecting) More...
 
static final int MDL_ORIGIN_X = 259
 auxiliary label to be used as an index (long) More...
 
static final int MDL_ORIGIN_Y = 260
 < Origin for the image in the X axis (double) More...
 
static final int MDL_ORIGIN_Z = 261
 < Origin for the image in the Y axis (double) More...
 
static final int MDL_OPTICALFLOW_MEANX = 262
 < Origin for the image in the Z axis (double) More...
 
static final int MDL_OPTICALFLOW_MEANY = 263
 <Mean of="" the="" movement="" in="" x="" direction="" of="" the="" motion="" map>=""> (double) More...
 
static final int MDL_OPTICALFLOW_STDX = 264
 <Mean of="" the="" movement="" in="" y="" direction="" of="" the="" motion="" map>=""> (double) More...
 
static final int MDL_OPTICALFLOW_STDY = 265
 <Standatd deviation="" of="" the="" movement="" in="" x="" direction="" of="" the="" motion="" map>=""> (double) More...
 
static final int MDL_PARTICLE_ID = 266
 <Standard deviation="" of="" the="" movement="" in="" y="" direction="" of="" the="" motion="" map>=""> (double) More...
 
static final int MDL_PHANTOM_BGDENSITY = 267
 < Particle unique identifier for reference. (The MDL_ITEM_ID should be used when particle list) More...
 
static final int MDL_PHANTOM_FEATURE_CENTER = 268
 < Phantom background density (double) More...
 
static final int MDL_PHANTOM_FEATURE_DENSITY = 269
 < Center of the feature (vector double) More...
 
static final int MDL_PHANTOM_FEATURE_OPERATION = 270
 < The density of the feature (double) More...
 
static final int MDL_PHANTOM_FEATURE_SPECIFIC = 271
 < Operation in case of overlapping features (+,-) More...
 
static final int MDL_PHANTOM_FEATURE_TYPE = 272
 < Specific parameters for a feature (vector double) More...
 
static final int MDL_PHANTOM_SCALE = 273
 < Type of the feature (Sphere, Blob, ...) (std::string) More...
 
static final int MDL_MACRO_CMD = 274
 < Number which will multiply all features (double) More...
 
static final int MDL_MACRO_CMD_ARGS = 275
 
static final int MDL_COLOR = 276
 
static final int MDL_PICKING_TEMPLATES = 277
 < Color for particle picking More...
 
static final int MDL_PICKING_STATE = 278
 < Number of templates More...
 
static final int MDL_PICKING_MICROGRAPH_STATE = 279
 < State for particle picking More...
 
static final int MDL_PICKING_AUTOPICKPERCENT = 280
 < Micrograph state for particle picking More...
 
static final int MDL_PICKING_PARTICLE_SIZE = 281
 
static final int MDL_PICKING_AUTOPARTICLES_SIZE = 282
 < Particle size for particle picking More...
 
static final int MDL_PICKING_MANUALPARTICLES_SIZE = 283
 < Number of automatic particles picked More...
 
static final int MDL_PMAX = 284
 < Number of manual particles picked More...
 
static final int MDL_POINTSASYMETRICUNIT = 285
 < Maximum value of normalized probability function (now called "Pmax/sumP") (double) More...
 
static final int MDL_PRJ_DIMENSIONS = 286
 < Number of non-redundant projections directions (size_t) More...
 
static final int MDL_PRJ_ANGFILE = 287
 
static final int MDL_PRJ_PSI_NOISE = 288
 < File for generated angles More...
 
static final int MDL_PRJ_PSI_RANDSTR = 289
 < Psi angle dev and mean noise (vector double) More...
 
static final int MDL_PRJ_PSI_RANGE = 290
 < Type of randomness for Psi (std::string) More...
 
static final int MDL_PRJ_ROT_NOISE = 291
 < Psi angle range (vector double) More...
 
static final int MDL_PRJ_ROT_RANDSTR = 292
 < Rotational angle dev and mean noise (vector double) More...
 
static final int MDL_PRJ_ROT_RANGE = 293
 < Type of randomness for Rotational (std::string) More...
 
static final int MDL_PRJ_TILT_NOISE = 294
 
static final int MDL_PRJ_TILT_RANDSTR = 295
 < Tilt angle dev and mean noise (vector double) More...
 
static final int MDL_PRJ_TILT_RANGE = 296
 < Type of randomness for Tilt (std::string) More...
 
static final int MDL_PRJ_VOL = 297
 
static final int MDL_PROGRAM = 298
 
static final int MDL_USER = 299
 
static final int MDL_DIMENSIONS_3D = 300
 
static final int MDL_DIMENSIONS_2D = 301
 
static final int MDL_PSD = 302
 
static final int MDL_PSD_ENHANCED = 303
 < A Power Spectrum Density file name (std::string) More...
 
static final int MDL_RANDOMSEED = 304
 < A enhanced Power Spectrum Density file name (std::string) More...
 
static final int MDL_REF3D = 305
 < Seed for random number generator More...
 
static final int MDL_REF = 306
 < 3D Class to which the image belongs (int) More...
 
static final int MDL_REF2 = 307
 < Class to which the image belongs (int) More...
 
static final int MDL_REFMD = 308
 < Store a second class (int) More...
 
static final int MDL_ASSIGNED_DIR_REF_CC = 309
 < Name of Metadata file for all references(string) More...
 
static final int MDL_RESIDUE = 310
 < correlation of references assigned by two methods More...
 
static final int MDL_RESOLUTION_ANISOTROPY = 311
 
static final int MDL_RESOLUTION_DPR = 312
 <Resolution anisotropy used to store the significance of the Bingham Test (double) More...
 
static final int MDL_RESOLUTION_ERRORL2 = 313
 <differential phase residual (double) More...
 
static final int MDL_RESOLUTION_FRC = 314
 <Error in l2 (double) More...
 
static final int MDL_RESOLUTION_FRCRANDOMNOISE = 315
 <Fourier shell correlation (double) More...
 
static final int MDL_RESOLUTION_FREQ = 316
 <Fourier shell correlation noise (double) More...
 
static final int MDL_RESOLUTION_FREQ2 = 317
 <Frequency in 1/A (double) More...
 
static final int MDL_RESOLUTION_FREQREAL = 318
 < Frequency in 1/A squared (double) More...
 
static final int MDL_RESOLUTION_FSO = 319
 < Frequency in A (double) More...
 
static final int MDL_RESOLUTION_LOCAL_RESIDUE = 320
 <Fourier shell occupancy (double) More...
 
static final int MDL_RESOLUTION_LOG_STRUCTURE_FACTOR = 321
 < Frequency in A of the local resolution of a residue (double) More...
 
static final int MDL_RESOLUTION_SSNR = 322
 <Logarithm of the structure factor More...
 
static final int MDL_RESOLUTION_STRUCTURE_FACTOR = 323
 <Fourier shell correlation (double) More...
 
static final int MDL_RESOLUTION_RFACTOR = 324
 <Structure factor More...
 
static final int MDL_SAMPLINGRATE = 325
 rfactor More...
 
static final int MDL_SAMPLINGRATE_ORIGINAL = 326
 < sampling rate in A/pixel (double) More...
 
static final int MDL_SAMPLINGRATE_X = 327
 < original sampling rate in A/pixel (double) More...
 
static final int MDL_SAMPLINGRATE_Y = 328
 < sampling rate in A/pixel (double) More...
 
static final int MDL_SAMPLINGRATE_Z = 329
 < sampling rate in A/pixel (double) More...
 
static final int MDL_SCALE = 330
 < sampling rate in A/pixel (double) More...
 
static final int MDL_SCORE_BY_PCA_RESIDUAL_PROJ = 331
 < scaling factor for an image or volume (double) More...
 
static final int MDL_SCORE_BY_PCA_RESIDUAL_EXP = 332
 
static final int MDL_SCORE_BY_PCA_RESIDUAL = 333
 
static final int MDL_SCORE_BY_ALIGNABILITY = 334
 
static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION = 335
 < score by alignability (double) More...
 
static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY = 336
 < score by alignability (double) More...
 
static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXP = 337
 < score by alignability (double) More...
 
static final int MDL_SCORE_BY_ALIGNABILITY_PRECISION_REF = 338
 < score by alignability experimental particles (double) More...
 
static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXP = 339
 < score by alignability references (double) More...
 
static final int MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REF = 340
 < score by alignability experimental particles (double) More...
 
static final int MDL_SCORE_BY_ALIGNABILITY_NOISE = 341
 < score by alignability references (double) More...
 
static final int MDL_SCORE_BY_EMPTINESS = 342
 < score by alignability noise (double) More...
 
static final int MDL_SCORE_BY_ENTROPY = 343
 < Small values represent worse particles. Much larger than 1 for good particles More...
 
static final int MDL_SCORE_BY_GRANULO = 344
 < Feature vectors used to classify particles (vector double) More...
 
static final int MDL_SCORE_BY_HISTDIST = 345
 < Feature vectors used to classify particles (vector double) More...
 
static final int MDL_SCORE_BY_LBP = 346
 < Feature vectors used to classify particles (vector double) More...
 
static final int MDL_SCORE_BY_MIRROR = 347
 < Feature vectors used to classify particles (vector double) More...
 
static final int MDL_SCORE_BY_RAMP = 348
 < score by mirror (double) More...
 
static final int MDL_SCORE_BY_SCREENING = 349
 < Feature vectors used to classify particles (vector double) More...
 
static final int MDL_SCORE_BY_VARIANCE = 350
 < Feature vectors used to classify particles (vector double) More...
 
static final int MDL_SCORE_BY_VAR = 351
 < Feature vectors used to classify particles (vector double) More...
 
static final int MDL_SCORE_BY_GINI = 352
 < Particle variance (double) More...
 
static final int MDL_SCORE_BY_ZERNIKE = 353
 < Micrographs Gini Coeff. (double) More...
 
static final int MDL_SCORE_BY_ZSCORE = 354
 < Feature vectors used to classify particles (vector double) More...
 
static final int MDL_SELFILE = 355
 
static final int MDL_SERIE = 356
 < Name of an image (std::string) More...
 
static final int MDL_SHIFT_X = 357
 < A collection of micrographs, e.g. a tilt serie (std::string) More...
 
static final int MDL_SHIFT_X2 = 358
 < Shift for the image in the X axis (double) More...
 
static final int MDL_SHIFT_X3 = 359
 < Shift for the image in the X axis (double) More...
 
static final int MDL_SHIFT_X_DIFF = 360
 < Shift for the image in the X axis (double) More...
 
static final int MDL_SHIFT_Y = 361
 < difference in Shift along X axis (double) More...
 
static final int MDL_SHIFT_Y2 = 362
 < Shift for the image in the Y axis (double) More...
 
static final int MDL_SHIFT_Y3 = 363
 < Shift for the image in the Y axis (double) More...
 
static final int MDL_SHIFT_Y_DIFF = 364
 < Shift for the image in the Y axis (double) More...
 
static final int MDL_SHIFT_Z = 365
 < difference in Shift along Y axis (double) More...
 
static final int MDL_SHIFT_Z2 = 366
 < Shift for the image in the Z axis (double) More...
 
static final int MDL_SHIFT_Z3 = 367
 < Shift for the image in the Z axis (double) More...
 
static final int MDL_SHIFT_DIFF0 = 368
 < Shift for the image in the Z axis (double) More...
 
static final int MDL_SHIFT_DIFF = 369
 < shift difference (double) More...
 
static final int MDL_SHIFT_DIFF2 = 370
 < shift difference (double) More...
 
static final int MDL_SIGMANOISE = 371
 < shift difference (double) More...
 
static final int MDL_SIGMAOFFSET = 372
 < Standard deviation of the noise in ML model More...
 
static final int MDL_SIGNALCHANGE = 373
 < Standard deviation of the offsets in ML model More...
 
static final int MDL_SPH_COEFFICIENTS = 374
 < Signal change for an image More...
 
static final int MDL_SPH_DEFORMATION = 375
 < Deformation coefficients More...
 
static final int MDL_SPH_TSNE_COEFF1D = 376
 < Deformation in voxels More...
 
static final int MDL_SPH_TSNE_COEFF2D = 377
 tsne coefficicient in 1D More...
 
static final int MDL_STDDEV = 378
 tsne coefficients in 2D More...
 
static final int MDL_STAR_COMMENT = 379
 <stdandard deviation value (double) More...
 
static final int MDL_SUBTRACTION_R2 = 380
 < A comment for this object /*** NOTE THIS IS A SPECIAL CASE AND SO IS TREATED ***/ More...
 
static final int MDL_SUBTRACTION_BETA0 = 381
 < R2 coefficient of subtracted particle More...
 
static final int MDL_SUBTRACTION_BETA1 = 382
 < Beta 0 coefficient of adjusted model for subtract particle More...
 
static final int MDL_SUM = 383
 < Beta 1 coefficient of adjusted model for subtract particle More...
 
static final int MDL_SUMWEIGHT = 384
 < Sum of elements of a given type (double) [this is a genereic type do not use to transfer information to another program] More...
 
static final int MDL_SYMNO = 385
 < Sum of all weights in ML model More...
 
static final int MDL_TOMOGRAM_VOLUME = 386
 < Symmetry number for a projection (used in ART) More...
 
static final int MDL_TOMOGRAMMD = 387
 < Name for the reconstructed tomogram volume (std::string) More...
 
static final int MDL_TRANSFORM_MATRIX = 388
 < Name for a Metadata file (std::string) More...
 
static final int MDL_TSID = 389
 < transformation matrix in numpy string format or space separated (std::string) More...
 
static final int MDL_TEST_SIZE = 390
 <Tilt series id (std::string) More...
 
static final int MDL_TILT_ANALYSIS_MEAN = 391
 
static final int MDL_TILT_ANALYSIS_STD = 392
 
static final int MDL_TILT_ANALYSIS_MIN = 393
 
static final int MDL_TILT_ANALYSIS_MAX = 394
 
static final int MDL_TILT_ANALYSIS_PSDs = 395
 
static final int MDL_VOLUME_SCORE_SUM = 396
 
static final int MDL_VOLUME_SCORE_SUM_TH = 397
 < Score corresponding to the sum of cc with cc>threshold More...
 
static final int MDL_VOLUME_SCORE_MEAN = 398
 < Score corresponding to the sum of cc-threshold with cc>threshold More...
 
static final int MDL_VOLUME_SCORE_MIN = 399
 < Score corresponding to the mean of cc with cc>threshold More...
 
static final int MDL_VOLUME_SCORE1 = 400
 < Score corresponding to the min of cc with cc>threshold More...
 
static final int MDL_VOLUME_SCORE2 = 401
 < Score 1 for volumes More...
 
static final int MDL_VOLUME_SCORE3 = 402
 < Score 2 for volumes More...
 
static final int MDL_VOLUME_SCORE4 = 403
 < Score 3 for volumes More...
 
static final int MDL_WEIGHT = 404
 < Score 4 for volumes More...
 
static final int MDL_WEIGHT_P = 405
 < Weight assigned to the image (double) More...
 
static final int MDL_WEIGHT_CONTINUOUS2 = 406
 < Weight assigned to the image accordint to its clusterability with a significance with respect noise (double) More...
 
static final int MDL_WEIGHT_JUMPER0 = 407
 < Weight due to angular continuous assignment More...
 
static final int MDL_WEIGHT_JUMPER = 408
 < Weight due to angular jumping More...
 
static final int MDL_WEIGHT_JUMPER2 = 409
 < Weight due to angular jumping More...
 
static final int MDL_WEIGHT_REALCORR = 410
 < Weight due to angular jumping More...
 
static final int MDL_WEIGHT_PHASECORR = 411
 < Weight due correlation between two images/subtomos More...
 
static final int MDL_WEIGHT_SIGNIFICANT = 412
 < Weight due phase correlation between two images/subtomos More...
 
static final int MDL_WEIGHT_SSNR = 413
 < Weight due to Angular significance More...
 
static final int MDL_WEIGHT_PRECISION_ALIGNABILITY = 414
 < Weight due to SSNR More...
 
static final int MDL_WEIGHT_ALIGNABILITY = 415
 < Weight due to Alignability Precision More...
 
static final int MDL_WEIGHT_ACCURACY_ALIGNABILITY = 416
 < Weight due to Alignability Precision and Accuracy More...
 
static final int MDL_WEIGHT_PRECISION_MIRROR = 417
 < Weight due to Alignability Accuracy More...
 
static final int MDL_WROBUST = 418
 < Weight due to Mirror Precision More...
 
static final int MDL_X = 419
 < Weight of t-student distribution in robust Maximum likelihood More...
 
static final int MDL_XCOOR = 420
 < X component (double) More...
 
static final int MDL_XCOOR_TILT = 421
 < X component (int) More...
 
static final int MDL_XSIZE = 422
 < X component in tilted micrograph (int) More...
 
static final int MDL_Y = 423
 < X size (int) More...
 
static final int MDL_YCOOR = 424
 < Y component (double) More...
 
static final int MDL_YCOOR_TILT = 425
 < Y component (int) More...
 
static final int MDL_YSIZE = 426
 < Y component in tilted micrograph (int) More...
 
static final int MDL_Z = 427
 < Y size (int) More...
 
static final int MDL_ZCOOR = 428
 < Z component (double) More...
 
static final int MDL_ZSCORE = 429
 < Z component (int) More...
 
static final int MDL_ZSCORE_DEEPLEARNING1 = 430
 < Global Z Score (double) More...
 
static final int MDL_GOOD_REGION_SCORE = 431
 < Z Score (double) More...
 
static final int MDL_ZSCORE_HISTOGRAM = 432
 < Z Score (double) More...
 
static final int MDL_ZSCORE_RESMEAN = 433
 < Z Score (double) More...
 
static final int MDL_ZSCORE_RESVAR = 434
 < Z Score of the mean of the residuals (double) More...
 
static final int MDL_ZSCORE_RESCOV = 435
 < Z Score of the stddev of the residuals (double) More...
 
static final int MDL_ZSCORE_SHAPE1 = 436
 < Z Score of the covariance matrix of the residuals (double) More...
 
static final int MDL_ZSCORE_SHAPE2 = 437
 < Z Score (double) More...
 
static final int MDL_ZSCORE_SNR1 = 438
 < Z Score (double) More...
 
static final int MDL_ZSCORE_SNR2 = 439
 < Z Score (double) More...
 
static final int MDL_ZSIZE = 440
 < Z Score (double) More...
 
static final int RLN_AREA_ID = 441
 < Z size (int) More...
 
static final int RLN_AREA_NAME = 442
 < ID for the area (or field of view). If one does not use (tilt) series, area would be the same as micrograph... More...
 
static final int RLN_COMMENT = 443
 < Name for the area (or field of view). If one does not use (tilt) series, area would be the same as micrograph... More...
 
static final int RLN_CTF_BFACTOR = 444
 
static final int RLN_CTF_SCALEFACTOR = 445
 < B-factor More...
 
static final int RLN_CTF_SAMPLING_RATE = 446
 < linear scale-factor More...
 
static final int RLN_CTF_VOLTAGE = 447
 < Sampling rate More...
 
static final int RLN_CTF_DEFOCUSU = 448
 < Microscope voltage (kV) More...
 
static final int RLN_CTF_DEFOCUSV = 449
 < Defocus U (Angstroms) More...
 
static final int RLN_CTF_DEFOCUS_ANGLE = 450
 < Defocus V (Angstroms) More...
 
static final int RLN_CTF_CS = 451
 < Defocus angle (degrees) More...
 
static final int RLN_CTF_CA = 452
 < Spherical aberration More...
 
static final int RLN_CTF_DETECTOR_PIXEL_SIZE = 453
 < Chromatic aberration More...
 
static final int RLN_CTF_ENERGY_LOSS = 454
 < Pixel size for detector as used in CTF-determination More...
 
static final int RLN_CTF_FOM = 455
 < Energy loss More...
 
static final int RLN_CTF_IMAGE = 456
 < ctffind3 FOM (CC) for quality of CTF-fit More...
 
static final int RLN_CTF_LENS_STABILITY = 457
 < name of an image describing the CTF model More...
 
static final int RLN_CTF_MAGNIFICATION = 458
 < Lens stability More...
 
static final int RLN_CTF_MAXRES = 459
 < Magnification used for CTF-determination More...
 
static final int RLN_CTF_CONVERGENCE_CONE = 460
 < Maximum resolution with Thon rings More...
 
static final int RLN_CTF_LONGITUDINAL_DISPLACEMENT = 461
 < Convergence cone More...
 
static final int RLN_CTF_TRANSVERSAL_DISPLACEMENT = 462
 < Longitudinal displacement More...
 
static final int RLN_CTF_Q0 = 463
 < Transversal displacemente More...
 
static final int RLN_CTF_K = 464
 < Amplitude contrast More...
 
static final int RLN_CTF_VALUE = 465
 < CTF gain More...
 
static final int RLN_CTF_VALIDATIONSCORE = 466
 < CTF value More...
 
static final int RLN_CTF_PHASESHIFT = 467
 < Gctf-based validation score for CTF fit More...
 
static final int RLN_IMAGE_NAME = 468
 < Phase-shift from a phase-plate (in degrees) More...
 
static final int RLN_IMAGE_RECONSTRUCT_NAME = 469
 
static final int RLN_IMAGE_ID = 470
 
static final int RLN_IMAGE_ENABLED = 471
 
static final int RLN_IMAGE_DATATYPE = 472
 
static final int RLN_IMAGE_DIMENSIONALITY = 473
 
static final int RLN_IMAGE_BEAMTILT_X = 474
 
static final int RLN_IMAGE_BEAMTILT_Y = 475
 
static final int RLN_IMAGE_BEAMTILT_GROUP = 476
 
static final int RLN_IMAGE_COORD_X = 477
 
static final int RLN_IMAGE_COORD_Y = 478
 
static final int RLN_IMAGE_COORD_Z = 479
 
static final int RLN_IMAGE_FRAME_NR = 480
 
static final int RLN_IMAGE_MAGNIFICATION_CORRECTION = 481
 
static final int RLN_IMAGE_NORM_CORRECTION = 482
 
static final int RLN_IMAGE_ORI_NAME = 483
 
static final int RLN_IMAGE_SAMPLINGRATE = 484
 
static final int RLN_IMAGE_SAMPLINGRATE_X = 485
 
static final int RLN_IMAGE_SAMPLINGRATE_Y = 486
 
static final int RLN_IMAGE_SAMPLINGRATE_Z = 487
 
static final int RLN_IMAGE_SIZE = 488
 
static final int RLN_IMAGE_SIZEX = 489
 
static final int RLN_IMAGE_SIZEY = 490
 
static final int RLN_IMAGE_SIZEZ = 491
 
static final int RLN_IMAGE_STATS_MIN = 492
 
static final int RLN_IMAGE_STATS_MAX = 493
 
static final int RLN_IMAGE_STATS_AVG = 494
 
static final int RLN_IMAGE_STATS_STDDEV = 495
 
static final int RLN_IMAGE_STATS_SKEW = 496
 
static final int RLN_IMAGE_STATS_KURT = 497
 
static final int RLN_IMAGE_WEIGHT = 498
 
static final int RLN_MASK_NAME = 499
 
static final int RLN_MATRIX_1_1 = 500
 
static final int RLN_MATRIX_1_2 = 501
 
static final int RLN_MATRIX_1_3 = 502
 
static final int RLN_MATRIX_2_1 = 503
 
static final int RLN_MATRIX_2_2 = 504
 
static final int RLN_MATRIX_2_3 = 505
 
static final int RLN_MATRIX_3_1 = 506
 
static final int RLN_MATRIX_3_2 = 507
 
static final int RLN_MATRIX_3_3 = 508
 
static final int RLN_MICROGRAPH_ID = 509
 
static final int RLN_MICROGRAPH_MOVIE_NAME = 510
 
static final int RLN_MICROGRAPH_NAME = 511
 
static final int RLN_MICROGRAPH_NAME_WODOSE = 512
 
static final int RLN_MICROGRAPH_TILT_ANGLE = 513
 
static final int RLN_MICROGRAPH_TILT_AXIS_DIRECTION = 514
 
static final int RLN_MICROGRAPH_TILT_AXIS_OUTOFPLANE = 515
 
static final int RLN_MLMODEL_ACCURACY_ROT = 516
 
static final int RLN_MLMODEL_ACCURACY_TRANS = 517
 
static final int RLN_MLMODEL_AVE_PMAX = 518
 
static final int RLN_MLMODEL_CURRENT_RESOLUTION = 519
 
static final int RLN_MLMODEL_CURRENT_SIZE = 520
 
static final int RLN_MLMODEL_DATA_VS_PRIOR_REF = 521
 
static final int RLN_MLMODEL_DIMENSIONALITY = 522
 
static final int RLN_MLMODEL_DIMENSIONALITY_DATA = 523
 
static final int RLN_MLMODEL_DIFF2_HALVES_REF = 524
 
static final int RLN_MLMODEL_ESTIM_RESOL_REF = 525
 
static final int RLN_MLMODEL_FOURIER_COVERAGE_REF = 526
 
static final int RLN_MLMODEL_FOURIER_COVERAGE_TOTAL_REF = 527
 
static final int RLN_MLMODEL_FSC_HALVES_REF = 528
 
static final int RLN_MLMODEL_GROUP_NAME = 529
 
static final int RLN_MLMODEL_GROUP_NO = 530
 
static final int RLN_MLMODEL_GROUP_NR_PARTICLES = 531
 
static final int RLN_MLMODEL_GROUP_SCALE_CORRECTION = 532
 
static final int RLN_MLMODEL_HELICAL_NR_ASU = 533
 
static final int RLN_MLMODEL_HELICAL_TWIST = 534
 
static final int RLN_MLMODEL_HELICAL_TWIST_MIN = 535
 
static final int RLN_MLMODEL_HELICAL_TWIST_MAX = 536
 
static final int RLN_MLMODEL_HELICAL_TWIST_INITIAL_STEP = 537
 
static final int RLN_MLMODEL_HELICAL_RISE = 538
 
static final int RLN_MLMODEL_HELICAL_RISE_MIN = 539
 
static final int RLN_MLMODEL_HELICAL_RISE_MAX = 540
 
static final int RLN_MLMODEL_HELICAL_RISE_INITIAL_STEP = 541
 
static final int RLN_MLMODEL_IS_HELIX = 542
 
static final int RLN_MLMODEL_INTERPOLATOR = 543
 
static final int RLN_MLMODEL_LL = 544
 
static final int RLN_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION = 545
 
static final int RLN_MLMODEL_NORM_CORRECTION_AVG = 546
 
static final int RLN_MLMODEL_NR_BODIES = 547
 
static final int RLN_MLMODEL_NR_CLASSES = 548
 
static final int RLN_MLMODEL_NR_GROUPS = 549
 
static final int RLN_MLMODEL_ORIGINAL_SIZE = 550
 
static final int RLN_MLMODEL_ORIENTABILITY_CONTRIBUTION = 551
 
static final int RLN_MLMODEL_PADDING_FACTOR = 552
 
static final int RLN_MLMODEL_PDF_CLASS = 553
 
static final int RLN_MLMODEL_PRIOR_OFFX_CLASS = 554
 
static final int RLN_MLMODEL_PRIOR_OFFY_CLASS = 555
 
static final int RLN_MLMODEL_PDF_ORIENT = 556
 
static final int RLN_MLMODEL_PIXEL_SIZE = 557
 
static final int RLN_MLMODEL_POWER_REF = 558
 
static final int RLN_MLMODEL_PRIOR_MODE = 559
 
static final int RLN_MLMODEL_SGD_GRADIENT_IMAGE = 560
 
static final int RLN_MLMODEL_SIGMA_OFFSET = 561
 
static final int RLN_MLMODEL_SIGMA_ROT = 562
 
static final int RLN_MLMODEL_SIGMA_TILT = 563
 
static final int RLN_MLMODEL_SIGMA_PSI = 564
 
static final int RLN_MLMODEL_REF_IMAGE = 565
 
static final int RLN_MLMODEL_SIGMA2_NOISE = 566
 
static final int RLN_MLMODEL_SIGMA2_REF = 567
 
static final int RLN_MLMODEL_SSNR_REF = 568
 
static final int RLN_MLMODEL_TAU2_FUDGE_FACTOR = 569
 
static final int RLN_MLMODEL_TAU2_REF = 570
 
static final int RLN_OPTIMISER_ACCURACY_ROT = 571
 
static final int RLN_OPTIMISER_ACCURACY_TRANS = 572
 
static final int RLN_OPTIMISER_ADAPTIVE_FRACTION = 573
 
static final int RLN_OPTIMISER_ADAPTIVE_OVERSAMPLING = 574
 
static final int RLN_OPTIMISER_AUTO_LOCAL_HP_ORDER = 575
 
static final int RLN_OPTIMISER_AVAILABLE_MEMORY = 576
 
static final int RLN_OPTIMISER_BEST_RESOL_THUS_FAR = 577
 
static final int RLN_OPTIMISER_CHANGES_OPTIMAL_OFFSETS = 578
 
static final int RLN_OPTIMISER_CHANGES_OPTIMAL_ORIENTS = 579
 
static final int RLN_OPTIMISER_CHANGES_OPTIMAL_CLASSES = 580
 
static final int RLN_OPTIMISER_COARSE_SIZE = 581
 
static final int RLN_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED = 582
 
static final int RLN_OPTIMISER_DATA_ARE_CTF_PREMULTIPLIED = 583
 
static final int RLN_OPTIMISER_DATA_STARFILE = 584
 
static final int RLN_OPTIMISER_DO_AUTO_REFINE = 585
 
static final int RLN_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES = 586
 
static final int RLN_OPTIMISER_DO_CORRECT_CTF = 587
 
static final int RLN_OPTIMISER_DO_CORRECT_MAGNIFICATION = 588
 
static final int RLN_OPTIMISER_DO_CORRECT_NORM = 589
 
static final int RLN_OPTIMISER_DO_CORRECT_SCALE = 590
 
static final int RLN_OPTIMISER_DO_HELICAL_REFINE = 591
 
static final int RLN_OPTIMISER_DO_REALIGN_MOVIES = 592
 
static final int RLN_OPTIMISER_DO_MAP = 593
 
static final int RLN_OPTIMISER_DO_SGD = 594
 
static final int RLN_OPTIMISER_DO_SOLVENT_FLATTEN = 595
 
static final int RLN_OPTIMISER_DO_SKIP_ALIGN = 596
 
static final int RLN_OPTIMISER_DO_SKIP_ROTATE = 597
 
static final int RLN_OPTIMISER_DO_SPLIT_RANDOM_HALVES = 598
 
static final int RLN_OPTIMISER_DO_ZERO_MASK = 599
 
static final int RLN_OPTIMISER_FIX_SIGMA_NOISE = 600
 
static final int RLN_OPTIMISER_FIX_SIGMA_OFFSET = 601
 
static final int RLN_OPTIMISER_FIX_TAU = 602
 
static final int RLN_OPTIMISER_HAS_CONVERGED = 603
 
static final int RLN_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT = 604
 
static final int RLN_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO = 605
 
static final int RLN_OPTIMISER_HELICAL_TWIST_INITIAL = 606
 
static final int RLN_OPTIMISER_HELICAL_RISE_INITIAL = 607
 
static final int RLN_OPTIMISER_HELICAL_Z_PERCENTAGE = 608
 
static final int RLN_OPTIMISER_HELICAL_TUBE_INNER_DIAMETER = 609
 
static final int RLN_OPTIMISER_HELICAL_TUBE_OUTER_DIAMETER = 610
 
static final int RLN_OPTIMISER_HELICAL_SYMMETRY_LOCAL_REFINEMENT = 611
 
static final int RLN_OPTIMISER_HELICAL_SIGMA_DISTANCE = 612
 
static final int RLN_OPTIMISER_HIGHRES_LIMIT_SGD = 613
 
static final int RLN_OPTIMISER_IGNORE_HELICAL_SYMMETRY = 614
 
static final int RLN_OPTIMISER_HELICAL_KEEP_TILT_PRIOR_FIXED = 615
 
static final int RLN_OPTIMISER_HIGHRES_LIMIT_EXP = 616
 
static final int RLN_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK = 617
 
static final int RLN_OPTIMISER_INCR_SIZE = 618
 
static final int RLN_OPTIMISER_ITERATION_NO = 619
 
static final int RLN_OPTIMISER_LOCAL_SYMMETRY_FILENAME = 620
 
static final int RLN_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES = 621
 
static final int RLN_OPTIMISER_MAGNIFICATION_RANGE = 622
 
static final int RLN_OPTIMISER_MAGNIFICATION_STEP = 623
 
static final int RLN_OPTIMISER_MAX_COARSE_SIZE = 624
 
static final int RLN_OPTIMISER_MAX_NR_POOL = 625
 
static final int RLN_OPTIMISER_MODEL_STARFILE = 626
 
static final int RLN_OPTIMISER_MODEL_STARFILE2 = 627
 
static final int RLN_OPTIMISER_NR_ITERATIONS = 628
 
static final int RLN_OPTIMISER_NR_ITER_WO_RESOL_GAIN = 629
 
static final int RLN_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES = 630
 
static final int RLN_OPTIMISER_OUTPUT_ROOTNAME = 631
 
static final int RLN_OPTIMISER_PARTICLE_DIAMETER = 632
 
static final int RLN_OPTIMISER_RADIUS_MASK_3D_MAP = 633
 
static final int RLN_OPTIMISER_RADIUS_MASK_EXP_PARTICLES = 634
 
static final int RLN_OPTIMISER_RANDOM_SEED = 635
 
static final int RLN_OPTIMISER_REFS_ARE_CTF_CORRECTED = 636
 
static final int RLN_OPTIMISER_SAMPLING_STARFILE = 637
 
static final int RLN_OPTIMISER_SGD_MU = 638
 
static final int RLN_OPTIMISER_SGD_SIGMA2FUDGE_INI = 639
 
static final int RLN_OPTIMISER_SGD_SIGMA2FUDGE_HALFLIFE = 640
 
static final int RLN_OPTIMISER_SGD_SUBSET_START = 641
 
static final int RLN_OPTIMISER_SGD_SUBSET_SIZE = 642
 
static final int RLN_OPTIMISER_SGD_WRITE_EVERY_SUBSET = 643
 
static final int RLN_OPTIMISER_SGD_MAX_SUBSETS = 644
 
static final int RLN_OPTIMISER_SGD_STEPSIZE = 645
 
static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES = 646
 
static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS = 647
 
static final int RLN_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS = 648
 
static final int RLN_OPTIMISER_SOLVENT_MASK_NAME = 649
 
static final int RLN_OPTIMISER_SOLVENT_MASK2_NAME = 650
 
static final int RLN_OPTIMISER_TAU_SPECTRUM_NAME = 651
 
static final int RLN_OPTIMISER_USE_TOO_COARSE_SAMPLING = 652
 
static final int RLN_OPTIMISER_WIDTH_MASK_EDGE = 653
 
static final int RLN_ORIENT_FLIP = 654
 
static final int RLN_ORIENT_ID = 655
 
static final int RLN_ORIENT_ORIGIN_X = 656
 
static final int RLN_ORIENT_ORIGIN_X_PRIOR = 657
 
static final int RLN_ORIENT_ORIGIN_Y = 658
 
static final int RLN_ORIENT_ORIGIN_Y_PRIOR = 659
 
static final int RLN_ORIENT_ORIGIN_Z = 660
 
static final int RLN_ORIENT_ORIGIN_Z_PRIOR = 661
 
static final int RLN_ORIENT_ROT = 662
 
static final int RLN_ORIENT_ROT_PRIOR = 663
 
static final int RLN_ORIENT_TILT = 664
 
static final int RLN_ORIENT_TILT_PRIOR = 665
 
static final int RLN_ORIENT_PSI = 666
 
static final int RLN_ORIENT_PSI_PRIOR = 667
 
static final int RLN_ORIENT_PSI_PRIOR_FLIP_RATIO = 668
 
static final int RLN_PARTICLE_AUTOPICK_FOM = 669
 
static final int RLN_PARTICLE_CLASS = 670
 
static final int RLN_PARTICLE_DLL = 671
 
static final int RLN_PARTICLE_ID = 672
 
static final int RLN_PARTICLE_FOM = 673
 
static final int RLN_PARTICLE_KL_DIVERGENCE = 674
 
static final int RLN_PARTICLE_MOVIE_RUNNING_AVG = 675
 
static final int RLN_PARTICLE_RANDOM_SUBSET = 676
 
static final int RLN_PARTICLE_NAME = 677
 
static final int RLN_PARTICLE_ORI_NAME = 678
 
static final int RLN_PARTICLE_NR_SIGNIFICANT_SAMPLES = 679
 
static final int RLN_PARTICLE_NR_FRAMES = 680
 
static final int RLN_PARTICLE_NR_FRAMES_AVG = 681
 
static final int RLN_PARTICLE_PMAX = 682
 
static final int RLN_PARTICLE_HELICAL_TUBE_ID = 683
 
static final int RLN_PARTICLE_HELICAL_TUBE_PITCH = 684
 
static final int RLN_PARTICLE_HELICAL_TRACK_LENGTH = 685
 
static final int RLN_PIPELINE_JOB_COUNTER = 686
 
static final int RLN_PIPELINE_NODE_NAME = 687
 
static final int RLN_PIPELINE_NODE_TYPE = 688
 
static final int RLN_PIPELINE_PROCESS_ALIAS = 689
 
static final int RLN_PIPELINE_PROCESS_NAME = 690
 
static final int RLN_PIPELINE_PROCESS_TYPE = 691
 
static final int RLN_PIPELINE_PROCESS_STATUS = 692
 
static final int RLN_PIPELINE_EDGE_FROM = 693
 
static final int RLN_PIPELINE_EDGE_TO = 694
 
static final int RLN_PIPELINE_EDGE_PROCESS = 695
 
static final int RLN_POSTPROCESS_AMPLCORR_MASKED = 696
 
static final int RLN_POSTPROCESS_AMPLCORR_UNMASKED = 697
 
static final int RLN_POSTPROCESS_BFACTOR = 698
 
static final int RLN_POSTPROCESS_DPR_MASKED = 699
 
static final int RLN_POSTPROCESS_DPR_UNMASKED = 700
 
static final int RLN_POSTPROCESS_FINAL_RESOLUTION = 701
 
static final int RLN_POSTPROCESS_FSC_GENERAL = 702
 
static final int RLN_POSTPROCESS_FSC_TRUE = 703
 
static final int RLN_POSTPROCESS_FSC_MASKED = 704
 
static final int RLN_POSTPROCESS_FSC_UNMASKED = 705
 
static final int RLN_POSTPROCESS_FSC_RANDOM_MASKED = 706
 
static final int RLN_POSTPROCESS_GUINIER_FIT_CORRELATION = 707
 
static final int RLN_POSTPROCESS_GUINIER_FIT_INTERCEPT = 708
 
static final int RLN_POSTPROCESS_GUINIER_FIT_SLOPE = 709
 
static final int RLN_POSTPROCESS_GUINIER_VALUE_IN = 710
 
static final int RLN_POSTPROCESS_GUINIER_VALUE_INVMTF = 711
 
static final int RLN_POSTPROCESS_GUINIER_VALUE_WEIGHTED = 712
 
static final int RLN_POSTPROCESS_GUINIER_VALUE_SHARPENED = 713
 
static final int RLN_POSTPROCESS_GUINIER_VALUE_INTERCEPT = 714
 
static final int RLN_POSTPROCESS_GUINIER_RESOL_SQUARED = 715
 
static final int RLN_POSTPROCESS_MTF_VALUE = 716
 
static final int RLN_SAMPLING_IS_3D = 717
 < Detector MTF value More...
 
static final int RLN_SAMPLING_IS_3D_TRANS = 718
 
static final int RLN_SAMPLING_HEALPIX_ORDER = 719
 
static final int RLN_SAMPLING_HELICAL_OFFSET_STEP = 720
 
static final int RLN_SAMPLING_LIMIT_TILT = 721
 
static final int RLN_SAMPLING_OFFSET_RANGE = 722
 
static final int RLN_SAMPLING_OFFSET_STEP = 723
 
static final int RLN_SAMPLING_PERTURB = 724
 
static final int RLN_SAMPLING_PERTURBATION_FACTOR = 725
 
static final int RLN_SAMPLING_PRIOR_MODE = 726
 
static final int RLN_SAMPLING_PSI_STEP = 727
 
static final int RLN_SAMPLING_SIGMA_ROT = 728
 
static final int RLN_SAMPLING_SIGMA_TILT = 729
 
static final int RLN_SAMPLING_SIGMA_PSI = 730
 
static final int RLN_SAMPLING_SYMMETRY = 731
 
static final int RLN_SELECTED = 732
 
static final int RLN_SELECT_PARTICLES_ZSCORE = 733
 
static final int RLN_SORTED_IDX = 734
 
static final int RLN_STARFILE_MOVIE_PARTICLES = 735
 
static final int RLN_PERFRAME_CUMULATIVE_WEIGHT = 736
 
static final int RLN_PERFRAME_RELATIVE_WEIGHT = 737
 
static final int RLN_RESOLUTION = 738
 
static final int RLN_RESOLUTION_ANGSTROM = 739
 
static final int RLN_RESOLUTION_INVPIXEL = 740
 
static final int RLN_SPECTRAL_IDX = 741
 
static final int MDL_LAST_LABEL = 742
 
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Detailed Description

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Definition at line 3 of file MDLabel.java.

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Member Data Documentation

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◆ MDL_ANGLE_DIFF

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final int xmipp.jni.MDLabel.MDL_ANGLE_DIFF = 15
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< difference between two angles (double,degrees)

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Definition at line 21 of file MDLabel.java.

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◆ MDL_ANGLE_DIFF0

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final int xmipp.jni.MDLabel.MDL_ANGLE_DIFF0 = 14
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< difference between tilt angles (double,degrees)

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Definition at line 20 of file MDLabel.java.

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◆ MDL_ANGLE_DIFF2

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final int xmipp.jni.MDLabel.MDL_ANGLE_DIFF2 = 16
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< difference between two angles (double,degrees)

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Definition at line 22 of file MDLabel.java.

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◆ MDL_ANGLE_PSI

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final int xmipp.jni.MDLabel.MDL_ANGLE_PSI = 2
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Special label to be used when gathering MDs in MpiMetadataPrograms.

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Definition at line 8 of file MDLabel.java.

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- -

◆ MDL_ANGLE_PSI2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_PSI2 = 3
- 		-static
-
- -

< Psi angle of an image (double,degrees)

- -

Definition at line 9 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_PSI3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_PSI3 = 4
- 		-static
-
- -

< Psi angle of an image (double,degrees)

- -

Definition at line 10 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_PSI_DIFF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_PSI_DIFF = 5
- 		-static
-
- -

< Psi angle of an image (double,degrees)

- -

Definition at line 11 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_ROT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_ROT = 6
- 		-static
-
- -

< difference between psi angles (double,degrees)

- -

Definition at line 12 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_ROT2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_ROT2 = 7
- 		-static
-
- -

< Rotation angle of an image (double,degrees)

- -

Definition at line 13 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_ROT3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_ROT3 = 8
- 		-static
-
- -

< Rotation angle of an image (double,degrees)

- -

Definition at line 14 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_ROT_DIFF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_ROT_DIFF = 9
- 		-static
-
- -

< Rotation angle of an image (double,degrees)

- -

Definition at line 15 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_TEMPERATURE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_TEMPERATURE = 19
- 		-static
-
- -

< Angle between y-axis and tilt-axis (double, degrees) for tilted micrographs

- -

Definition at line 25 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_TILT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_TILT = 10
- 		-static
-
- -

< difference between rot angles (double,degrees)

- -

Definition at line 16 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_TILT2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_TILT2 = 11
- 		-static
-
- -

< Tilting angle of an image (double,degrees)

- -

Definition at line 17 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_TILT3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_TILT3 = 12
- 		-static
-
- -

< Tilting angle of an image (double,degrees)

- -

Definition at line 18 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_TILT_DIFF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_TILT_DIFF = 13
- 		-static
-
- -

< Tilting angle of an image (double,degrees)

- -

Definition at line 19 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_Y = 17
- 		-static
-
- -

< difference between two angles (double,degrees)

- -

Definition at line 23 of file MDLabel.java.

- -
-
- -

◆ MDL_ANGLE_Y2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ANGLE_Y2 = 18
- 		-static
-
- -

< Angle between y-axis and tilt-axis (double, degrees) for untilted micrographs

- -

Definition at line 24 of file MDLabel.java.

- -
-
- -

◆ MDL_APPLY_SHIFT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_APPLY_SHIFT = 20
- 		-static
-
- -

< Angular temperature (double,degrees)

- -

Definition at line 26 of file MDLabel.java.

- -
-
- -

◆ MDL_ASSIGNED_DIR_REF_CC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ASSIGNED_DIR_REF_CC = 309
- 		-static
-
- -

< Name of Metadata file for all references(string)

- -

Definition at line 315 of file MDLabel.java.

- -
-
- -

◆ MDL_AVG

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_AVG = 21
- 		-static
-
- -

<Apply shift when project the volume ,

- -

Definition at line 27 of file MDLabel.java.

- -
-
- -

◆ MDL_AVG_CHANGES_CLASSES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_AVG_CHANGES_CLASSES = 24
- 		-static
-
- -

Average change in offset (double pixels)

- -

Definition at line 30 of file MDLabel.java.

- -
-
- -

◆ MDL_AVG_CHANGES_OFFSETS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_AVG_CHANGES_OFFSETS = 23
- 		-static
-
- -

Average change in angular orientation (double degrees)

- -

Definition at line 29 of file MDLabel.java.

- -
-
- -

◆ MDL_AVG_CHANGES_ORIENTATIONS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_AVG_CHANGES_ORIENTATIONS = 22
- 		-static
-
- -

< average value (double)

- -

Definition at line 28 of file MDLabel.java.

- -
-
- -

◆ MDL_AVGPMAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_AVGPMAX = 25
- 		-static
-
- -

Average change in class assignment(double dimensionaless)

- -

Definition at line 31 of file MDLabel.java.

- -
-
- -

◆ MDL_BFACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_BFACTOR = 26
- 		-static
-
- -

< Average (per class) of the maximum value of normalized probability function) (double)

- -

Definition at line 32 of file MDLabel.java.

- -
-
- -

◆ MDL_BGMEAN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_BGMEAN = 27
- 		-static
-
- -

<Bfactor of a map, or even a local bfactor

- -

Definition at line 33 of file MDLabel.java.

- -
-
- -

◆ MDL_BLOCK_NUMBER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_BLOCK_NUMBER = 28
- 		-static
-
- -

< Mean background value for an image

- -

Definition at line 34 of file MDLabel.java.

- -
-
- -

◆ MDL_CL2D_CHANGES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CL2D_CHANGES = 29
- 		-static
-
- -

< Current block number (for incremental EM)

- -

Definition at line 35 of file MDLabel.java.

- -
-
- -

◆ MDL_CL2D_SIMILARITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CL2D_SIMILARITY = 30
- 		-static
-
- -

< Number of changes between iterations

- -

Definition at line 36 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASS_COUNT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASS_COUNT = 31
- 		-static
-
- -

< Average cross-correlation for the image (double)

- -

Definition at line 37 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASS_INTERSECTION_RELATIVE_SIZE_PVALUE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASS_INTERSECTION_RELATIVE_SIZE_PVALUE = 47
- 		-static
-
- -

< P-value (1-percentile) of the class size compared to a random distribution (double in [0, 1])

- -

Definition at line 53 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASS_INTERSECTION_SIZE_PVALUE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASS_INTERSECTION_SIZE_PVALUE = 46
- 		-static
-
- -

<Correlation between the denoised image and the noisy version

- -

Definition at line 52 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASS_PERCENTAGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASS_PERCENTAGE = 32
- 		-static
-
- -

< Number of images assigned to the same class as this image

- -

Definition at line 38 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASSIFICATION_DATA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASSIFICATION_DATA = 33
- 		-static
-
- -

< Percentage of images assigned to the same class as this image

- -

Definition at line 39 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASSIFICATION_DATA_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASSIFICATION_DATA_SIZE = 34
- 		-static
-
- -

< Data vector for classification (vector double)

- -

Definition at line 40 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASSIFICATION_DPR_05

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASSIFICATION_DPR_05 = 35
- 		-static
-
- -

< Size of data vectors for classification (int)

- -

Definition at line 41 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASSIFICATION_FRC_05

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASSIFICATION_FRC_05 = 37
- 		-static
-
- -

< Average intraclass distance (double)

- -

Definition at line 43 of file MDLabel.java.

- -
-
- -

◆ MDL_CLASSIFICATION_INTRACLASS_DISTANCE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CLASSIFICATION_INTRACLASS_DISTANCE = 36
- 		-static
-
- -

< Differential Phase Residual evaluated at FRC=0.5

- -

Definition at line 42 of file MDLabel.java.

- -
-
- -

◆ MDL_COLOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_COLOR = 276
- 		-static
-
- -

Definition at line 282 of file MDLabel.java.

- -
-
- -

◆ MDL_COMMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_COMMENT = 38
- 		-static
-
- -

< Digital frequency at which the FRC drops below 0.5 (double)

- -

Definition at line 44 of file MDLabel.java.

- -
-
- -

◆ MDL_CONTINUOUS_FLIP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CONTINUOUS_FLIP = 62
- 		-static
-
- -

< Y shift of continuous assignment

- -

Definition at line 68 of file MDLabel.java.

- -
-
- -

◆ MDL_CONTINUOUS_GRAY_A

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CONTINUOUS_GRAY_A = 63
- 		-static
-
- -

< Flip of continuous assignment

- -

Definition at line 69 of file MDLabel.java.

- -
-
- -

◆ MDL_CONTINUOUS_GRAY_B

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CONTINUOUS_GRAY_B = 64
- 		-static
-
- -

< a value of continuous assignment

- -

Definition at line 70 of file MDLabel.java.

- -
-
- -

◆ MDL_CONTINUOUS_SCALE_ANGLE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CONTINUOUS_SCALE_ANGLE = 65
- 		-static
-
- -

< b value of continuous assignment

- -

Definition at line 71 of file MDLabel.java.

- -
-
- -

◆ MDL_CONTINUOUS_SCALE_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CONTINUOUS_SCALE_X = 66
- 		-static
-
- -

< scale angle of continuous assignment

- -

Definition at line 72 of file MDLabel.java.

- -
-
- -

◆ MDL_CONTINUOUS_SCALE_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CONTINUOUS_SCALE_Y = 67
- 		-static
-
- -

< scale x of continuous assignment

- -

Definition at line 73 of file MDLabel.java.

- -
-
- -

◆ MDL_CONTINUOUS_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CONTINUOUS_X = 60
- 		-static
-
- -

< noise if center of unit cell (vector double)

- -

Definition at line 66 of file MDLabel.java.

- -
-
- -

◆ MDL_CONTINUOUS_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CONTINUOUS_Y = 61
- 		-static
-
- -

< X shift of continuous assignment

- -

Definition at line 67 of file MDLabel.java.

- -
-
- -

◆ MDL_COORD_CONSENSUS_SCORE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_COORD_CONSENSUS_SCORE = 39
- 		-static
-
- -

< Serve to make annotations on the metadata row

- -

Definition at line 45 of file MDLabel.java.

- -
-
- -

◆ MDL_CORR_DENOISED_NOISY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CORR_DENOISED_NOISY = 45
- 		-static
-
- -

<Correlation between the denoised image and the projection proposed

- -

Definition at line 51 of file MDLabel.java.

- -
-
- -

◆ MDL_CORR_DENOISED_PROJECTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CORR_DENOISED_PROJECTION = 44
- 		-static
-
- -

< Number of elements of a type (int) [this is a genereic type do not use to transfer information to another program]

- -

Definition at line 50 of file MDLabel.java.

- -
-
- -

◆ MDL_CORRELATION_IDX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CORRELATION_IDX = 68
- 		-static
-
- -

< scale y of continuous assignment

- -

Definition at line 74 of file MDLabel.java.

- -
-
- -

◆ MDL_CORRELATION_MASK

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CORRELATION_MASK = 69
- 		-static
-
- -

< correlation value between a particle and its assigned projection

- -

Definition at line 75 of file MDLabel.java.

- -
-
- -

◆ MDL_CORRELATION_WEIGHT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CORRELATION_WEIGHT = 70
- 		-static
-
- -

< masked correlation value between a particle and its assigned projection inside the region with pixel values higher than the standard deviation

- -

Definition at line 76 of file MDLabel.java.

- -
-
- -

◆ MDL_COST

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_COST = 40
- 		-static
-
- -

< Store a score for the coords. consensus (it will change the behavoir of the viewer)

- -

Definition at line 46 of file MDLabel.java.

- -
-
- -

◆ MDL_COST_PERCENTILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_COST_PERCENTILE = 41
- 		-static
-
- -

< Cost for the image (double)

- -

Definition at line 47 of file MDLabel.java.

- -
-
- -

◆ MDL_COUNT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_COUNT = 42
- 		-static
-
- -

< Cost percentile for the image (double)

- -

Definition at line 48 of file MDLabel.java.

- -
-
- -

◆ MDL_COUNT2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_COUNT2 = 43
- 		-static
-
- -

< Number of elements of a type (int) [this is a genereic type do not use to transfer information to another program]

- -

Definition at line 49 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_CELLX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_CELLX = 48
- 		-static
-
- -

< P-value (1-percentile) of the relative class size (size/max(original_classes)) compared to a random distribution (double in [0, 1])

- -

Definition at line 54 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_CELLY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_CELLY = 49
- 		-static
-
- -

< Cell location for crystals

- -

Definition at line 55 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_DISAPPEAR_THRE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_DISAPPEAR_THRE = 52
- 		-static
-
- -

< Lattice vector for projection (vector double)

- -

Definition at line 58 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_LATTICE_A

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_LATTICE_A = 50
- 		-static
-
- -

< Cell location for crystals

- -

Definition at line 56 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_LATTICE_B

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_LATTICE_B = 51
- 		-static
-
- -

< Lattice vector for projection (vector double)

- -

Definition at line 57 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_NOISE_SHIFT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_NOISE_SHIFT = 59
- 		-static
-
- -

< Shift for the image in the Z axis (double) for crystals

- -

Definition at line 65 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_ORTHO_PRJ

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_ORTHO_PRJ = 54
- 		-static
-
- -

< Shift file for crystal projection

- -

Definition at line 60 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_PROJ

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_PROJ = 55
- 		-static
-
- -

<Orthogonal projection or not (bool)

- -

Definition at line 61 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_SHFILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_SHFILE = 53
- 		-static
-
- -

< Disappearing threshold (double)

- -

Definition at line 59 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_SHIFTX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_SHIFTX = 56
- 		-static
-
- -

< Have a crystal projection (bool)

- -

Definition at line 62 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_SHIFTY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_SHIFTY = 57
- 		-static
-
- -

< Shift for the image in the X axis (double) for crystals

- -

Definition at line 63 of file MDLabel.java.

- -
-
- -

◆ MDL_CRYSTAL_SHIFTZ

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CRYSTAL_SHIFTZ = 58
- 		-static
-
- -

< Shift for the image in the Y axis (double) for crystals

- -

Definition at line 64 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_BASELINE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_BASELINE = 122
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 128 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN2_ANGLE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_ANGLE = 128
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 134 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN2_CU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_CU = 126
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 132 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN2_CV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_CV = 127
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 133 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN2_K

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_K = 123
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 129 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN2_SIGMAU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_SIGMAU = 124
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 130 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN2_SIGMAV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN2_SIGMAV = 125
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 131 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN_ANGLE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_ANGLE = 117
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 123 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN_CU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_CU = 115
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 121 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN_CV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_CV = 116
- 		-static
-
- -

<CTF_ CTF Background parameter

- -

Definition at line 122 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN_K

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_K = 112
- 		-static
-
- -

< CTF Envelope polynomial parameter

- -

Definition at line 118 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN_SIGMAU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_SIGMAU = 113
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 119 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_GAUSSIAN_SIGMAV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_GAUSSIAN_SIGMAV = 114
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 120 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_R1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_R1 = 129
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 135 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_R2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_R2 = 130
- 		-static
-
- -

< CTF Background polynomial parameter

- -

Definition at line 136 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_R3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_R3 = 131
- 		-static
-
- -

< CTF Background polynomial parameter

- -

Definition at line 137 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_SQRT_ANGLE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_SQRT_ANGLE = 121
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 127 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_SQRT_K

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_SQRT_K = 118
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 124 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_SQRT_U

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_SQRT_U = 119
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 125 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_BG_SQRT_V

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_BG_SQRT_V = 120
- 		-static
-
- -

< CTF Background parameter

- -

Definition at line 126 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CA = 98
- 		-static
-
- -

< Spherical aberration

- -

Definition at line 104 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CONVERGENCE_CONE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CONVERGENCE_CONE = 104
- 		-static
-
- -

< Lens stability

- -

Definition at line 110 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CORRECTED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CORRECTED = 72
- 		-static
-
- -

Definition at line 78 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_DAMPING

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_DAMPING = 140
- 		-static
-
- -

< Maximum frequency at which the envelope drops below 0.1 (in Angstroms)

- -

Definition at line 146 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_DIFF_RATIO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_DIFF_RATIO = 136
- 		-static
-
- -

< Ratio sigma(firstMinimum)/sigma(firstZero)

- -

Definition at line 142 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_RATIO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTMINIMUM_FIRSTZERO_RATIO = 135
- 		-static
-
- -

< First zero ratio

- -

Definition at line 141 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_FIRSTZEROAVG

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTZEROAVG = 137
- 		-static
-
- -

< Ratio sigma(firstMinimum-firstZero)/sigma(firstZero)

- -

Definition at line 143 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_FIRSTZERODISAGREEMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTZERODISAGREEMENT = 138
- 		-static
-
- -

< First zero average (in Angstroms)

- -

Definition at line 144 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_FIRSTZERORATIO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_FIRSTZERORATIO = 134
- 		-static
-
- -

< PSD correlation at 90 degrees

- -

Definition at line 140 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_FITTINGCORR13

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_FITTINGCORR13 = 143
- 		-static
-
- -

< Score of the fitting

- -

Definition at line 149 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_FITTINGSCORE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_FITTINGSCORE = 142
- 		-static
-
- -

< Integral of the radial PSD

- -

Definition at line 148 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_ICENESS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_ICENESS = 148
- 		-static
-
- -

< Normality test between histogram of micrography and gaussian distribution

- -

Definition at line 154 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_MAXFREQ

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_MAXFREQ = 139
- 		-static
-
- -

< First zero disagreement with second model (in Angstroms)

- -

Definition at line 145 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_NONASTIGMATICVALIDITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_NONASTIGMATICVALIDITY = 132
- 		-static
-
- -

< CTF Background polynomial parameter

- -

Definition at line 138 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_NORMALITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_NORMALITY = 147
- 		-static
-
- -

< Runs test on the projection of the PSD on the first principal component

- -

Definition at line 153 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_PSDCORRELATION90

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDCORRELATION90 = 133
- 		-static
-
- -

< Maximum frequency (in Angstroms) at which non-astigmatic CTF correction is valid

- -

Definition at line 139 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_PSDPCA1VARIANCE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDPCA1VARIANCE = 145
- 		-static
-
- -

< PSD variance

- -

Definition at line 151 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_PSDPCARUNSTEST

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDPCARUNSTEST = 146
- 		-static
-
- -

< Variance in the first principal component of the PSDs

- -

Definition at line 152 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_PSDRADIALINTEGRAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDRADIALINTEGRAL = 141
- 		-static
-
- -

< Minimum damping at border

- -

Definition at line 147 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CRIT_PSDVARIANCE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CRIT_PSDVARIANCE = 144
- 		-static
-
- -

< Correlation between the 1st and 3rd ring of the CTF

- -

Definition at line 150 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_CS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_CS = 97
- 		-static
-
- -

< Defocus angle (degrees)

- -

Definition at line 103 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DATA_PHASE_FLIPPED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DATA_PHASE_FLIPPED = 71
- 		-static
-
- -

< weighted correlation value between a particle and its assigned projection taking into the difference between both images

- -

Definition at line 77 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_ANGLE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_ANGLE = 96
- 		-static
-
- -

< Defocus = A*x+B*y+C

- -

Definition at line 102 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_CHANGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_CHANGE = 82
- 		-static
-
- -

< Defocus V (Angstroms)

- -

Definition at line 88 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_COEFS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_COEFS = 84
- 		-static
-
- -

< Defocus coefficient of determination

- -

Definition at line 90 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_PLANEUA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEUA = 90
- 		-static
-
- -

< The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates

- -

Definition at line 96 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_PLANEUB

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEUB = 91
- 		-static
-
- -

< Defocus = A*x+B*y+C

- -

Definition at line 97 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_PLANEUC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEUC = 92
- 		-static
-
- -

< Defocus = A*x+B*y+C

- -

Definition at line 98 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_PLANEVA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEVA = 93
- 		-static
-
- -

< Defocus = A*x+B*y+C

- -

Definition at line 99 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_PLANEVB

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEVB = 94
- 		-static
-
- -

< Defocus = A*x+B*y+C

- -

Definition at line 100 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_PLANEVC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_PLANEVC = 95
- 		-static
-
- -

< Defocus = A*x+B*y+C

- -

Definition at line 101 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_R2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_R2 = 83
- 		-static
-
- -

< Defocus change with respect to previous defoucs (Angstroms)

- -

Definition at line 89 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUS_RESIDUAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUS_RESIDUAL = 85
- 		-static
-
- -

< Coefficients of the defocus adjustment plane

- -

Definition at line 91 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUSA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUSA = 79
- 		-static
-
- -

< Microscope voltage (kV)

- -

Definition at line 85 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUSU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUSU = 80
- 		-static
-
- -

< average defocus (Angtroms)

- -

Definition at line 86 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DEFOCUSV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DEFOCUSV = 81
- 		-static
-
- -

< Defocus U (Angstroms)

- -

Definition at line 87 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DIMENSIONS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DIMENSIONS = 150
- 		-static
-
- -

< Downsampling performed to estimate the CTF

- -

Definition at line 156 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_DOWNSAMPLE_PERFORMED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED = 149
- 		-static
-
- -

< Iceness of the micrograph

- -

Definition at line 155 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_ENERGY_LOSS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_ENERGY_LOSS = 100
- 		-static
-
- -

< group images by defocus

- -

Definition at line 106 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_ENV_R0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_ENV_R0 = 109
- 		-static
-
- -

< CTF gain

- -

Definition at line 115 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_ENV_R1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_ENV_R1 = 110
- 		-static
-
- -

< CTF Envelope polynomial parameter

- -

Definition at line 116 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_ENV_R2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_ENV_R2 = 111
- 		-static
-
- -

< CTF Envelope polynomial parameter

- -

Definition at line 117 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_ENVELOPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_ENVELOPE = 101
- 		-static
-
- -

< Energy loss

- -

Definition at line 107 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_ENVELOPE_PLOT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_ENVELOPE_PLOT = 102
- 		-static
-
- -

Definition at line 108 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_GROUP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_GROUP = 99
- 		-static
-
- -

< Chromatic aberration

- -

Definition at line 105 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_INPUTPARAMS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_INPUTPARAMS = 73
- 		-static
-
- -

Definition at line 79 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_K

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_K = 108
- 		-static
-
- -

< Inelastic absorption

- -

Definition at line 114 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_LAMBDA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_LAMBDA = 151
- 		-static
-
- -

Definition at line 157 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_LENS_STABILITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_LENS_STABILITY = 103
- 		-static
-
- -

Definition at line 109 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_LONGITUDINAL_DISPLACEMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_LONGITUDINAL_DISPLACEMENT = 105
- 		-static
-
- -

< Convergence cone

- -

Definition at line 111 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_MODEL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_MODEL = 74
- 		-static
-
- -

< Parameters file for the CTF Model (std::string)

- -

Definition at line 80 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_MODEL2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_MODEL2 = 75
- 		-static
-
- -

< Name for the CTF Model (std::string)

- -

Definition at line 81 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_PHASE_SHIFT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_PHASE_SHIFT = 155
- 		-static
-
- -

Definition at line 161 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_Q0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_Q0 = 107
- 		-static
-
- -

< Transversal displacemente

- -

Definition at line 113 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_SAMPLING_RATE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_SAMPLING_RATE = 76
- 		-static
-
- -

< Name for another CTF model (std::string)

- -

Definition at line 82 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_SAMPLING_RATE_Z

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_SAMPLING_RATE_Z = 77
- 		-static
-
- -

< Sampling rate

- -

Definition at line 83 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_TRANSVERSAL_DISPLACEMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_TRANSVERSAL_DISPLACEMENT = 106
- 		-static
-
- -

< Longitudinal displacement

- -

Definition at line 112 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_VOLTAGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_VOLTAGE = 78
- 		-static
-
- -

< Sampling rate in Z direction

- -

Definition at line 84 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_VPP_RADIUS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_VPP_RADIUS = 156
- 		-static
-
- -

Definition at line 162 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_X0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_X0 = 86
- 		-static
-
- -

< Difference between the observed defocus value and the estimated defocus value

- -

Definition at line 92 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_XF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_XF = 88
- 		-static
-
- -

< The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates

- -

Definition at line 94 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_XRAY_LENS_TYPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_XRAY_LENS_TYPE = 152
- 		-static
-
- -

Wavelength (nm)

- -

Definition at line 158 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_XRAY_OUTER_ZONE_WIDTH

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_XRAY_OUTER_ZONE_WIDTH = 153
- 		-static
-
- -

Algorithm used to generate Xray PSF.

- -

Definition at line 159 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_XRAY_ZONES_NUMBER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_XRAY_ZONES_NUMBER = 154
- 		-static
-
- -

Outermost zone width of the X-ray Fresnel lens (nm)

- -

Definition at line 160 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_Y0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_Y0 = 87
- 		-static
-
- -

< The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates

- -

Definition at line 93 of file MDLabel.java.

- -
-
- -

◆ MDL_CTF_YF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CTF_YF = 89
- 		-static
-
- -

< The CTF is valid within (x0,y0) to (xF,yF) in the micrograph coordinates

- -

Definition at line 95 of file MDLabel.java.

- -
-
- -

◆ MDL_CUMULATIVE_SSNR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_CUMULATIVE_SSNR = 157
- 		-static
-
- -

Definition at line 163 of file MDLabel.java.

- -
-
- -

◆ MDL_DATATYPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DATATYPE = 158
- 		-static
-
- -

<Cumulative SSNR (double)

- -

Definition at line 164 of file MDLabel.java.

- -
-
- -

◆ MDL_DATE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DATE = 172
- 		-static
-
- -

< Is this image enabled? (int [-1 or 1])

- -

Definition at line 178 of file MDLabel.java.

- -
-
- -

◆ MDL_DEFGROUP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DEFGROUP = 159
- 		-static
-
- -

< if read from file original image datatype, this is an struct defined in image

- -

Definition at line 165 of file MDLabel.java.

- -
-
- -

◆ MDL_DIMENSIONS_2D

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DIMENSIONS_2D = 301
- 		-static
-
- -

Definition at line 307 of file MDLabel.java.

- -
-
- -

◆ MDL_DIMENSIONS_3D

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DIMENSIONS_3D = 300
- 		-static
-
- -

Definition at line 306 of file MDLabel.java.

- -
-
- -

◆ MDL_DIMRED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DIMRED = 160
- 		-static
-
- -

< Defocus group

- -

Definition at line 166 of file MDLabel.java.

- -
-
- -

◆ MDL_DIRECTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DIRECTION = 161
- 		-static
-
- -

< Projection onto a reduced manifold (vector double)

- -

Definition at line 167 of file MDLabel.java.

- -
-
- -

◆ MDL_DM3_IDTAG

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DM3_IDTAG = 162
- 		-static
-
- -

< Direction in 3D

- -

Definition at line 168 of file MDLabel.java.

- -
-
- -

◆ MDL_DM3_NODEID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DM3_NODEID = 163
- 		-static
-
- -

Definition at line 169 of file MDLabel.java.

- -
-
- -

◆ MDL_DM3_NUMBER_TYPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DM3_NUMBER_TYPE = 164
- 		-static
-
- -

Definition at line 170 of file MDLabel.java.

- -
-
- -

◆ MDL_DM3_PARENTID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DM3_PARENTID = 165
- 		-static
-
- -

Definition at line 171 of file MDLabel.java.

- -
-
- -

◆ MDL_DM3_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DM3_SIZE = 168
- 		-static
-
- -

Definition at line 174 of file MDLabel.java.

- -
-
- -

◆ MDL_DM3_TAGCLASS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DM3_TAGCLASS = 166
- 		-static
-
- -

Definition at line 172 of file MDLabel.java.

- -
-
- -

◆ MDL_DM3_TAGNAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DM3_TAGNAME = 167
- 		-static
-
- -

Definition at line 173 of file MDLabel.java.

- -
-
- -

◆ MDL_DM3_VALUE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DM3_VALUE = 169
- 		-static
-
- -

Definition at line 175 of file MDLabel.java.

- -
-
- -

◆ MDL_DOSE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_DOSE = 170
- 		-static
-
- -

Definition at line 176 of file MDLabel.java.

- -
-
- -

◆ MDL_ENABLED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ENABLED = 171
- 		-static
-
- -

< Dose e/A^2 (double)

- -

Definition at line 177 of file MDLabel.java.

- -
-
- -

◆ MDL_FIRST_LABEL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_FIRST_LABEL = 0
- 		-static
-
- -

Definition at line 5 of file MDLabel.java.

- -
-
- -

◆ MDL_FLIP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_FLIP = 174
- 		-static
-
- -

Definition at line 180 of file MDLabel.java.

- -
-
- -

◆ MDL_FOM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_FOM = 175
- 		-static
-
- -

< Flip the image? (bool)

- -

Definition at line 181 of file MDLabel.java.

- -
-
- -

◆ MDL_FRAME_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_FRAME_ID = 176
- 		-static
-
- -

< Figure of Merit in 0-1 range (double)

- -

Definition at line 182 of file MDLabel.java.

- -
-
- -

◆ MDL_GATHER_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_GATHER_ID = 1
- 		-static
-
- -

< object id (int), NOTE: This label is special and shouldn't be used

- -

Definition at line 7 of file MDLabel.java.

- -
-
- -

◆ MDL_GOOD_REGION_SCORE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_GOOD_REGION_SCORE = 431
- 		-static
-
- -

< Z Score (double)

- -

Definition at line 437 of file MDLabel.java.

- -
-
- -

◆ MDL_GRAPH_CC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_GRAPH_CC = 179
- 		-static
-
- -

< when previous assignment validation

- -

Definition at line 185 of file MDLabel.java.

- -
-
- -

◆ MDL_GRAPH_CC_PREVIOUS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_GRAPH_CC_PREVIOUS = 180
- 		-static
-
- -

< Correlation between assigned direction and graph filtered maximum

- -

Definition at line 186 of file MDLabel.java.

- -
-
- -

◆ MDL_GRAPH_DISTANCE2MAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_GRAPH_DISTANCE2MAX = 177
- 		-static
-
- -

< Unique id of frame inside a Movie

- -

Definition at line 183 of file MDLabel.java.

- -
-
- -

◆ MDL_GRAPH_DISTANCE2MAX_PREVIOUS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_GRAPH_DISTANCE2MAX_PREVIOUS = 178
- 		-static
-
- -

< Distance to graph filtered max

- -

Definition at line 184 of file MDLabel.java.

- -
-
- -

◆ MDL_HALF1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_HALF1 = 181
- 		-static
-
- -

< when previous assignment validation

- -

Definition at line 187 of file MDLabel.java.

- -
-
- -

◆ MDL_HALF2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_HALF2 = 182
- 		-static
-
- -

< Half map/image 1 file name (string)

- -

Definition at line 188 of file MDLabel.java.

- -
-
- -

◆ MDL_IDX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IDX = 183
- 		-static
-
- -

< Half map/image file name (string)

- -

Definition at line 189 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE = 184
- 		-static
-
- -

< Index within a list (size_t)

- -

Definition at line 190 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE1 = 193
- 		-static
-
- -

< Name of Metadata file for all images (string)

- -

Definition at line 199 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE2 = 194
- 		-static
-
- -

< Image associated to this object (std::string)

- -

Definition at line 200 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE3 = 195
- 		-static
-
- -

< Image associated to this object (std::string)

- -

Definition at line 201 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE4

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE4 = 196
- 		-static
-
- -

< Image associated to this object (std::string)

- -

Definition at line 202 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE5

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE5 = 197
- 		-static
-
- -

< Image associated to this object (std::string)

- -

Definition at line 203 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE_COVARIANCE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE_COVARIANCE = 185
- 		-static
-
- -

< Name of an image (std::string)

- -

Definition at line 191 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE_IDX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE_IDX = 186
- 		-static
-
- -

< Name of the covariance imagee associated to this image

- -

Definition at line 192 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE_ORIGINAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE_ORIGINAL = 187
- 		-static
-
- -

< Index of an image within a list (size_t)

- -

Definition at line 193 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE_REF = 188
- 		-static
-
- -

< Name of an image from which MDL_IMAGE is coming from

- -

Definition at line 194 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE_RESIDUAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE_RESIDUAL = 189
- 		-static
-
- -

< Name of of the class image from which MDL_IMAGE is coming from

- -

Definition at line 195 of file MDLabel.java.

- -
-
- -

◆ MDL_IMAGE_TILTED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMAGE_TILTED = 190
- 		-static
-
- -

< Name of a residual image associated to this image

- -

Definition at line 196 of file MDLabel.java.

- -
-
- -

◆ MDL_IMED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMED = 191
- 		-static
-
- -

< Name of the tilted images associated to MDL_IMAGE

- -

Definition at line 197 of file MDLabel.java.

- -
-
- -

◆ MDL_IMGMD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_IMGMD = 192
- 		-static
-
- -

< imed value between a particle and its assigned projection

- -

Definition at line 198 of file MDLabel.java.

- -
-
- -

◆ MDL_INTSCALE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_INTSCALE = 198
- 		-static
-
- -

< Image associated to this object (std::string)

- -

Definition at line 204 of file MDLabel.java.

- -
-
- -

◆ MDL_ITEM_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ITEM_ID = 199
- 		-static
-
- -

< Intensity scale for an image

- -

Definition at line 205 of file MDLabel.java.

- -
-
- -

◆ MDL_ITER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ITER = 200
- 		-static
-
- -

< Unique identifier for items inside a list or set (std::size_t)

- -

Definition at line 206 of file MDLabel.java.

- -
-
- -

◆ MDL_KERDENSOM_FUNCTIONAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_KERDENSOM_FUNCTIONAL = 201
- 		-static
-
- -

< Current iteration number (int)

- -

Definition at line 207 of file MDLabel.java.

- -
-
- -

◆ MDL_KERDENSOM_REGULARIZATION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_KERDENSOM_REGULARIZATION = 202
- 		-static
-
- -

< Functional value (double)

- -

Definition at line 208 of file MDLabel.java.

- -
-
- -

◆ MDL_KERDENSOM_SIGMA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_KERDENSOM_SIGMA = 203
- 		-static
-
- -

< Regularization value (double)

- -

Definition at line 209 of file MDLabel.java.

- -
-
- -

◆ MDL_KEYWORDS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_KEYWORDS = 204
- 		-static
-
- -

< Sigma value (double)

- -

Definition at line 210 of file MDLabel.java.

- -
-
- -

◆ MDL_KMEANS2D_CENTROID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_KMEANS2D_CENTROID = 205
- 		-static
-
- -

< Keywords associated to this line, should be a single string block (do not use spaces as separators)

- -

Definition at line 211 of file MDLabel.java.

- -
-
- -

◆ MDL_KSTEST

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_KSTEST = 206
- 		-static
-
- -

< Centroid of a cluster for the KMEANS2D classification

- -

Definition at line 212 of file MDLabel.java.

- -
-
- -

◆ MDL_LAST_LABEL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_LAST_LABEL = 742
- 		-static
-
- -

Definition at line 748 of file MDLabel.java.

- -
-
- -

◆ MDL_LL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_LL = 207
- 		-static
-
- -

<KS-test statistics

- -

Definition at line 213 of file MDLabel.java.

- -
-
- -

◆ MDL_LOCAL_ALIGNMENT_COEFFS_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_COEFFS_X = 209
- 		-static
-
- -

< Two values representing number of patches used for local alignment (X, Y)

- -

Definition at line 215 of file MDLabel.java.

- -
-
- -

◆ MDL_LOCAL_ALIGNMENT_COEFFS_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_COEFFS_Y = 210
- 		-static
-
- -

< BSpline coefficient in X dim

- -

Definition at line 216 of file MDLabel.java.

- -
-
- -

◆ MDL_LOCAL_ALIGNMENT_CONF_2_5_PERC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_CONF_2_5_PERC = 211
- 		-static
-
- -

< BSpline coefficient in Y dim

- -

Definition at line 217 of file MDLabel.java.

- -
-
- -

◆ MDL_LOCAL_ALIGNMENT_CONF_97_5_PERC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_CONF_97_5_PERC = 212
- 		-static
-
- -

< A shift amount at confidence level of 2.5%

- -

Definition at line 218 of file MDLabel.java.

- -
-
- -

◆ MDL_LOCAL_ALIGNMENT_CONTROL_POINTS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_CONTROL_POINTS = 213
- 		-static
-
- -

< A shift amount at confidence level of 95.5%

- -

Definition at line 219 of file MDLabel.java.

- -
-
- -

◆ MDL_LOCAL_ALIGNMENT_PATCHES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_LOCAL_ALIGNMENT_PATCHES = 208
- 		-static
-
- -

< contribution of an image to log-likelihood value

- -

Definition at line 214 of file MDLabel.java.

- -
-
- -

◆ MDL_MACRO_CMD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MACRO_CMD = 274
- 		-static
-
- -

< Number which will multiply all features (double)

- -

Definition at line 280 of file MDLabel.java.

- -
-
- -

◆ MDL_MACRO_CMD_ARGS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MACRO_CMD_ARGS = 275
- 		-static
-
- -

Definition at line 281 of file MDLabel.java.

- -
-
- -

◆ MDL_MAGNIFICATION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MAGNIFICATION = 214
- 		-static
-
- -

< Three values representing number of control points used for local alignment (X, Y, N)

- -

Definition at line 220 of file MDLabel.java.

- -
-
- -

◆ MDL_MAPTOPOLOGY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MAPTOPOLOGY = 215
- 		-static
-
- -

Magnification of microscope.

- -

Definition at line 221 of file MDLabel.java.

- -
-
- -

◆ MDL_MASK

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MASK = 216
- 		-static
-
- -

< Map topology (KerDenSOM, ...)

- -

Definition at line 222 of file MDLabel.java.

- -
-
- -

◆ MDL_MAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MAX = 219
- 		-static
-
- -

< Percentile of the maximum cross-correlation for the image (double)

- -

Definition at line 225 of file MDLabel.java.

- -
-
- -

◆ MDL_MAXCC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MAXCC = 217
- 		-static
-
- -

< Name of a mask associated to image

- -

Definition at line 223 of file MDLabel.java.

- -
-
- -

◆ MDL_MAXCC_PERCENTILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MAXCC_PERCENTILE = 218
- 		-static
-
- -

< Maximum cross-correlation for the image (double)

- -

Definition at line 224 of file MDLabel.java.

- -
-
- -

◆ MDL_MAXCC_PREVIOUS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MAXCC_PREVIOUS = 220
- 		-static
-
- -

< Maximum value (double)

- -

Definition at line 226 of file MDLabel.java.

- -
-
- -

◆ MDL_MICROGRAPH

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MICROGRAPH = 221
- 		-static
-
- -

< Correlation from previous alignment

- -

Definition at line 227 of file MDLabel.java.

- -
-
- -

◆ MDL_MICROGRAPH_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MICROGRAPH_ID = 222
- 		-static
-
- -

< Name of a micrograph (std::string)

- -

Definition at line 228 of file MDLabel.java.

- -
-
- -

◆ MDL_MICROGRAPH_MOVIE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MICROGRAPH_MOVIE = 223
- 		-static
-
- -

< Micrograph unique id for reference (MDL_ITEM_ID should be used for Micrographs list)

- -

Definition at line 229 of file MDLabel.java.

- -
-
- -

◆ MDL_MICROGRAPH_MOVIE_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MICROGRAPH_MOVIE_ID = 224
- 		-static
-
- -

< Name of a movie (std::string)

- -

Definition at line 230 of file MDLabel.java.

- -
-
- -

◆ MDL_MICROGRAPH_ORIGINAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MICROGRAPH_ORIGINAL = 226
- 		-static
-
- -

< Name of a position file (std::string)

- -

Definition at line 232 of file MDLabel.java.

- -
-
- -

◆ MDL_MICROGRAPH_PARTICLES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MICROGRAPH_PARTICLES = 225
- 		-static
-
- -

< Unique identifier of a movie.

- -

Definition at line 231 of file MDLabel.java.

- -
-
- -

◆ MDL_MICROGRAPH_TILTED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MICROGRAPH_TILTED = 227
- 		-static
-
- -

< Name of the original micrograph, MDL_MICROGRAPH is probably a downsampled version of this one (std::string)

- -

Definition at line 233 of file MDLabel.java.

- -
-
- -

◆ MDL_MICROGRAPH_TILTED_ORIGINAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MICROGRAPH_TILTED_ORIGINAL = 228
- 		-static
-
- -

< Name of the corresponding tilted micrograph (std::string)

- -

Definition at line 234 of file MDLabel.java.

- -
-
- -

◆ MDL_MIN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MIN = 229
- 		-static
-
- -

< Name of the corresponding original, tilted micrograph (std::string)

- -

Definition at line 235 of file MDLabel.java.

- -
-
- -

◆ MDL_MIRRORFRAC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MIRRORFRAC = 230
- 		-static
-
- -

< Minimum value (double)

- -

Definition at line 236 of file MDLabel.java.

- -
-
- -

◆ MDL_MISSINGREGION_NR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MISSINGREGION_NR = 231
- 		-static
-
- -

< Mirror fraction for a Maximum Likelihood model

- -

Definition at line 237 of file MDLabel.java.

- -
-
- -

◆ MDL_MISSINGREGION_THX0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MISSINGREGION_THX0 = 235
- 		-static
-
- -

< Final tilt angle in Y for missing region in subtomogram

- -

Definition at line 241 of file MDLabel.java.

- -
-
- -

◆ MDL_MISSINGREGION_THXF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MISSINGREGION_THXF = 236
- 		-static
-
- -

< Initial tilt angle in X for missing region in subtomogram

- -

Definition at line 242 of file MDLabel.java.

- -
-
- -

◆ MDL_MISSINGREGION_THY0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MISSINGREGION_THY0 = 233
- 		-static
-
- -

< Type of missing region in subtomogram

- -

Definition at line 239 of file MDLabel.java.

- -
-
- -

◆ MDL_MISSINGREGION_THYF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MISSINGREGION_THYF = 234
- 		-static
-
- -

< Initial tilt angle in Y for missing region in subtomogram

- -

Definition at line 240 of file MDLabel.java.

- -
-
- -

◆ MDL_MISSINGREGION_TYPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MISSINGREGION_TYPE = 232
- 		-static
-
- -

< Number of missing region in subtomogram

- -

Definition at line 238 of file MDLabel.java.

- -
-
- -

◆ MDL_MLF_CTF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MLF_CTF = 237
- 		-static
-
- -

< Final tilt angle in X for missing region in subtomogram

- -

Definition at line 243 of file MDLabel.java.

- -
-
- -

◆ MDL_MLF_NOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MLF_NOISE = 240
- 		-static
-
- -

< MLF signal (double)

- -

Definition at line 246 of file MDLabel.java.

- -
-
- -

◆ MDL_MLF_SIGNAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MLF_SIGNAL = 239
- 		-static
-
- -

< MLF Wiener filter (double)

- -

Definition at line 245 of file MDLabel.java.

- -
-
- -

◆ MDL_MLF_WIENER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MLF_WIENER = 238
- 		-static
-
- -

< MLF CTF estimated value (double)

- -

Definition at line 244 of file MDLabel.java.

- -
-
- -

◆ MDL_MODELFRAC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_MODELFRAC = 241
- 		-static
-
- -

< MLF Wiener filter (double)

- -

Definition at line 247 of file MDLabel.java.

- -
-
- -

◆ MDL_NEIGHBOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NEIGHBOR = 243
- 		-static
-
- -

< Vector of indexes to points some "neighbors"

- -

Definition at line 249 of file MDLabel.java.

- -
-
- -

◆ MDL_NEIGHBORHOOD_RADIUS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NEIGHBORHOOD_RADIUS = 244
- 		-static
-
- -

< Particular neighbor (pointed myNEIGHBORS)

- -

Definition at line 250 of file MDLabel.java.

- -
-
- -

◆ MDL_NEIGHBORS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NEIGHBORS = 242
- 		-static
-
- -

< Model fraction (alpha_k) for a Maximum Likelihood model

- -

Definition at line 248 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA = 245
- 		-static
-
- -

< Radius of the neighborhood (radians)

- -

Definition at line 251 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA_ATOMSHIFT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA_ATOMSHIFT = 247
- 		-static
-
- -

< NMA Collectivity of a given mode

- -

Definition at line 253 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA_COLLECTIVITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA_COLLECTIVITY = 246
- 		-static
-
- -

< Normal mode displacements (vector double)

- -

Definition at line 252 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA_EIGENVAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA_EIGENVAL = 253
- 		-static
-
- -

< NMA Score of a given mode

- -

Definition at line 259 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA_ENERGY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA_ENERGY = 248
- 		-static
-
- -

< NMA Atom shift in Angstroms

- -

Definition at line 254 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA_MAXRANGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA_MAXRANGE = 250
- 		-static
-
- -

< Minimum value observed for a given NMA mode

- -

Definition at line 256 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA_MINRANGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA_MINRANGE = 249
- 		-static
-
- -

< NMA energy contained in the NMA displacement vector

- -

Definition at line 255 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA_MODEFILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA_MODEFILE = 251
- 		-static
-
- -

< Maximum value observed for a given NMA mode

- -

Definition at line 257 of file MDLabel.java.

- -
-
- -

◆ MDL_NMA_SCORE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NMA_SCORE = 252
- 		-static
-
- -

< File with an NMA mode

- -

Definition at line 258 of file MDLabel.java.

- -
-
- -

◆ MDL_NOISE_ANGLES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NOISE_ANGLES = 254
- 		-static
-
- -

< NMA Eigenvalue of a given mode

- -

Definition at line 260 of file MDLabel.java.

- -
-
- -

◆ MDL_NOISE_COORD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NOISE_COORD = 256
- 		-static
-
- -

< Noise description for particle's center coordenates (when projecting)

- -

Definition at line 262 of file MDLabel.java.

- -
-
- -

◆ MDL_NOISE_PARTICLE_COORD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NOISE_PARTICLE_COORD = 255
- 		-static
-
- -

< Noise description for projected angles

- -

Definition at line 261 of file MDLabel.java.

- -
-
- -

◆ MDL_NOISE_PIXEL_LEVEL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_NOISE_PIXEL_LEVEL = 257
- 		-static
-
- -

Definition at line 263 of file MDLabel.java.

- -
-
- -

◆ MDL_OBJID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_OBJID = MDL_FIRST_LABEL
- 		-static
-
- -

< The label MDL_OBJID is special and should not be used

- -

Definition at line 6 of file MDLabel.java.

- -
-
- -

◆ MDL_OPTICALFLOW_MEANX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_OPTICALFLOW_MEANX = 262
- 		-static
-
- -

< Origin for the image in the Z axis (double)

- -

Definition at line 268 of file MDLabel.java.

- -
-
- -

◆ MDL_OPTICALFLOW_MEANY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_OPTICALFLOW_MEANY = 263
- 		-static
-
- -

<Mean of="" the="" movement="" in="" x="" direction="" of="" the="" motion="" map>=""> (double)

- -

Definition at line 269 of file MDLabel.java.

- -
-
- -

◆ MDL_OPTICALFLOW_STDX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_OPTICALFLOW_STDX = 264
- 		-static
-
- -

<Mean of="" the="" movement="" in="" y="" direction="" of="" the="" motion="" map>=""> (double)

- -

Definition at line 270 of file MDLabel.java.

- -
-
- -

◆ MDL_OPTICALFLOW_STDY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_OPTICALFLOW_STDY = 265
- 		-static
-
- -

<Standatd deviation="" of="" the="" movement="" in="" x="" direction="" of="" the="" motion="" map>=""> (double)

- -

Definition at line 271 of file MDLabel.java.

- -
-
- -

◆ MDL_ORDER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ORDER = 258
- 		-static
-
- -

< Noise description for pixels' gray level (when projecting)

- -

Definition at line 264 of file MDLabel.java.

- -
-
- -

◆ MDL_ORIGIN_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ORIGIN_X = 259
- 		-static
-
- -

auxiliary label to be used as an index (long)

- -

Definition at line 265 of file MDLabel.java.

- -
-
- -

◆ MDL_ORIGIN_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ORIGIN_Y = 260
- 		-static
-
- -

< Origin for the image in the X axis (double)

- -

Definition at line 266 of file MDLabel.java.

- -
-
- -

◆ MDL_ORIGIN_Z

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ORIGIN_Z = 261
- 		-static
-
- -

< Origin for the image in the Y axis (double)

- -

Definition at line 267 of file MDLabel.java.

- -
-
- -

◆ MDL_PARTICLE_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PARTICLE_ID = 266
- 		-static
-
- -

<Standard deviation="" of="" the="" movement="" in="" y="" direction="" of="" the="" motion="" map>=""> (double)

- -

Definition at line 272 of file MDLabel.java.

- -
-
- -

◆ MDL_PHANTOM_BGDENSITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PHANTOM_BGDENSITY = 267
- 		-static
-
- -

< Particle unique identifier for reference. (The MDL_ITEM_ID should be used when particle list)

- -

Definition at line 273 of file MDLabel.java.

- -
-
- -

◆ MDL_PHANTOM_FEATURE_CENTER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_CENTER = 268
- 		-static
-
- -

< Phantom background density (double)

- -

Definition at line 274 of file MDLabel.java.

- -
-
- -

◆ MDL_PHANTOM_FEATURE_DENSITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_DENSITY = 269
- 		-static
-
- -

< Center of the feature (vector double)

- -

Definition at line 275 of file MDLabel.java.

- -
-
- -

◆ MDL_PHANTOM_FEATURE_OPERATION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_OPERATION = 270
- 		-static
-
- -

< The density of the feature (double)

- -

Definition at line 276 of file MDLabel.java.

- -
-
- -

◆ MDL_PHANTOM_FEATURE_SPECIFIC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_SPECIFIC = 271
- 		-static
-
- -

< Operation in case of overlapping features (+,-)

- -

Definition at line 277 of file MDLabel.java.

- -
-
- -

◆ MDL_PHANTOM_FEATURE_TYPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PHANTOM_FEATURE_TYPE = 272
- 		-static
-
- -

< Specific parameters for a feature (vector double)

- -

Definition at line 278 of file MDLabel.java.

- -
-
- -

◆ MDL_PHANTOM_SCALE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PHANTOM_SCALE = 273
- 		-static
-
- -

< Type of the feature (Sphere, Blob, ...) (std::string)

- -

Definition at line 279 of file MDLabel.java.

- -
-
- -

◆ MDL_PICKING_AUTOPARTICLES_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE = 282
- 		-static
-
- -

< Particle size for particle picking

- -

Definition at line 288 of file MDLabel.java.

- -
-
- -

◆ MDL_PICKING_AUTOPICKPERCENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PICKING_AUTOPICKPERCENT = 280
- 		-static
-
- -

< Micrograph state for particle picking

- -

Definition at line 286 of file MDLabel.java.

- -
-
- -

◆ MDL_PICKING_MANUALPARTICLES_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE = 283
- 		-static
-
- -

< Number of automatic particles picked

- -

Definition at line 289 of file MDLabel.java.

- -
-
- -

◆ MDL_PICKING_MICROGRAPH_STATE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PICKING_MICROGRAPH_STATE = 279
- 		-static
-
- -

< State for particle picking

- -

Definition at line 285 of file MDLabel.java.

- -
-
- -

◆ MDL_PICKING_PARTICLE_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PICKING_PARTICLE_SIZE = 281
- 		-static
-
- -

Definition at line 287 of file MDLabel.java.

- -
-
- -

◆ MDL_PICKING_STATE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PICKING_STATE = 278
- 		-static
-
- -

< Number of templates

- -

Definition at line 284 of file MDLabel.java.

- -
-
- -

◆ MDL_PICKING_TEMPLATES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PICKING_TEMPLATES = 277
- 		-static
-
- -

< Color for particle picking

- -

Definition at line 283 of file MDLabel.java.

- -
-
- -

◆ MDL_PMAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PMAX = 284
- 		-static
-
- -

< Number of manual particles picked

- -

Definition at line 290 of file MDLabel.java.

- -
-
- -

◆ MDL_POINTSASYMETRICUNIT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_POINTSASYMETRICUNIT = 285
- 		-static
-
- -

< Maximum value of normalized probability function (now called "Pmax/sumP") (double)

- -

Definition at line 291 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_ANGFILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_ANGFILE = 287
- 		-static
-
- -

Definition at line 293 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_DIMENSIONS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_DIMENSIONS = 286
- 		-static
-
- -

< Number of non-redundant projections directions (size_t)

- -

Definition at line 292 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_PSI_NOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_PSI_NOISE = 288
- 		-static
-
- -

< File for generated angles

- -

Definition at line 294 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_PSI_RANDSTR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_PSI_RANDSTR = 289
- 		-static
-
- -

< Psi angle dev and mean noise (vector double)

- -

Definition at line 295 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_PSI_RANGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_PSI_RANGE = 290
- 		-static
-
- -

< Type of randomness for Psi (std::string)

- -

Definition at line 296 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_ROT_NOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_ROT_NOISE = 291
- 		-static
-
- -

< Psi angle range (vector double)

- -

Definition at line 297 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_ROT_RANDSTR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_ROT_RANDSTR = 292
- 		-static
-
- -

< Rotational angle dev and mean noise (vector double)

- -

Definition at line 298 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_ROT_RANGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_ROT_RANGE = 293
- 		-static
-
- -

< Type of randomness for Rotational (std::string)

- -

Definition at line 299 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_TILT_NOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_TILT_NOISE = 294
- 		-static
-
- -

Definition at line 300 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_TILT_RANDSTR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_TILT_RANDSTR = 295
- 		-static
-
- -

< Tilt angle dev and mean noise (vector double)

- -

Definition at line 301 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_TILT_RANGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_TILT_RANGE = 296
- 		-static
-
- -

< Type of randomness for Tilt (std::string)

- -

Definition at line 302 of file MDLabel.java.

- -
-
- -

◆ MDL_PRJ_VOL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PRJ_VOL = 297
- 		-static
-
- -

Definition at line 303 of file MDLabel.java.

- -
-
- -

◆ MDL_PROGRAM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PROGRAM = 298
- 		-static
-
- -

Definition at line 304 of file MDLabel.java.

- -
-
- -

◆ MDL_PSD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PSD = 302
- 		-static
-
- -

Definition at line 308 of file MDLabel.java.

- -
-
- -

◆ MDL_PSD_ENHANCED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_PSD_ENHANCED = 303
- 		-static
-
- -

< A Power Spectrum Density file name (std::string)

- -

Definition at line 309 of file MDLabel.java.

- -
-
- -

◆ MDL_RANDOMSEED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RANDOMSEED = 304
- 		-static
-
- -

< A enhanced Power Spectrum Density file name (std::string)

- -

Definition at line 310 of file MDLabel.java.

- -
-
- -

◆ MDL_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_REF = 306
- 		-static
-
- -

< 3D Class to which the image belongs (int)

- -

Definition at line 312 of file MDLabel.java.

- -
-
- -

◆ MDL_REF2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_REF2 = 307
- 		-static
-
- -

< Class to which the image belongs (int)

- -

Definition at line 313 of file MDLabel.java.

- -
-
- -

◆ MDL_REF3D

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_REF3D = 305
- 		-static
-
- -

< Seed for random number generator

- -

Definition at line 311 of file MDLabel.java.

- -
-
- -

◆ MDL_REFMD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_REFMD = 308
- 		-static
-
- -

< Store a second class (int)

- -

Definition at line 314 of file MDLabel.java.

- -
-
- -

◆ MDL_RESIDUE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESIDUE = 310
- 		-static
-
- -

< correlation of references assigned by two methods

- -

Definition at line 316 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_ANISOTROPY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_ANISOTROPY = 311
- 		-static
-
- -

Definition at line 317 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_DPR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_DPR = 312
- 		-static
-
- -

<Resolution anisotropy used to store the significance of the Bingham Test (double)

- -

Definition at line 318 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_ERRORL2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_ERRORL2 = 313
- 		-static
-
- -

<differential phase residual (double)

- -

Definition at line 319 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_FRC

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_FRC = 314
- 		-static
-
- -

<Error in l2 (double)

- -

Definition at line 320 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_FRCRANDOMNOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_FRCRANDOMNOISE = 315
- 		-static
-
- -

<Fourier shell correlation (double)

- -

Definition at line 321 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_FREQ

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_FREQ = 316
- 		-static
-
- -

<Fourier shell correlation noise (double)

- -

Definition at line 322 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_FREQ2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_FREQ2 = 317
- 		-static
-
- -

<Frequency in 1/A (double)

- -

Definition at line 323 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_FREQREAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_FREQREAL = 318
- 		-static
-
- -

< Frequency in 1/A squared (double)

- -

Definition at line 324 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_FSO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_FSO = 319
- 		-static
-
- -

< Frequency in A (double)

- -

Definition at line 325 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_LOCAL_RESIDUE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_LOCAL_RESIDUE = 320
- 		-static
-
- -

<Fourier shell occupancy (double)

- -

Definition at line 326 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_LOG_STRUCTURE_FACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_LOG_STRUCTURE_FACTOR = 321
- 		-static
-
- -

< Frequency in A of the local resolution of a residue (double)

- -

Definition at line 327 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_RFACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_RFACTOR = 324
- 		-static
-
- -

<Structure factor

- -

Definition at line 330 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_SSNR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_SSNR = 322
- 		-static
-
- -

<Logarithm of the structure factor

- -

Definition at line 328 of file MDLabel.java.

- -
-
- -

◆ MDL_RESOLUTION_STRUCTURE_FACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_RESOLUTION_STRUCTURE_FACTOR = 323
- 		-static
-
- -

<Fourier shell correlation (double)

- -

Definition at line 329 of file MDLabel.java.

- -
-
- -

◆ MDL_SAMPLINGRATE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SAMPLINGRATE = 325
- 		-static
-
- -

rfactor

- -

Definition at line 331 of file MDLabel.java.

- -
-
- -

◆ MDL_SAMPLINGRATE_ORIGINAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SAMPLINGRATE_ORIGINAL = 326
- 		-static
-
- -

< sampling rate in A/pixel (double)

- -

Definition at line 332 of file MDLabel.java.

- -
-
- -

◆ MDL_SAMPLINGRATE_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SAMPLINGRATE_X = 327
- 		-static
-
- -

< original sampling rate in A/pixel (double)

- -

Definition at line 333 of file MDLabel.java.

- -
-
- -

◆ MDL_SAMPLINGRATE_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SAMPLINGRATE_Y = 328
- 		-static
-
- -

< sampling rate in A/pixel (double)

- -

Definition at line 334 of file MDLabel.java.

- -
-
- -

◆ MDL_SAMPLINGRATE_Z

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SAMPLINGRATE_Z = 329
- 		-static
-
- -

< sampling rate in A/pixel (double)

- -

Definition at line 335 of file MDLabel.java.

- -
-
- -

◆ MDL_SCALE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCALE = 330
- 		-static
-
- -

< sampling rate in A/pixel (double)

- -

Definition at line 336 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ALIGNABILITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY = 334
- 		-static
-
- -

Definition at line 340 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ALIGNABILITY_ACCURACY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_ACCURACY = 336
- 		-static
-
- -

< score by alignability (double)

- -

Definition at line 342 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_ACCURACY_EXP = 339
- 		-static
-
- -

< score by alignability references (double)

- -

Definition at line 345 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_ACCURACY_REF = 340
- 		-static
-
- -

< score by alignability experimental particles (double)

- -

Definition at line 346 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ALIGNABILITY_NOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_NOISE = 341
- 		-static
-
- -

< score by alignability references (double)

- -

Definition at line 347 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ALIGNABILITY_PRECISION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_PRECISION = 335
- 		-static
-
- -

< score by alignability (double)

- -

Definition at line 341 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_PRECISION_EXP = 337
- 		-static
-
- -

< score by alignability (double)

- -

Definition at line 343 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ALIGNABILITY_PRECISION_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ALIGNABILITY_PRECISION_REF = 338
- 		-static
-
- -

< score by alignability experimental particles (double)

- -

Definition at line 344 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_EMPTINESS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_EMPTINESS = 342
- 		-static
-
- -

< score by alignability noise (double)

- -

Definition at line 348 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ENTROPY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ENTROPY = 343
- 		-static
-
- -

< Small values represent worse particles. Much larger than 1 for good particles

- -

Definition at line 349 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_GINI

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_GINI = 352
- 		-static
-
- -

< Particle variance (double)

- -

Definition at line 358 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_GRANULO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_GRANULO = 344
- 		-static
-
- -

< Feature vectors used to classify particles (vector double)

- -

Definition at line 350 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_HISTDIST

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_HISTDIST = 345
- 		-static
-
- -

< Feature vectors used to classify particles (vector double)

- -

Definition at line 351 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_LBP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_LBP = 346
- 		-static
-
- -

< Feature vectors used to classify particles (vector double)

- -

Definition at line 352 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_MIRROR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_MIRROR = 347
- 		-static
-
- -

< Feature vectors used to classify particles (vector double)

- -

Definition at line 353 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_PCA_RESIDUAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_PCA_RESIDUAL = 333
- 		-static
-
- -

Definition at line 339 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_PCA_RESIDUAL_EXP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_PCA_RESIDUAL_EXP = 332
- 		-static
-
- -

Definition at line 338 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_PCA_RESIDUAL_PROJ

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_PCA_RESIDUAL_PROJ = 331
- 		-static
-
- -

< scaling factor for an image or volume (double)

- -

Definition at line 337 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_RAMP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_RAMP = 348
- 		-static
-
- -

< score by mirror (double)

- -

Definition at line 354 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_SCREENING

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_SCREENING = 349
- 		-static
-
- -

< Feature vectors used to classify particles (vector double)

- -

Definition at line 355 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_VAR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_VAR = 351
- 		-static
-
- -

< Feature vectors used to classify particles (vector double)

- -

Definition at line 357 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_VARIANCE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_VARIANCE = 350
- 		-static
-
- -

< Feature vectors used to classify particles (vector double)

- -

Definition at line 356 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ZERNIKE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ZERNIKE = 353
- 		-static
-
- -

< Micrographs Gini Coeff. (double)

- -

Definition at line 359 of file MDLabel.java.

- -
-
- -

◆ MDL_SCORE_BY_ZSCORE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SCORE_BY_ZSCORE = 354
- 		-static
-
- -

< Feature vectors used to classify particles (vector double)

- -

Definition at line 360 of file MDLabel.java.

- -
-
- -

◆ MDL_SELFILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SELFILE = 355
- 		-static
-
- -

Definition at line 361 of file MDLabel.java.

- -
-
- -

◆ MDL_SERIE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SERIE = 356
- 		-static
-
- -

< Name of an image (std::string)

- -

Definition at line 362 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_DIFF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_DIFF = 369
- 		-static
-
- -

< shift difference (double)

- -

Definition at line 375 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_DIFF0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_DIFF0 = 368
- 		-static
-
- -

< Shift for the image in the Z axis (double)

- -

Definition at line 374 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_DIFF2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_DIFF2 = 370
- 		-static
-
- -

< shift difference (double)

- -

Definition at line 376 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_X = 357
- 		-static
-
- -

< A collection of micrographs, e.g. a tilt serie (std::string)

- -

Definition at line 363 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_X2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_X2 = 358
- 		-static
-
- -

< Shift for the image in the X axis (double)

- -

Definition at line 364 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_X3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_X3 = 359
- 		-static
-
- -

< Shift for the image in the X axis (double)

- -

Definition at line 365 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_X_DIFF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_X_DIFF = 360
- 		-static
-
- -

< Shift for the image in the X axis (double)

- -

Definition at line 366 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_Y = 361
- 		-static
-
- -

< difference in Shift along X axis (double)

- -

Definition at line 367 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_Y2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_Y2 = 362
- 		-static
-
- -

< Shift for the image in the Y axis (double)

- -

Definition at line 368 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_Y3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_Y3 = 363
- 		-static
-
- -

< Shift for the image in the Y axis (double)

- -

Definition at line 369 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_Y_DIFF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_Y_DIFF = 364
- 		-static
-
- -

< Shift for the image in the Y axis (double)

- -

Definition at line 370 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_Z

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_Z = 365
- 		-static
-
- -

< difference in Shift along Y axis (double)

- -

Definition at line 371 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_Z2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_Z2 = 366
- 		-static
-
- -

< Shift for the image in the Z axis (double)

- -

Definition at line 372 of file MDLabel.java.

- -
-
- -

◆ MDL_SHIFT_Z3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SHIFT_Z3 = 367
- 		-static
-
- -

< Shift for the image in the Z axis (double)

- -

Definition at line 373 of file MDLabel.java.

- -
-
- -

◆ MDL_SIGMANOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SIGMANOISE = 371
- 		-static
-
- -

< shift difference (double)

- -

Definition at line 377 of file MDLabel.java.

- -
-
- -

◆ MDL_SIGMAOFFSET

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SIGMAOFFSET = 372
- 		-static
-
- -

< Standard deviation of the noise in ML model

- -

Definition at line 378 of file MDLabel.java.

- -
-
- -

◆ MDL_SIGNALCHANGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SIGNALCHANGE = 373
- 		-static
-
- -

< Standard deviation of the offsets in ML model

- -

Definition at line 379 of file MDLabel.java.

- -
-
- -

◆ MDL_SPH_COEFFICIENTS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SPH_COEFFICIENTS = 374
- 		-static
-
- -

< Signal change for an image

- -

Definition at line 380 of file MDLabel.java.

- -
-
- -

◆ MDL_SPH_DEFORMATION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SPH_DEFORMATION = 375
- 		-static
-
- -

< Deformation coefficients

- -

Definition at line 381 of file MDLabel.java.

- -
-
- -

◆ MDL_SPH_TSNE_COEFF1D

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SPH_TSNE_COEFF1D = 376
- 		-static
-
- -

< Deformation in voxels

- -

Definition at line 382 of file MDLabel.java.

- -
-
- -

◆ MDL_SPH_TSNE_COEFF2D

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SPH_TSNE_COEFF2D = 377
- 		-static
-
- -

tsne coefficicient in 1D

- -

Definition at line 383 of file MDLabel.java.

- -
-
- -

◆ MDL_STAR_COMMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_STAR_COMMENT = 379
- 		-static
-
- -

<stdandard deviation value (double)

- -

Definition at line 385 of file MDLabel.java.

- -
-
- -

◆ MDL_STDDEV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_STDDEV = 378
- 		-static
-
- -

tsne coefficients in 2D

- -

Definition at line 384 of file MDLabel.java.

- -
-
- -

◆ MDL_SUBTRACTION_BETA0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SUBTRACTION_BETA0 = 381
- 		-static
-
- -

< R2 coefficient of subtracted particle

- -

Definition at line 387 of file MDLabel.java.

- -
-
- -

◆ MDL_SUBTRACTION_BETA1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SUBTRACTION_BETA1 = 382
- 		-static
-
- -

< Beta 0 coefficient of adjusted model for subtract particle

- -

Definition at line 388 of file MDLabel.java.

- -
-
- -

◆ MDL_SUBTRACTION_R2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SUBTRACTION_R2 = 380
- 		-static
-
- -

< A comment for this object /*** NOTE THIS IS A SPECIAL CASE AND SO IS TREATED ***/

- -

Definition at line 386 of file MDLabel.java.

- -
-
- -

◆ MDL_SUM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SUM = 383
- 		-static
-
- -

< Beta 1 coefficient of adjusted model for subtract particle

- -

Definition at line 389 of file MDLabel.java.

- -
-
- -

◆ MDL_SUMWEIGHT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SUMWEIGHT = 384
- 		-static
-
- -

< Sum of elements of a given type (double) [this is a genereic type do not use to transfer information to another program]

- -

Definition at line 390 of file MDLabel.java.

- -
-
- -

◆ MDL_SYMNO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_SYMNO = 385
- 		-static
-
- -

< Sum of all weights in ML model

- -

Definition at line 391 of file MDLabel.java.

- -
-
- -

◆ MDL_TEST_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TEST_SIZE = 390
- 		-static
-
- -

<Tilt series id (std::string)

- -

Definition at line 396 of file MDLabel.java.

- -
-
- -

◆ MDL_TILT_ANALYSIS_MAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_MAX = 394
- 		-static
-
- -

Definition at line 400 of file MDLabel.java.

- -
-
- -

◆ MDL_TILT_ANALYSIS_MEAN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_MEAN = 391
- 		-static
-
- -

Definition at line 397 of file MDLabel.java.

- -
-
- -

◆ MDL_TILT_ANALYSIS_MIN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_MIN = 393
- 		-static
-
- -

Definition at line 399 of file MDLabel.java.

- -
-
- -

◆ MDL_TILT_ANALYSIS_PSDs

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_PSDs = 395
- 		-static
-
- -

Definition at line 401 of file MDLabel.java.

- -
-
- -

◆ MDL_TILT_ANALYSIS_STD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TILT_ANALYSIS_STD = 392
- 		-static
-
- -

Definition at line 398 of file MDLabel.java.

- -
-
- -

◆ MDL_TIME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TIME = 173
- 		-static
-
- -

Definition at line 179 of file MDLabel.java.

- -
-
- -

◆ MDL_TOMOGRAM_VOLUME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TOMOGRAM_VOLUME = 386
- 		-static
-
- -

< Symmetry number for a projection (used in ART)

- -

Definition at line 392 of file MDLabel.java.

- -
-
- -

◆ MDL_TOMOGRAMMD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TOMOGRAMMD = 387
- 		-static
-
- -

< Name for the reconstructed tomogram volume (std::string)

- -

Definition at line 393 of file MDLabel.java.

- -
-
- -

◆ MDL_TRANSFORM_MATRIX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TRANSFORM_MATRIX = 388
- 		-static
-
- -

< Name for a Metadata file (std::string)

- -

Definition at line 394 of file MDLabel.java.

- -
-
- -

◆ MDL_TSID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_TSID = 389
- 		-static
-
- -

< transformation matrix in numpy string format or space separated (std::string)

- -

Definition at line 395 of file MDLabel.java.

- -
-
- -

◆ MDL_UNDEFINED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_UNDEFINED = -1
- 		-static
-
- -

Definition at line 4 of file MDLabel.java.

- -
-
- -

◆ MDL_USER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_USER = 299
- 		-static
-
- -

Definition at line 305 of file MDLabel.java.

- -
-
- -

◆ MDL_VOLUME_SCORE1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_VOLUME_SCORE1 = 400
- 		-static
-
- -

< Score corresponding to the min of cc with cc>threshold

- -

Definition at line 406 of file MDLabel.java.

- -
-
- -

◆ MDL_VOLUME_SCORE2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_VOLUME_SCORE2 = 401
- 		-static
-
- -

< Score 1 for volumes

- -

Definition at line 407 of file MDLabel.java.

- -
-
- -

◆ MDL_VOLUME_SCORE3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_VOLUME_SCORE3 = 402
- 		-static
-
- -

< Score 2 for volumes

- -

Definition at line 408 of file MDLabel.java.

- -
-
- -

◆ MDL_VOLUME_SCORE4

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_VOLUME_SCORE4 = 403
- 		-static
-
- -

< Score 3 for volumes

- -

Definition at line 409 of file MDLabel.java.

- -
-
- -

◆ MDL_VOLUME_SCORE_MEAN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_VOLUME_SCORE_MEAN = 398
- 		-static
-
- -

< Score corresponding to the sum of cc-threshold with cc>threshold

- -

Definition at line 404 of file MDLabel.java.

- -
-
- -

◆ MDL_VOLUME_SCORE_MIN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_VOLUME_SCORE_MIN = 399
- 		-static
-
- -

< Score corresponding to the mean of cc with cc>threshold

- -

Definition at line 405 of file MDLabel.java.

- -
-
- -

◆ MDL_VOLUME_SCORE_SUM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_VOLUME_SCORE_SUM = 396
- 		-static
-
- -

Definition at line 402 of file MDLabel.java.

- -
-
- -

◆ MDL_VOLUME_SCORE_SUM_TH

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_VOLUME_SCORE_SUM_TH = 397
- 		-static
-
- -

< Score corresponding to the sum of cc with cc>threshold

- -

Definition at line 403 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT = 404
- 		-static
-
- -

< Score 4 for volumes

- -

Definition at line 410 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_ACCURACY_ALIGNABILITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_ACCURACY_ALIGNABILITY = 416
- 		-static
-
- -

< Weight due to Alignability Precision and Accuracy

- -

Definition at line 422 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_ALIGNABILITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_ALIGNABILITY = 415
- 		-static
-
- -

< Weight due to Alignability Precision

- -

Definition at line 421 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_CONTINUOUS2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_CONTINUOUS2 = 406
- 		-static
-
- -

< Weight assigned to the image accordint to its clusterability with a significance with respect noise (double)

- -

Definition at line 412 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_JUMPER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_JUMPER = 408
- 		-static
-
- -

< Weight due to angular jumping

- -

Definition at line 414 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_JUMPER0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_JUMPER0 = 407
- 		-static
-
- -

< Weight due to angular continuous assignment

- -

Definition at line 413 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_JUMPER2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_JUMPER2 = 409
- 		-static
-
- -

< Weight due to angular jumping

- -

Definition at line 415 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_P

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_P = 405
- 		-static
-
- -

< Weight assigned to the image (double)

- -

Definition at line 411 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_PHASECORR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_PHASECORR = 411
- 		-static
-
- -

< Weight due correlation between two images/subtomos

- -

Definition at line 417 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_PRECISION_ALIGNABILITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_PRECISION_ALIGNABILITY = 414
- 		-static
-
- -

< Weight due to SSNR

- -

Definition at line 420 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_PRECISION_MIRROR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_PRECISION_MIRROR = 417
- 		-static
-
- -

< Weight due to Alignability Accuracy

- -

Definition at line 423 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_REALCORR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_REALCORR = 410
- 		-static
-
- -

< Weight due to angular jumping

- -

Definition at line 416 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_SIGNIFICANT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_SIGNIFICANT = 412
- 		-static
-
- -

< Weight due phase correlation between two images/subtomos

- -

Definition at line 418 of file MDLabel.java.

- -
-
- -

◆ MDL_WEIGHT_SSNR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WEIGHT_SSNR = 413
- 		-static
-
- -

< Weight due to Angular significance

- -

Definition at line 419 of file MDLabel.java.

- -
-
- -

◆ MDL_WROBUST

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_WROBUST = 418
- 		-static
-
- -

< Weight due to Mirror Precision

- -

Definition at line 424 of file MDLabel.java.

- -
-
- -

◆ MDL_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_X = 419
- 		-static
-
- -

< Weight of t-student distribution in robust Maximum likelihood

- -

Definition at line 425 of file MDLabel.java.

- -
-
- -

◆ MDL_XCOOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_XCOOR = 420
- 		-static
-
- -

< X component (double)

- -

Definition at line 426 of file MDLabel.java.

- -
-
- -

◆ MDL_XCOOR_TILT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_XCOOR_TILT = 421
- 		-static
-
- -

< X component (int)

- -

Definition at line 427 of file MDLabel.java.

- -
-
- -

◆ MDL_XSIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_XSIZE = 422
- 		-static
-
- -

< X component in tilted micrograph (int)

- -

Definition at line 428 of file MDLabel.java.

- -
-
- -

◆ MDL_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_Y = 423
- 		-static
-
- -

< X size (int)

- -

Definition at line 429 of file MDLabel.java.

- -
-
- -

◆ MDL_YCOOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_YCOOR = 424
- 		-static
-
- -

< Y component (double)

- -

Definition at line 430 of file MDLabel.java.

- -
-
- -

◆ MDL_YCOOR_TILT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_YCOOR_TILT = 425
- 		-static
-
- -

< Y component (int)

- -

Definition at line 431 of file MDLabel.java.

- -
-
- -

◆ MDL_YSIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_YSIZE = 426
- 		-static
-
- -

< Y component in tilted micrograph (int)

- -

Definition at line 432 of file MDLabel.java.

- -
-
- -

◆ MDL_Z

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_Z = 427
- 		-static
-
- -

< Y size (int)

- -

Definition at line 433 of file MDLabel.java.

- -
-
- -

◆ MDL_ZCOOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZCOOR = 428
- 		-static
-
- -

< Z component (double)

- -

Definition at line 434 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE = 429
- 		-static
-
- -

< Z component (int)

- -

Definition at line 435 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_DEEPLEARNING1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_DEEPLEARNING1 = 430
- 		-static
-
- -

< Global Z Score (double)

- -

Definition at line 436 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_HISTOGRAM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_HISTOGRAM = 432
- 		-static
-
- -

< Z Score (double)

- -

Definition at line 438 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_RESCOV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_RESCOV = 435
- 		-static
-
- -

< Z Score of the stddev of the residuals (double)

- -

Definition at line 441 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_RESMEAN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_RESMEAN = 433
- 		-static
-
- -

< Z Score (double)

- -

Definition at line 439 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_RESVAR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_RESVAR = 434
- 		-static
-
- -

< Z Score of the mean of the residuals (double)

- -

Definition at line 440 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_SHAPE1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE1 = 436
- 		-static
-
- -

< Z Score of the covariance matrix of the residuals (double)

- -

Definition at line 442 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_SHAPE2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE2 = 437
- 		-static
-
- -

< Z Score (double)

- -

Definition at line 443 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_SNR1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_SNR1 = 438
- 		-static
-
- -

< Z Score (double)

- -

Definition at line 444 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSCORE_SNR2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSCORE_SNR2 = 439
- 		-static
-
- -

< Z Score (double)

- -

Definition at line 445 of file MDLabel.java.

- -
-
- -

◆ MDL_ZSIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.MDL_ZSIZE = 440
- 		-static
-
- -

< Z Score (double)

- -

Definition at line 446 of file MDLabel.java.

- -
-
- -

◆ RLN_AREA_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_AREA_ID = 441
- 		-static
-
- -

< Z size (int)

- -

Definition at line 447 of file MDLabel.java.

- -
-
- -

◆ RLN_AREA_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_AREA_NAME = 442
- 		-static
-
- -

< ID for the area (or field of view). If one does not use (tilt) series, area would be the same as micrograph...

- -

Definition at line 448 of file MDLabel.java.

- -
-
- -

◆ RLN_COMMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_COMMENT = 443
- 		-static
-
- -

< Name for the area (or field of view). If one does not use (tilt) series, area would be the same as micrograph...

- -

Definition at line 449 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_BFACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_BFACTOR = 444
- 		-static
-
- -

Definition at line 450 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_CA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_CA = 452
- 		-static
-
- -

< Spherical aberration

- -

Definition at line 458 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_CONVERGENCE_CONE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_CONVERGENCE_CONE = 460
- 		-static
-
- -

< Maximum resolution with Thon rings

- -

Definition at line 466 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_CS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_CS = 451
- 		-static
-
- -

< Defocus angle (degrees)

- -

Definition at line 457 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_DEFOCUS_ANGLE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_DEFOCUS_ANGLE = 450
- 		-static
-
- -

< Defocus V (Angstroms)

- -

Definition at line 456 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_DEFOCUSU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_DEFOCUSU = 448
- 		-static
-
- -

< Microscope voltage (kV)

- -

Definition at line 454 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_DEFOCUSV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_DEFOCUSV = 449
- 		-static
-
- -

< Defocus U (Angstroms)

- -

Definition at line 455 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_DETECTOR_PIXEL_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_DETECTOR_PIXEL_SIZE = 453
- 		-static
-
- -

< Chromatic aberration

- -

Definition at line 459 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_ENERGY_LOSS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_ENERGY_LOSS = 454
- 		-static
-
- -

< Pixel size for detector as used in CTF-determination

- -

Definition at line 460 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_FOM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_FOM = 455
- 		-static
-
- -

< Energy loss

- -

Definition at line 461 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_IMAGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_IMAGE = 456
- 		-static
-
- -

< ctffind3 FOM (CC) for quality of CTF-fit

- -

Definition at line 462 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_K

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_K = 464
- 		-static
-
- -

< Amplitude contrast

- -

Definition at line 470 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_LENS_STABILITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_LENS_STABILITY = 457
- 		-static
-
- -

< name of an image describing the CTF model

- -

Definition at line 463 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_LONGITUDINAL_DISPLACEMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_LONGITUDINAL_DISPLACEMENT = 461
- 		-static
-
- -

< Convergence cone

- -

Definition at line 467 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_MAGNIFICATION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_MAGNIFICATION = 458
- 		-static
-
- -

< Lens stability

- -

Definition at line 464 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_MAXRES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_MAXRES = 459
- 		-static
-
- -

< Magnification used for CTF-determination

- -

Definition at line 465 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_PHASESHIFT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_PHASESHIFT = 467
- 		-static
-
- -

< Gctf-based validation score for CTF fit

- -

Definition at line 473 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_Q0

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_Q0 = 463
- 		-static
-
- -

< Transversal displacemente

- -

Definition at line 469 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_SAMPLING_RATE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_SAMPLING_RATE = 446
- 		-static
-
- -

< linear scale-factor

- -

Definition at line 452 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_SCALEFACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_SCALEFACTOR = 445
- 		-static
-
- -

< B-factor

- -

Definition at line 451 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_TRANSVERSAL_DISPLACEMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_TRANSVERSAL_DISPLACEMENT = 462
- 		-static
-
- -

< Longitudinal displacement

- -

Definition at line 468 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_VALIDATIONSCORE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_VALIDATIONSCORE = 466
- 		-static
-
- -

< CTF value

- -

Definition at line 472 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_VALUE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_VALUE = 465
- 		-static
-
- -

< CTF gain

- -

Definition at line 471 of file MDLabel.java.

- -
-
- -

◆ RLN_CTF_VOLTAGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_CTF_VOLTAGE = 447
- 		-static
-
- -

< Sampling rate

- -

Definition at line 453 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_BEAMTILT_GROUP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_BEAMTILT_GROUP = 476
- 		-static
-
- -

Definition at line 482 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_BEAMTILT_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_BEAMTILT_X = 474
- 		-static
-
- -

Definition at line 480 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_BEAMTILT_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_BEAMTILT_Y = 475
- 		-static
-
- -

Definition at line 481 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_COORD_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_COORD_X = 477
- 		-static
-
- -

Definition at line 483 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_COORD_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_COORD_Y = 478
- 		-static
-
- -

Definition at line 484 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_COORD_Z

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_COORD_Z = 479
- 		-static
-
- -

Definition at line 485 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_DATATYPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_DATATYPE = 472
- 		-static
-
- -

Definition at line 478 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_DIMENSIONALITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_DIMENSIONALITY = 473
- 		-static
-
- -

Definition at line 479 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_ENABLED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_ENABLED = 471
- 		-static
-
- -

Definition at line 477 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_FRAME_NR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_FRAME_NR = 480
- 		-static
-
- -

Definition at line 486 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_ID = 470
- 		-static
-
- -

Definition at line 476 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_MAGNIFICATION_CORRECTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_MAGNIFICATION_CORRECTION = 481
- 		-static
-
- -

Definition at line 487 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_NAME = 468
- 		-static
-
- -

< Phase-shift from a phase-plate (in degrees)

- -

Definition at line 474 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_NORM_CORRECTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_NORM_CORRECTION = 482
- 		-static
-
- -

Definition at line 488 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_ORI_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_ORI_NAME = 483
- 		-static
-
- -

Definition at line 489 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_RECONSTRUCT_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_RECONSTRUCT_NAME = 469
- 		-static
-
- -

Definition at line 475 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_SAMPLINGRATE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_SAMPLINGRATE = 484
- 		-static
-
- -

Definition at line 490 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_SAMPLINGRATE_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_SAMPLINGRATE_X = 485
- 		-static
-
- -

Definition at line 491 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_SAMPLINGRATE_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_SAMPLINGRATE_Y = 486
- 		-static
-
- -

Definition at line 492 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_SAMPLINGRATE_Z

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_SAMPLINGRATE_Z = 487
- 		-static
-
- -

Definition at line 493 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_SIZE = 488
- 		-static
-
- -

Definition at line 494 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_SIZEX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_SIZEX = 489
- 		-static
-
- -

Definition at line 495 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_SIZEY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_SIZEY = 490
- 		-static
-
- -

Definition at line 496 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_SIZEZ

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_SIZEZ = 491
- 		-static
-
- -

Definition at line 497 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_STATS_AVG

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_STATS_AVG = 494
- 		-static
-
- -

Definition at line 500 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_STATS_KURT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_STATS_KURT = 497
- 		-static
-
- -

Definition at line 503 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_STATS_MAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_STATS_MAX = 493
- 		-static
-
- -

Definition at line 499 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_STATS_MIN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_STATS_MIN = 492
- 		-static
-
- -

Definition at line 498 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_STATS_SKEW

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_STATS_SKEW = 496
- 		-static
-
- -

Definition at line 502 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_STATS_STDDEV

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_STATS_STDDEV = 495
- 		-static
-
- -

Definition at line 501 of file MDLabel.java.

- -
-
- -

◆ RLN_IMAGE_WEIGHT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_IMAGE_WEIGHT = 498
- 		-static
-
- -

Definition at line 504 of file MDLabel.java.

- -
-
- -

◆ RLN_MASK_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MASK_NAME = 499
- 		-static
-
- -

Definition at line 505 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_1_1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_1_1 = 500
- 		-static
-
- -

Definition at line 506 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_1_2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_1_2 = 501
- 		-static
-
- -

Definition at line 507 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_1_3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_1_3 = 502
- 		-static
-
- -

Definition at line 508 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_2_1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_2_1 = 503
- 		-static
-
- -

Definition at line 509 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_2_2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_2_2 = 504
- 		-static
-
- -

Definition at line 510 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_2_3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_2_3 = 505
- 		-static
-
- -

Definition at line 511 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_3_1

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_3_1 = 506
- 		-static
-
- -

Definition at line 512 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_3_2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_3_2 = 507
- 		-static
-
- -

Definition at line 513 of file MDLabel.java.

- -
-
- -

◆ RLN_MATRIX_3_3

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MATRIX_3_3 = 508
- 		-static
-
- -

Definition at line 514 of file MDLabel.java.

- -
-
- -

◆ RLN_MICROGRAPH_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MICROGRAPH_ID = 509
- 		-static
-
- -

Definition at line 515 of file MDLabel.java.

- -
-
- -

◆ RLN_MICROGRAPH_MOVIE_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MICROGRAPH_MOVIE_NAME = 510
- 		-static
-
- -

Definition at line 516 of file MDLabel.java.

- -
-
- -

◆ RLN_MICROGRAPH_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MICROGRAPH_NAME = 511
- 		-static
-
- -

Definition at line 517 of file MDLabel.java.

- -
-
- -

◆ RLN_MICROGRAPH_NAME_WODOSE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MICROGRAPH_NAME_WODOSE = 512
- 		-static
-
- -

Definition at line 518 of file MDLabel.java.

- -
-
- -

◆ RLN_MICROGRAPH_TILT_ANGLE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MICROGRAPH_TILT_ANGLE = 513
- 		-static
-
- -

Definition at line 519 of file MDLabel.java.

- -
-
- -

◆ RLN_MICROGRAPH_TILT_AXIS_DIRECTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MICROGRAPH_TILT_AXIS_DIRECTION = 514
- 		-static
-
- -

Definition at line 520 of file MDLabel.java.

- -
-
- -

◆ RLN_MICROGRAPH_TILT_AXIS_OUTOFPLANE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MICROGRAPH_TILT_AXIS_OUTOFPLANE = 515
- 		-static
-
- -

Definition at line 521 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_ACCURACY_ROT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_ACCURACY_ROT = 516
- 		-static
-
- -

Definition at line 522 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_ACCURACY_TRANS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_ACCURACY_TRANS = 517
- 		-static
-
- -

Definition at line 523 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_AVE_PMAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_AVE_PMAX = 518
- 		-static
-
- -

Definition at line 524 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_CURRENT_RESOLUTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_CURRENT_RESOLUTION = 519
- 		-static
-
- -

Definition at line 525 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_CURRENT_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_CURRENT_SIZE = 520
- 		-static
-
- -

Definition at line 526 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_DATA_VS_PRIOR_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_DATA_VS_PRIOR_REF = 521
- 		-static
-
- -

Definition at line 527 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_DIFF2_HALVES_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_DIFF2_HALVES_REF = 524
- 		-static
-
- -

Definition at line 530 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_DIMENSIONALITY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_DIMENSIONALITY = 522
- 		-static
-
- -

Definition at line 528 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_DIMENSIONALITY_DATA

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_DIMENSIONALITY_DATA = 523
- 		-static
-
- -

Definition at line 529 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_ESTIM_RESOL_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_ESTIM_RESOL_REF = 525
- 		-static
-
- -

Definition at line 531 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_FOURIER_COVERAGE_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_FOURIER_COVERAGE_REF = 526
- 		-static
-
- -

Definition at line 532 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_FOURIER_COVERAGE_TOTAL_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_FOURIER_COVERAGE_TOTAL_REF = 527
- 		-static
-
- -

Definition at line 533 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_FSC_HALVES_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_FSC_HALVES_REF = 528
- 		-static
-
- -

Definition at line 534 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_GROUP_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_GROUP_NAME = 529
- 		-static
-
- -

Definition at line 535 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_GROUP_NO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_GROUP_NO = 530
- 		-static
-
- -

Definition at line 536 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_GROUP_NR_PARTICLES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_GROUP_NR_PARTICLES = 531
- 		-static
-
- -

Definition at line 537 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_GROUP_SCALE_CORRECTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_GROUP_SCALE_CORRECTION = 532
- 		-static
-
- -

Definition at line 538 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_NR_ASU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_NR_ASU = 533
- 		-static
-
- -

Definition at line 539 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_RISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_RISE = 538
- 		-static
-
- -

Definition at line 544 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_RISE_INITIAL_STEP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_RISE_INITIAL_STEP = 541
- 		-static
-
- -

Definition at line 547 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_RISE_MAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_RISE_MAX = 540
- 		-static
-
- -

Definition at line 546 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_RISE_MIN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_RISE_MIN = 539
- 		-static
-
- -

Definition at line 545 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_TWIST

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_TWIST = 534
- 		-static
-
- -

Definition at line 540 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_TWIST_INITIAL_STEP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_TWIST_INITIAL_STEP = 537
- 		-static
-
- -

Definition at line 543 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_TWIST_MAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_TWIST_MAX = 536
- 		-static
-
- -

Definition at line 542 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_HELICAL_TWIST_MIN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_HELICAL_TWIST_MIN = 535
- 		-static
-
- -

Definition at line 541 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_INTERPOLATOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_INTERPOLATOR = 543
- 		-static
-
- -

Definition at line 549 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_IS_HELIX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_IS_HELIX = 542
- 		-static
-
- -

Definition at line 548 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_LL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_LL = 544
- 		-static
-
- -

Definition at line 550 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION = 545
- 		-static
-
- -

Definition at line 551 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_NORM_CORRECTION_AVG

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_NORM_CORRECTION_AVG = 546
- 		-static
-
- -

Definition at line 552 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_NR_BODIES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_NR_BODIES = 547
- 		-static
-
- -

Definition at line 553 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_NR_CLASSES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_NR_CLASSES = 548
- 		-static
-
- -

Definition at line 554 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_NR_GROUPS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_NR_GROUPS = 549
- 		-static
-
- -

Definition at line 555 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_ORIENTABILITY_CONTRIBUTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_ORIENTABILITY_CONTRIBUTION = 551
- 		-static
-
- -

Definition at line 557 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_ORIGINAL_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_ORIGINAL_SIZE = 550
- 		-static
-
- -

Definition at line 556 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_PADDING_FACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_PADDING_FACTOR = 552
- 		-static
-
- -

Definition at line 558 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_PDF_CLASS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_PDF_CLASS = 553
- 		-static
-
- -

Definition at line 559 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_PDF_ORIENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_PDF_ORIENT = 556
- 		-static
-
- -

Definition at line 562 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_PIXEL_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_PIXEL_SIZE = 557
- 		-static
-
- -

Definition at line 563 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_POWER_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_POWER_REF = 558
- 		-static
-
- -

Definition at line 564 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_PRIOR_MODE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_PRIOR_MODE = 559
- 		-static
-
- -

Definition at line 565 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_PRIOR_OFFX_CLASS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_PRIOR_OFFX_CLASS = 554
- 		-static
-
- -

Definition at line 560 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_PRIOR_OFFY_CLASS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_PRIOR_OFFY_CLASS = 555
- 		-static
-
- -

Definition at line 561 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_REF_IMAGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_REF_IMAGE = 565
- 		-static
-
- -

Definition at line 571 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_SGD_GRADIENT_IMAGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_SGD_GRADIENT_IMAGE = 560
- 		-static
-
- -

Definition at line 566 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_SIGMA2_NOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA2_NOISE = 566
- 		-static
-
- -

Definition at line 572 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_SIGMA2_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA2_REF = 567
- 		-static
-
- -

Definition at line 573 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_SIGMA_OFFSET

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA_OFFSET = 561
- 		-static
-
- -

Definition at line 567 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_SIGMA_PSI

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA_PSI = 564
- 		-static
-
- -

Definition at line 570 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_SIGMA_ROT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA_ROT = 562
- 		-static
-
- -

Definition at line 568 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_SIGMA_TILT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_SIGMA_TILT = 563
- 		-static
-
- -

Definition at line 569 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_SSNR_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_SSNR_REF = 568
- 		-static
-
- -

Definition at line 574 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_TAU2_FUDGE_FACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_TAU2_FUDGE_FACTOR = 569
- 		-static
-
- -

Definition at line 575 of file MDLabel.java.

- -
-
- -

◆ RLN_MLMODEL_TAU2_REF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_MLMODEL_TAU2_REF = 570
- 		-static
-
- -

Definition at line 576 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_ACCURACY_ROT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_ACCURACY_ROT = 571
- 		-static
-
- -

Definition at line 577 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_ACCURACY_TRANS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_ACCURACY_TRANS = 572
- 		-static
-
- -

Definition at line 578 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_ADAPTIVE_FRACTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_ADAPTIVE_FRACTION = 573
- 		-static
-
- -

Definition at line 579 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_ADAPTIVE_OVERSAMPLING

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_ADAPTIVE_OVERSAMPLING = 574
- 		-static
-
- -

Definition at line 580 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_AUTO_LOCAL_HP_ORDER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_AUTO_LOCAL_HP_ORDER = 575
- 		-static
-
- -

Definition at line 581 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_AVAILABLE_MEMORY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_AVAILABLE_MEMORY = 576
- 		-static
-
- -

Definition at line 582 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_BEST_RESOL_THUS_FAR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_BEST_RESOL_THUS_FAR = 577
- 		-static
-
- -

Definition at line 583 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_CHANGES_OPTIMAL_CLASSES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_CHANGES_OPTIMAL_CLASSES = 580
- 		-static
-
- -

Definition at line 586 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_CHANGES_OPTIMAL_OFFSETS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_CHANGES_OPTIMAL_OFFSETS = 578
- 		-static
-
- -

Definition at line 584 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_CHANGES_OPTIMAL_ORIENTS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_CHANGES_OPTIMAL_ORIENTS = 579
- 		-static
-
- -

Definition at line 585 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_COARSE_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_COARSE_SIZE = 581
- 		-static
-
- -

Definition at line 587 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED = 582
- 		-static
-
- -

Definition at line 588 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DATA_ARE_CTF_PREMULTIPLIED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DATA_ARE_CTF_PREMULTIPLIED = 583
- 		-static
-
- -

Definition at line 589 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DATA_STARFILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DATA_STARFILE = 584
- 		-static
-
- -

Definition at line 590 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_AUTO_REFINE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_AUTO_REFINE = 585
- 		-static
-
- -

Definition at line 591 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_CORRECT_CTF

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_CORRECT_CTF = 587
- 		-static
-
- -

Definition at line 593 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_CORRECT_MAGNIFICATION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_CORRECT_MAGNIFICATION = 588
- 		-static
-
- -

Definition at line 594 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_CORRECT_NORM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_CORRECT_NORM = 589
- 		-static
-
- -

Definition at line 595 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_CORRECT_SCALE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_CORRECT_SCALE = 590
- 		-static
-
- -

Definition at line 596 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_HELICAL_REFINE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_HELICAL_REFINE = 591
- 		-static
-
- -

Definition at line 597 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_MAP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_MAP = 593
- 		-static
-
- -

Definition at line 599 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES = 586
- 		-static
-
- -

Definition at line 592 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_REALIGN_MOVIES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_REALIGN_MOVIES = 592
- 		-static
-
- -

Definition at line 598 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_SGD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SGD = 594
- 		-static
-
- -

Definition at line 600 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_SKIP_ALIGN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SKIP_ALIGN = 596
- 		-static
-
- -

Definition at line 602 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_SKIP_ROTATE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SKIP_ROTATE = 597
- 		-static
-
- -

Definition at line 603 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_SOLVENT_FLATTEN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SOLVENT_FLATTEN = 595
- 		-static
-
- -

Definition at line 601 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_SPLIT_RANDOM_HALVES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_SPLIT_RANDOM_HALVES = 598
- 		-static
-
- -

Definition at line 604 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_DO_ZERO_MASK

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_DO_ZERO_MASK = 599
- 		-static
-
- -

Definition at line 605 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_FIX_SIGMA_NOISE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_FIX_SIGMA_NOISE = 600
- 		-static
-
- -

Definition at line 606 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_FIX_SIGMA_OFFSET

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_FIX_SIGMA_OFFSET = 601
- 		-static
-
- -

Definition at line 607 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_FIX_TAU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_FIX_TAU = 602
- 		-static
-
- -

Definition at line 608 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HAS_CONVERGED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HAS_CONVERGED = 603
- 		-static
-
- -

Definition at line 609 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT = 604
- 		-static
-
- -

Definition at line 610 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO = 605
- 		-static
-
- -

Definition at line 611 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HELICAL_KEEP_TILT_PRIOR_FIXED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_KEEP_TILT_PRIOR_FIXED = 615
- 		-static
-
- -

Definition at line 621 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HELICAL_RISE_INITIAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_RISE_INITIAL = 607
- 		-static
-
- -

Definition at line 613 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HELICAL_SIGMA_DISTANCE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_SIGMA_DISTANCE = 612
- 		-static
-
- -

Definition at line 618 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HELICAL_SYMMETRY_LOCAL_REFINEMENT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_SYMMETRY_LOCAL_REFINEMENT = 611
- 		-static
-
- -

Definition at line 617 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HELICAL_TUBE_INNER_DIAMETER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_TUBE_INNER_DIAMETER = 609
- 		-static
-
- -

Definition at line 615 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HELICAL_TUBE_OUTER_DIAMETER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_TUBE_OUTER_DIAMETER = 610
- 		-static
-
- -

Definition at line 616 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HELICAL_TWIST_INITIAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_TWIST_INITIAL = 606
- 		-static
-
- -

Definition at line 612 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HELICAL_Z_PERCENTAGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HELICAL_Z_PERCENTAGE = 608
- 		-static
-
- -

Definition at line 614 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HIGHRES_LIMIT_EXP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HIGHRES_LIMIT_EXP = 616
- 		-static
-
- -

Definition at line 622 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_HIGHRES_LIMIT_SGD

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_HIGHRES_LIMIT_SGD = 613
- 		-static
-
- -

Definition at line 619 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK = 617
- 		-static
-
- -

Definition at line 623 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_IGNORE_HELICAL_SYMMETRY

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_IGNORE_HELICAL_SYMMETRY = 614
- 		-static
-
- -

Definition at line 620 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_INCR_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_INCR_SIZE = 618
- 		-static
-
- -

Definition at line 624 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_ITERATION_NO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_ITERATION_NO = 619
- 		-static
-
- -

Definition at line 625 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_LOCAL_SYMMETRY_FILENAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_LOCAL_SYMMETRY_FILENAME = 620
- 		-static
-
- -

Definition at line 626 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES = 621
- 		-static
-
- -

Definition at line 627 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_MAGNIFICATION_RANGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_MAGNIFICATION_RANGE = 622
- 		-static
-
- -

Definition at line 628 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_MAGNIFICATION_STEP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_MAGNIFICATION_STEP = 623
- 		-static
-
- -

Definition at line 629 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_MAX_COARSE_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_MAX_COARSE_SIZE = 624
- 		-static
-
- -

Definition at line 630 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_MAX_NR_POOL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_MAX_NR_POOL = 625
- 		-static
-
- -

Definition at line 631 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_MODEL_STARFILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_MODEL_STARFILE = 626
- 		-static
-
- -

Definition at line 632 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_MODEL_STARFILE2

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_MODEL_STARFILE2 = 627
- 		-static
-
- -

Definition at line 633 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES = 630
- 		-static
-
- -

Definition at line 636 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_NR_ITER_WO_RESOL_GAIN

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_NR_ITER_WO_RESOL_GAIN = 629
- 		-static
-
- -

Definition at line 635 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_NR_ITERATIONS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_NR_ITERATIONS = 628
- 		-static
-
- -

Definition at line 634 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_OUTPUT_ROOTNAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_OUTPUT_ROOTNAME = 631
- 		-static
-
- -

Definition at line 637 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_PARTICLE_DIAMETER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_PARTICLE_DIAMETER = 632
- 		-static
-
- -

Definition at line 638 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_RADIUS_MASK_3D_MAP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_RADIUS_MASK_3D_MAP = 633
- 		-static
-
- -

Definition at line 639 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_RADIUS_MASK_EXP_PARTICLES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_RADIUS_MASK_EXP_PARTICLES = 634
- 		-static
-
- -

Definition at line 640 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_RANDOM_SEED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_RANDOM_SEED = 635
- 		-static
-
- -

Definition at line 641 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_REFS_ARE_CTF_CORRECTED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_REFS_ARE_CTF_CORRECTED = 636
- 		-static
-
- -

Definition at line 642 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SAMPLING_STARFILE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SAMPLING_STARFILE = 637
- 		-static
-
- -

Definition at line 643 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SGD_MAX_SUBSETS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_MAX_SUBSETS = 644
- 		-static
-
- -

Definition at line 650 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SGD_MU

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_MU = 638
- 		-static
-
- -

Definition at line 644 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SGD_SIGMA2FUDGE_HALFLIFE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_SIGMA2FUDGE_HALFLIFE = 640
- 		-static
-
- -

Definition at line 646 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SGD_SIGMA2FUDGE_INI

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_SIGMA2FUDGE_INI = 639
- 		-static
-
- -

Definition at line 645 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SGD_STEPSIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_STEPSIZE = 645
- 		-static
-
- -

Definition at line 651 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SGD_SUBSET_SIZE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_SUBSET_SIZE = 642
- 		-static
-
- -

Definition at line 648 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SGD_SUBSET_START

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_SUBSET_START = 641
- 		-static
-
- -

Definition at line 647 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SGD_WRITE_EVERY_SUBSET

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SGD_WRITE_EVERY_SUBSET = 643
- 		-static
-
- -

Definition at line 649 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES = 646
- 		-static
-
- -

Definition at line 652 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS = 647
- 		-static
-
- -

Definition at line 653 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS = 648
- 		-static
-
- -

Definition at line 654 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SOLVENT_MASK2_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SOLVENT_MASK2_NAME = 650
- 		-static
-
- -

Definition at line 656 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_SOLVENT_MASK_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_SOLVENT_MASK_NAME = 649
- 		-static
-
- -

Definition at line 655 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_TAU_SPECTRUM_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_TAU_SPECTRUM_NAME = 651
- 		-static
-
- -

Definition at line 657 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_USE_TOO_COARSE_SAMPLING

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_USE_TOO_COARSE_SAMPLING = 652
- 		-static
-
- -

Definition at line 658 of file MDLabel.java.

- -
-
- -

◆ RLN_OPTIMISER_WIDTH_MASK_EDGE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_OPTIMISER_WIDTH_MASK_EDGE = 653
- 		-static
-
- -

Definition at line 659 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_FLIP

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_FLIP = 654
- 		-static
-
- -

Definition at line 660 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ID = 655
- 		-static
-
- -

Definition at line 661 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ORIGIN_X

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_X = 656
- 		-static
-
- -

Definition at line 662 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ORIGIN_X_PRIOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_X_PRIOR = 657
- 		-static
-
- -

Definition at line 663 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ORIGIN_Y

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Y = 658
- 		-static
-
- -

Definition at line 664 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ORIGIN_Y_PRIOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Y_PRIOR = 659
- 		-static
-
- -

Definition at line 665 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ORIGIN_Z

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Z = 660
- 		-static
-
- -

Definition at line 666 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ORIGIN_Z_PRIOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ORIGIN_Z_PRIOR = 661
- 		-static
-
- -

Definition at line 667 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_PSI

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_PSI = 666
- 		-static
-
- -

Definition at line 672 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_PSI_PRIOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_PSI_PRIOR = 667
- 		-static
-
- -

Definition at line 673 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_PSI_PRIOR_FLIP_RATIO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_PSI_PRIOR_FLIP_RATIO = 668
- 		-static
-
- -

Definition at line 674 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ROT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ROT = 662
- 		-static
-
- -

Definition at line 668 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_ROT_PRIOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_ROT_PRIOR = 663
- 		-static
-
- -

Definition at line 669 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_TILT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_TILT = 664
- 		-static
-
- -

Definition at line 670 of file MDLabel.java.

- -
-
- -

◆ RLN_ORIENT_TILT_PRIOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_ORIENT_TILT_PRIOR = 665
- 		-static
-
- -

Definition at line 671 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_AUTOPICK_FOM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_AUTOPICK_FOM = 669
- 		-static
-
- -

Definition at line 675 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_CLASS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_CLASS = 670
- 		-static
-
- -

Definition at line 676 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_DLL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_DLL = 671
- 		-static
-
- -

Definition at line 677 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_FOM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_FOM = 673
- 		-static
-
- -

Definition at line 679 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_HELICAL_TRACK_LENGTH

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_HELICAL_TRACK_LENGTH = 685
- 		-static
-
- -

Definition at line 691 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_HELICAL_TUBE_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_HELICAL_TUBE_ID = 683
- 		-static
-
- -

Definition at line 689 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_HELICAL_TUBE_PITCH

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_HELICAL_TUBE_PITCH = 684
- 		-static
-
- -

Definition at line 690 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_ID

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_ID = 672
- 		-static
-
- -

Definition at line 678 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_KL_DIVERGENCE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_KL_DIVERGENCE = 674
- 		-static
-
- -

Definition at line 680 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_MOVIE_RUNNING_AVG

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_MOVIE_RUNNING_AVG = 675
- 		-static
-
- -

Definition at line 681 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_NAME = 677
- 		-static
-
- -

Definition at line 683 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_NR_FRAMES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_NR_FRAMES = 680
- 		-static
-
- -

Definition at line 686 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_NR_FRAMES_AVG

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_NR_FRAMES_AVG = 681
- 		-static
-
- -

Definition at line 687 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_NR_SIGNIFICANT_SAMPLES

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_NR_SIGNIFICANT_SAMPLES = 679
- 		-static
-
- -

Definition at line 685 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_ORI_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_ORI_NAME = 678
- 		-static
-
- -

Definition at line 684 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_PMAX

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_PMAX = 682
- 		-static
-
- -

Definition at line 688 of file MDLabel.java.

- -
-
- -

◆ RLN_PARTICLE_RANDOM_SUBSET

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PARTICLE_RANDOM_SUBSET = 676
- 		-static
-
- -

Definition at line 682 of file MDLabel.java.

- -
-
- -

◆ RLN_PERFRAME_CUMULATIVE_WEIGHT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PERFRAME_CUMULATIVE_WEIGHT = 736
- 		-static
-
- -

Definition at line 742 of file MDLabel.java.

- -
-
- -

◆ RLN_PERFRAME_RELATIVE_WEIGHT

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PERFRAME_RELATIVE_WEIGHT = 737
- 		-static
-
- -

Definition at line 743 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_EDGE_FROM

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_EDGE_FROM = 693
- 		-static
-
- -

Definition at line 699 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_EDGE_PROCESS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_EDGE_PROCESS = 695
- 		-static
-
- -

Definition at line 701 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_EDGE_TO

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_EDGE_TO = 694
- 		-static
-
- -

Definition at line 700 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_JOB_COUNTER

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_JOB_COUNTER = 686
- 		-static
-
- -

Definition at line 692 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_NODE_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_NODE_NAME = 687
- 		-static
-
- -

Definition at line 693 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_NODE_TYPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_NODE_TYPE = 688
- 		-static
-
- -

Definition at line 694 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_PROCESS_ALIAS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_PROCESS_ALIAS = 689
- 		-static
-
- -

Definition at line 695 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_PROCESS_NAME

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_PROCESS_NAME = 690
- 		-static
-
- -

Definition at line 696 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_PROCESS_STATUS

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_PROCESS_STATUS = 692
- 		-static
-
- -

Definition at line 698 of file MDLabel.java.

- -
-
- -

◆ RLN_PIPELINE_PROCESS_TYPE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_PIPELINE_PROCESS_TYPE = 691
- 		-static
-
- -

Definition at line 697 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_AMPLCORR_MASKED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_AMPLCORR_MASKED = 696
- 		-static
-
- -

Definition at line 702 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_AMPLCORR_UNMASKED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_AMPLCORR_UNMASKED = 697
- 		-static
-
- -

Definition at line 703 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_BFACTOR

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_BFACTOR = 698
- 		-static
-
- -

Definition at line 704 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_DPR_MASKED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_DPR_MASKED = 699
- 		-static
-
- -

Definition at line 705 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_DPR_UNMASKED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_DPR_UNMASKED = 700
- 		-static
-
- -

Definition at line 706 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_FINAL_RESOLUTION

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_FINAL_RESOLUTION = 701
- 		-static
-
- -

Definition at line 707 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_FSC_GENERAL

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_GENERAL = 702
- 		-static
-
- -

Definition at line 708 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_FSC_MASKED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_MASKED = 704
- 		-static
-
- -

Definition at line 710 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_FSC_RANDOM_MASKED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_RANDOM_MASKED = 706
- 		-static
-
- -

Definition at line 712 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_FSC_TRUE

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_TRUE = 703
- 		-static
-
- -

Definition at line 709 of file MDLabel.java.

- -
-
- -

◆ RLN_POSTPROCESS_FSC_UNMASKED

- -
-
- - - - - -
- - - - -
final int xmipp.jni.MDLabel.RLN_POSTPROCESS_FSC_UNMASKED = 705
- 		-static
-
- -

Definition at line 711 of file MDLabel.java.

- -
-
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◆ RLN_POSTPROCESS_GUINIER_FIT_CORRELATION

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_FIT_CORRELATION = 707
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Definition at line 713 of file MDLabel.java.

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◆ RLN_POSTPROCESS_GUINIER_FIT_INTERCEPT

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_FIT_INTERCEPT = 708
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Definition at line 714 of file MDLabel.java.

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◆ RLN_POSTPROCESS_GUINIER_FIT_SLOPE

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_FIT_SLOPE = 709
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Definition at line 715 of file MDLabel.java.

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◆ RLN_POSTPROCESS_GUINIER_RESOL_SQUARED

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_RESOL_SQUARED = 715
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Definition at line 721 of file MDLabel.java.

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◆ RLN_POSTPROCESS_GUINIER_VALUE_IN

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_IN = 710
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Definition at line 716 of file MDLabel.java.

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◆ RLN_POSTPROCESS_GUINIER_VALUE_INTERCEPT

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_INTERCEPT = 714
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Definition at line 720 of file MDLabel.java.

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◆ RLN_POSTPROCESS_GUINIER_VALUE_INVMTF

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_INVMTF = 711
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Definition at line 717 of file MDLabel.java.

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◆ RLN_POSTPROCESS_GUINIER_VALUE_SHARPENED

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_SHARPENED = 713
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Definition at line 719 of file MDLabel.java.

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◆ RLN_POSTPROCESS_GUINIER_VALUE_WEIGHTED

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_GUINIER_VALUE_WEIGHTED = 712
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Definition at line 718 of file MDLabel.java.

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◆ RLN_POSTPROCESS_MTF_VALUE

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final int xmipp.jni.MDLabel.RLN_POSTPROCESS_MTF_VALUE = 716
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Definition at line 722 of file MDLabel.java.

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◆ RLN_RESOLUTION

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final int xmipp.jni.MDLabel.RLN_RESOLUTION = 738
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Definition at line 744 of file MDLabel.java.

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◆ RLN_RESOLUTION_ANGSTROM

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final int xmipp.jni.MDLabel.RLN_RESOLUTION_ANGSTROM = 739
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Definition at line 745 of file MDLabel.java.

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◆ RLN_RESOLUTION_INVPIXEL

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final int xmipp.jni.MDLabel.RLN_RESOLUTION_INVPIXEL = 740
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Definition at line 746 of file MDLabel.java.

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◆ RLN_SAMPLING_HEALPIX_ORDER

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final int xmipp.jni.MDLabel.RLN_SAMPLING_HEALPIX_ORDER = 719
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Definition at line 725 of file MDLabel.java.

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◆ RLN_SAMPLING_HELICAL_OFFSET_STEP

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final int xmipp.jni.MDLabel.RLN_SAMPLING_HELICAL_OFFSET_STEP = 720
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Definition at line 726 of file MDLabel.java.

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final int xmipp.jni.MDLabel.RLN_SAMPLING_IS_3D = 717
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< Detector MTF value

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Definition at line 723 of file MDLabel.java.

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◆ RLN_SAMPLING_IS_3D_TRANS

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final int xmipp.jni.MDLabel.RLN_SAMPLING_IS_3D_TRANS = 718
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Definition at line 724 of file MDLabel.java.

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◆ RLN_SAMPLING_LIMIT_TILT

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final int xmipp.jni.MDLabel.RLN_SAMPLING_LIMIT_TILT = 721
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Definition at line 727 of file MDLabel.java.

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◆ RLN_SAMPLING_OFFSET_RANGE

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final int xmipp.jni.MDLabel.RLN_SAMPLING_OFFSET_RANGE = 722
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Definition at line 728 of file MDLabel.java.

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◆ RLN_SAMPLING_OFFSET_STEP

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final int xmipp.jni.MDLabel.RLN_SAMPLING_OFFSET_STEP = 723
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Definition at line 729 of file MDLabel.java.

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◆ RLN_SAMPLING_PERTURB

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final int xmipp.jni.MDLabel.RLN_SAMPLING_PERTURB = 724
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Definition at line 730 of file MDLabel.java.

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◆ RLN_SAMPLING_PERTURBATION_FACTOR

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final int xmipp.jni.MDLabel.RLN_SAMPLING_PERTURBATION_FACTOR = 725
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Definition at line 731 of file MDLabel.java.

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◆ RLN_SAMPLING_PRIOR_MODE

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final int xmipp.jni.MDLabel.RLN_SAMPLING_PRIOR_MODE = 726
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Definition at line 732 of file MDLabel.java.

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◆ RLN_SAMPLING_PSI_STEP

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Definition at line 733 of file MDLabel.java.

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◆ RLN_SAMPLING_SIGMA_PSI

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final int xmipp.jni.MDLabel.RLN_SAMPLING_SIGMA_PSI = 730
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Definition at line 736 of file MDLabel.java.

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◆ RLN_SAMPLING_SIGMA_ROT

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final int xmipp.jni.MDLabel.RLN_SAMPLING_SIGMA_ROT = 728
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Definition at line 734 of file MDLabel.java.

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◆ RLN_SAMPLING_SIGMA_TILT

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final int xmipp.jni.MDLabel.RLN_SAMPLING_SIGMA_TILT = 729
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Definition at line 735 of file MDLabel.java.

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◆ RLN_SAMPLING_SYMMETRY

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final int xmipp.jni.MDLabel.RLN_SAMPLING_SYMMETRY = 731
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Definition at line 737 of file MDLabel.java.

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◆ RLN_SELECT_PARTICLES_ZSCORE

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final int xmipp.jni.MDLabel.RLN_SELECT_PARTICLES_ZSCORE = 733
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Definition at line 739 of file MDLabel.java.

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◆ RLN_SELECTED

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final int xmipp.jni.MDLabel.RLN_SELECTED = 732
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Definition at line 738 of file MDLabel.java.

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◆ RLN_SORTED_IDX

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final int xmipp.jni.MDLabel.RLN_SORTED_IDX = 734
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Definition at line 740 of file MDLabel.java.

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◆ RLN_SPECTRAL_IDX

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final int xmipp.jni.MDLabel.RLN_SPECTRAL_IDX = 741
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Definition at line 747 of file MDLabel.java.

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◆ RLN_STARFILE_MOVIE_PARTICLES

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final int xmipp.jni.MDLabel.RLN_STARFILE_MOVIE_PARTICLES = 735
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Definition at line 741 of file MDLabel.java.

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This is the complete list of members for xmipp.jni.MDRow, including all inherited members.

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addLabel(int label)xmipp.jni.MDRow
clear()xmipp.jni.MDRow
containsLabel(int label)xmipp.jni.MDRow
destroy()xmipp.jni.MDRow
finalize()xmipp.jni.MDRowinlineprotected
getEnabled(long objId)xmipp.jni.MDRowinline
getValueDouble(int label)xmipp.jni.MDRow
getValueInt(int label)xmipp.jni.MDRow
getValueLong(int label)xmipp.jni.MDRow
getValueString(int label)xmipp.jni.MDRow
MDRow()xmipp.jni.MDRowinline
MDRow(long peer)xmipp.jni.MDRowinline
removeLabel(int label)xmipp.jni.MDRow
setEnabled(boolean value)xmipp.jni.MDRowinline
setValueBoolean(int label, boolean value)xmipp.jni.MDRow
setValueDouble(int label, double value)xmipp.jni.MDRow
setValueInt(int label, int value)xmipp.jni.MDRow
setValueLong(int label, long value)xmipp.jni.MDRow
setValueString(int label, String value)xmipp.jni.MDRow
size()xmipp.jni.MDRow
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-Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.jni.MDRow Class Reference
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-Public Member Functions

synchronized native void destroy ()
 
native void clear ()
 
native int size ()
 
native boolean containsLabel (int label)
 
native boolean removeLabel (int label)
 
native int getValueInt (int label)
 
native long getValueLong (int label)
 
native double getValueDouble (int label)
 
native String getValueString (int label)
 
boolean setEnabled (boolean value)
 
boolean getEnabled (long objId)
 
native boolean setValueInt (int label, int value)
 
native boolean setValueLong (int label, long value)
 
native boolean setValueDouble (int label, double value)
 
native boolean setValueString (int label, String value)
 
native boolean setValueBoolean (int label, boolean value)
 
native void addLabel (int label)
 
 MDRow ()
 
 MDRow (long peer)
 
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-Protected Member Functions

void finalize () throws Throwable
 
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Detailed Description

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Binding class for accessing C++ MDRow implementation.

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Definition at line 31 of file MDRow.java.

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Constructor & Destructor Documentation

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◆ MDRow() [1/2]

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xmipp.jni.MDRow.MDRow ()
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Create empty metadata

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Definition at line 93 of file MDRow.java.

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93  {
94  create();
95  }
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◆ MDRow() [2/2]

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xmipp.jni.MDRow.MDRow (long peer)
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Definition at line 97 of file MDRow.java.

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97  {
98  createRef(peer);
99 
100  }
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Member Function Documentation

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◆ addLabel()

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native void xmipp.jni.MDRow.addLabel (int label)
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◆ clear()

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◆ containsLabel()

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◆ destroy()

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synchronized native void xmipp.jni.MDRow.destroy ()
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◆ finalize()

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void xmipp.jni.MDRow.finalize () throws Throwable
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Will be called by GarbageCollector before destroying. Needed to free C++ object memory.

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Definition at line 107 of file MDRow.java.

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107  {
108  super.finalize();
109  destroy();
110  }
xmipp.jni.MDRow.destroy
synchronized native void destroy()
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◆ getEnabled()

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boolean xmipp.jni.MDRow.getEnabled (long objId)
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Definition at line 75 of file MDRow.java.

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75  {
76  return getValueInt(MDLabel.MDL_ENABLED) > 0;
77  }
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native int getValueInt(int label)
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native String xmipp.jni.MDRow.getValueString (int label)
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Return the value of some label as String

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◆ removeLabel()

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◆ setEnabled()

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boolean xmipp.jni.MDRow.setEnabled (boolean value)
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Definition at line 71 of file MDRow.java.

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71  {
72  return setValueInt(MDLabel.MDL_ENABLED, value ? 1 : -1);
73  }
xmipp.jni.MDRow.setValueInt
native boolean setValueInt(int label, int value)
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◆ setValueBoolean()

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native boolean xmipp.jni.MDRow.setValueBoolean (int label,
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◆ setValueDouble()

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◆ setValueInt()

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◆ setValueLong()

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◆ setValueString()

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◆ size()

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native int xmipp.jni.MDRow.size ()
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- - diff --git a/html/classxmipp_1_1jni_1_1MetaData-members.html b/html/classxmipp_1_1jni_1_1MetaData-members.html deleted file mode 100644 index dbfa343c..00000000 --- a/html/classxmipp_1_1jni_1_1MetaData-members.html +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.jni.MetaData Member List
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This is the complete list of members for xmipp.jni.MetaData, including all inherited members.

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addLabel(int label)xmipp.jni.MetaData
addObject()xmipp.jni.MetaData
clear()xmipp.jni.MetaData
computeFourierStatistics(MetaData mdIn, int label)xmipp.jni.MetaData
containsBlock(String file, String block)xmipp.jni.MetaDatainlinestatic
containsCTF(long id)xmipp.jni.MetaDatainline
containsGeometryInfo(String type)xmipp.jni.MetaDatainline
containsLabel(int label)xmipp.jni.MetaData
containsLabel(int[] labels)xmipp.jni.MetaDatainline
containsMicrographParticles()xmipp.jni.MetaDatainline
containsMicrographsInfo()xmipp.jni.MetaDatainline
ctfsxmipp.jni.MetaDataprotected
destroy()xmipp.jni.MetaData
enableDebug()xmipp.jni.MetaData
filenamexmipp.jni.MetaDataprotected
FILL_CONSTANTxmipp.jni.MetaDatastatic
FILL_LINEARxmipp.jni.MetaDatastatic
FILL_RAND_GAUSSIANxmipp.jni.MetaDatastatic
FILL_RAND_UNIFORMxmipp.jni.MetaDatastatic
fillConstant(int label, String value)xmipp.jni.MetaData
fillLinear(int label, double start, double step)xmipp.jni.MetaData
fillRandom(int label, String mode, double op1, double op2)xmipp.jni.MetaData
finalize()xmipp.jni.MetaDatainlineprotected
findObjects()xmipp.jni.MetaData
firstObject()xmipp.jni.MetaData
fixPath(String value)xmipp.jni.MetaDatainline
fixPath(String value, String baseDir)xmipp.jni.MetaDatainline
GEOMETRY_LABELSxmipp.jni.MetaDatastatic
GEOMETRY_RELION_LABELSxmipp.jni.MetaDatastatic
getActiveLabels()xmipp.jni.MetaData
getBaseDir()xmipp.jni.MetaDatainline
getBlock()xmipp.jni.MetaDatainline
getBlocksInMetaDataFile(String filename)xmipp.jni.MetaDatastatic
getClassForType(int type)xmipp.jni.MetaDatainlinestatic
getColumnMax(int column)xmipp.jni.MetaData
getColumnMin(int column)xmipp.jni.MetaData
getColumnValues(int label)xmipp.jni.MetaData
getCTFDescription(long id)xmipp.jni.MetaDatainline
getCTFFile(long id)xmipp.jni.MetaDatainline
getEllipseCTF(long id)xmipp.jni.MetaDatainline
getEllipseCTF(long id, int D)xmipp.jni.MetaDatainline
getEnabled(long objId)xmipp.jni.MetaDatainline
getFilename()xmipp.jni.MetaDatainline
getLabelClass(int label)xmipp.jni.MetaDatainlinestatic
getLabelComment(int label)xmipp.jni.MetaDatastatic
getLabelName(int label)xmipp.jni.MetaDatainlinestatic
getLabelType(int label)xmipp.jni.MetaDatastatic
getLabelTypeString(int labelType)xmipp.jni.MetaDatainlinestatic
getMetaDataRow()xmipp.jni.MetaDatainline
getPath()xmipp.jni.MetaDatainline
getPCAbasis(ImageGeneric basis, int label)xmipp.jni.MetaData
getPSDEnhanced(long id)xmipp.jni.MetaDatainline
getPSDFile(long id)xmipp.jni.MetaDatainline
getRow(MDRow mdRow, long objId)xmipp.jni.MetaData
getRowValues(long objId)xmipp.jni.MetaDatainline
getStatistics(boolean applyGeo, int label)xmipp.jni.MetaData
getStatsImages(ImageGeneric imageAvg, ImageGeneric imageStd, boolean applyGeo, boolean wrap, int label)xmipp.jni.MetaData
getValueBoolean(int label, long objId)xmipp.jni.MetaData
getValueDouble(int label, long objId)xmipp.jni.MetaData
getValueInt(int label, long objId)xmipp.jni.MetaData
getValueLong(int label, long objId)xmipp.jni.MetaData
getValueString(int label, long objId)xmipp.jni.MetaData
getValueString(int label, long objId, boolean fixPaths)xmipp.jni.MetaDatainline
hasRecalculateCTF()xmipp.jni.MetaDatainline
importObjects(MetaData from, long ids[])xmipp.jni.MetaData
isColumnFormat()xmipp.jni.MetaData
isCTFMd()xmipp.jni.MetaDatainline
isCtfParam(int label)xmipp.jni.MetaDatastatic
isImage(int label)xmipp.jni.MetaDatastatic
isMetadata(int label)xmipp.jni.MetaDatastatic
isMetadataFile()xmipp.jni.MetaData
isMicrograph(int label)xmipp.jni.MetaDatastatic
isPathField(int label)xmipp.jni.MetaDatainlinestatic
isPlainPos(String file)xmipp.jni.MetaDatainlinestatic
isPSD(int label)xmipp.jni.MetaDatastatic
isStack(int label)xmipp.jni.MetaDatastatic
isTextFile(int label)xmipp.jni.MetaDatastatic
label2Str(int label)xmipp.jni.MetaDatastatic
LABEL_BOOLxmipp.jni.MetaDatastatic
LABEL_DOUBLExmipp.jni.MetaDatastatic
LABEL_INTxmipp.jni.MetaDatastatic
LABEL_NOTYPExmipp.jni.MetaDatastatic
LABEL_SIZETxmipp.jni.MetaDatastatic
LABEL_STRINGxmipp.jni.MetaDatastatic
LABEL_VECTOR_DOUBLExmipp.jni.MetaDatastatic
LABEL_VECTOR_SIZETxmipp.jni.MetaDatastatic
makeAbsPath(int label)xmipp.jni.MetaData
MD_APPENDxmipp.jni.MetaDatastatic
MD_OVERWRITExmipp.jni.MetaDatastatic
MetaData()xmipp.jni.MetaDatainline
MetaData(String filename)xmipp.jni.MetaDatainline
MICROGRAPH_BASIC_LABELSxmipp.jni.MetaDatastatic
operate(String operateStr)xmipp.jni.MetaData
print()xmipp.jni.MetaData
putCTF(long id, EllipseCTF ellipseCTF)xmipp.jni.MetaDatainline
read(String filename)xmipp.jni.MetaDatainline
read_(String filename)xmipp.jni.MetaData
readPlain(String file, String columns)xmipp.jni.MetaData
removeCTF(long id)xmipp.jni.MetaDatainline
removeDisabled()xmipp.jni.MetaData
removeLabel(int label)xmipp.jni.MetaData
removeObject(long objId)xmipp.jni.MetaData
renameColumn(int oldLabel, int newLabel)xmipp.jni.MetaData
setColumnFormat(boolean format)xmipp.jni.MetaData
setEnabled(boolean value, long objId)xmipp.jni.MetaDatainline
setRow(MDRow mdRow, long objId)xmipp.jni.MetaData
setValueBoolean(int label, boolean value, long objId)xmipp.jni.MetaData
setValueDouble(int label, double value, long objId)xmipp.jni.MetaData
setValueInt(int label, int value, long objId)xmipp.jni.MetaData
setValueLong(int label, long value, long objId)xmipp.jni.MetaData
setValueString(int label, String value, long objId)xmipp.jni.MetaData
size()xmipp.jni.MetaData
sort(int sortLabel, boolean ascending)xmipp.jni.MetaData
str2Label(String labelName)xmipp.jni.MetaDatastatic
unionAll(MetaData mdIn)xmipp.jni.MetaData
write(String filename)xmipp.jni.MetaData
writeBlock(String filename)xmipp.jni.MetaData
writeMdToStack(String filename, boolean applyGeo, boolean wrap, int label)xmipp.jni.MetaData
writeWithException(String xmippFilename)xmipp.jni.MetaDatainline
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-Public Member Functions | -Static Public Member Functions | -Static Public Attributes | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.jni.MetaData Class Reference
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-Public Member Functions

 MetaData ()
 
synchronized native void destroy ()
 
native void clear ()
 
native void read_ (String filename)
 
final void read (String filename)
 
native int size ()
 
native void setColumnFormat (boolean format)
 
native void write (String filename)
 
native void writeBlock (String filename)
 
native void print ()
 
native boolean isColumnFormat ()
 
native boolean containsLabel (int label)
 
native boolean removeLabel (int label)
 
boolean containsGeometryInfo (String type)
 
boolean containsLabel (int[] labels)
 
boolean containsMicrographParticles ()
 
boolean containsMicrographsInfo ()
 
native int [] getActiveLabels ()
 
native boolean isMetadataFile ()
 
native void makeAbsPath (int label)
 
native int getValueInt (int label, long objId)
 
native long getValueLong (int label, long objId)
 
native double getValueDouble (int label, long objId)
 
native String getValueString (int label, long objId)
 
String getValueString (int label, long objId, boolean fixPaths)
 
String [] getRowValues (long objId)
 
native void getRow (MDRow mdRow, long objId)
 
native void setRow (MDRow mdRow, long objId)
 
MetaData getMetaDataRow ()
 
String fixPath (String value)
 
String fixPath (String value, String baseDir)
 
native boolean getValueBoolean (int label, long objId)
 
String getFilename ()
 
String getBlock ()
 
String getPath ()
 
String getBaseDir ()
 
native double [] getStatistics (boolean applyGeo, int label)
 
native double [] getColumnValues (int label)
 
boolean setEnabled (boolean value, long objId)
 
boolean getEnabled (long objId)
 
native boolean setValueInt (int label, int value, long objId)
 
native boolean setValueLong (int label, long value, long objId)
 
native boolean setValueDouble (int label, double value, long objId)
 
native boolean setValueString (int label, String value, long objId)
 
native boolean setValueBoolean (int label, boolean value, long objId)
 
native long [] findObjects ()
 
native void sort (int sortLabel, boolean ascending)
 
native void importObjects (MetaData from, long ids[])
 
native long firstObject ()
 
native long addObject ()
 
native boolean removeObject (long objId)
 
native void removeDisabled ()
 
native void addLabel (int label)
 
native void renameColumn (int oldLabel, int newLabel)
 
native void getStatsImages (ImageGeneric imageAvg, ImageGeneric imageStd, boolean applyGeo, boolean wrap, int label)
 
native void writeMdToStack (String filename, boolean applyGeo, boolean wrap, int label)
 
native void getPCAbasis (ImageGeneric basis, int label)
 
native void computeFourierStatistics (MetaData mdIn, int label)
 
native void unionAll (MetaData mdIn)
 
native void fillConstant (int label, String value)
 
native void fillRandom (int label, String mode, double op1, double op2)
 
native void fillLinear (int label, double start, double step)
 
native void enableDebug ()
 
 MetaData (String filename)
 
native void readPlain (String file, String columns)
 
native void operate (String operateStr)
 
native double getColumnMin (int column)
 
native double getColumnMax (int column)
 
boolean isCTFMd ()
 
String getCTFFile (long id)
 
EllipseCTF getEllipseCTF (long id)
 
EllipseCTF getEllipseCTF (long id, int D)
 
String getPSDFile (long id)
 
String getPSDEnhanced (long id)
 
CTFDescription getCTFDescription (long id)
 
boolean hasRecalculateCTF ()
 
void removeCTF (long id)
 
boolean containsCTF (long id)
 
void putCTF (long id, EllipseCTF ellipseCTF)
 
void writeWithException (String xmippFilename) throws IOException
 
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-Static Public Member Functions

static boolean containsBlock (String file, String block)
 
static native String label2Str (int label)
 
static native int str2Label (String labelName)
 
static String getLabelName (int label)
 
static native String [] getBlocksInMetaDataFile (String filename)
 
static native int getLabelType (int label)
 
static Class getClassForType (int type)
 
static Class getLabelClass (int label)
 
static String getLabelTypeString (int labelType)
 
static native String getLabelComment (int label)
 
static native boolean isTextFile (int label)
 
static native boolean isMetadata (int label)
 
static native boolean isCtfParam (int label)
 
static native boolean isImage (int label)
 
static native boolean isStack (int label)
 
static native boolean isMicrograph (int label)
 
static native boolean isPSD (int label)
 
static boolean isPathField (int label)
 
static boolean isPlainPos (String file)
 
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-Static Public Attributes

static final int LABEL_NOTYPE = -1
 
static final int LABEL_INT = 0
 
static final int LABEL_BOOL = 1
 
static final int LABEL_DOUBLE = 2
 
static final int LABEL_STRING = 3
 
static final int LABEL_VECTOR_DOUBLE = 4
 
static final int LABEL_SIZET = 5
 
static final int LABEL_VECTOR_SIZET = 6
 
static final String FILL_CONSTANT = "constant"
 
static final String FILL_LINEAR = "linear"
 
static final String FILL_RAND_UNIFORM = "random uniform"
 
static final String FILL_RAND_GAUSSIAN = "random gaussian"
 
static final int GEOMETRY_LABELS []
 
static final int GEOMETRY_RELION_LABELS [] = { MDLabel.RLN_ORIENT_ORIGIN_X, MDLabel.RLN_ORIENT_ORIGIN_Y, MDLabel.RLN_ORIENT_PSI, MDLabel.RLN_ORIENT_FLIP}
 
static final int MICROGRAPH_BASIC_LABELS []
 
static final int MD_OVERWRITE = 0
 
static final int MD_APPEND = 1
 
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-Protected Member Functions

void finalize () throws Throwable
 
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-Protected Attributes

String filename
 
HashMap< Long, EllipseCTF > ctfs = new HashMap<Long, EllipseCTF>()
 
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Detailed Description

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Binding class for accessing C++ MetaData implementation.

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Definition at line 41 of file MetaData.java.

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Constructor & Destructor Documentation

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◆ MetaData() [1/2]

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xmipp.jni.MetaData.MetaData ()
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Create empty metadata

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Definition at line 103 of file MetaData.java.

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103  {
104  //System.out.format("Java: Creating metadata\n");
105  //Exception ex = new Exception();
106  //ex.printStackTrace();
107  create();
108  }
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◆ MetaData() [2/2]

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xmipp.jni.MetaData.MetaData (String filename)
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Create a metadata and read data from filename

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Definition at line 544 of file MetaData.java.

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544  {
545  //DEBUG.printFormat("Java: Creating metadata from filename: %s\n", filename);
546  //DEBUG.printStackTrace();
547 
548  create();
549  read(filename);
550  }
xmipp.jni.MetaData.read
final void read(String filename)
Definition: MetaData.java:125
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Member Function Documentation

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◆ addLabel()

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native void xmipp.jni.MetaData.addLabel (int label)
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Add new column to MetaData

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Add a new object entry and return new id

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◆ computeFourierStatistics()

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native void xmipp.jni.MetaData.computeFourierStatistics (MetaData mdIn,
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◆ containsBlock()

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static boolean xmipp.jni.MetaData.containsBlock (String file,
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Definition at line 230 of file MetaData.java.

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231  {
232  try
233  {
234  return Arrays.asList(MetaData.getBlocksInMetaDataFile(file)).contains(block);
235  }
236  catch (Exception e)
237  {
238  throw new IllegalArgumentException(e);
239  }
240  }// function containsBlock
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◆ containsCTF()

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boolean xmipp.jni.MetaData.containsCTF (long id)
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Definition at line 690 of file MetaData.java.

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690  {
691  return ctfs.containsKey(id);
692  }
xmipp.jni.MetaData.ctfs
HashMap< Long, EllipseCTF > ctfs
Definition: MetaData.java:94
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Definition at line 147 of file MetaData.java.

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147  {
148 
149 
150  if (type.equals("2D")) {
151  return containsGeometryInfo2D();
152 
153  } else {
154 
155  return containsGeometryInfo3D();
156  }
157 
158  }
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boolean xmipp.jni.MetaData.containsLabel (int [] labels)
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Definition at line 193 of file MetaData.java.

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193  {
194  try {
195  for (int i = 0; i < labels.length; i++)
196  if (containsLabel(labels[i]))
197  return true;
198 
199  } catch (Exception e) {
200  e.printStackTrace();
201  }
202  return false;
203  }
xmipp.jni.MetaData.containsLabel
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boolean xmipp.jni.MetaData.containsMicrographParticles ()
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Definition at line 206 of file MetaData.java.

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206  {
207  try {
208  int[] labels = new int[]{MDLabel.MDL_MICROGRAPH, MDLabel.MDL_XCOOR, MDLabel.MDL_YCOOR, MDLabel.MDL_ENABLED};
209  for (int i = 0; i < labels.length; i++)
210  if (!containsLabel(labels[i]))
211  return false;
212  } catch (Exception e) {
213  e.printStackTrace();
214  }
215  return true;
216  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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◆ containsMicrographsInfo()

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boolean xmipp.jni.MetaData.containsMicrographsInfo ()
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Definition at line 218 of file MetaData.java.

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218  {
219  try {
220  // Should contain some micrographs labels
221  for (int i = 0; i < MICROGRAPH_BASIC_LABELS.length; i++)
222  if (!containsLabel(MICROGRAPH_BASIC_LABELS[i]))
223  return false;
224  } catch (Exception e) {
225  e.printStackTrace();
226  }
227  return true;
228  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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static final int MICROGRAPH_BASIC_LABELS[]
Definition: MetaData.java:82
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Just for debugging purposes

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◆ fillConstant()

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native void xmipp.jni.MetaData.fillConstant (int label,
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Fill all values in a column(label). Different types of fill are: Constant Linear Random uniform Random gaussian

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native void xmipp.jni.MetaData.fillRandom (int label,
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double op1,
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Fill column in a random way

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labelcolumn to be filled
modecan be "uniform" or "gaussian"
op1min for uniform and mean for gaussian
op2max for uniform and std for gaussian
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Will be called by GarbageCollector before destroying. Needed to free C++ object memory.

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Definition at line 557 of file MetaData.java.

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557  {
558  super.finalize();
559  destroy();
560  }
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◆ findObjects()

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Obtain all the objects ids in the MetaData

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Definition at line 408 of file MetaData.java.

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408  {
409  return Filename.findImagePath(value, getBaseDir(), true);
410  }
xmipp.jni.MetaData.getBaseDir
String getBaseDir()
Definition: MetaData.java:430
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Definition at line 412 of file MetaData.java.

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412  {
413  return Filename.findImagePath(value, baseDir, false);
414  }
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Definition at line 430 of file MetaData.java.

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430  {
431  File f = new File(getFilename());
432  f = new File(f.toURI().normalize().getPath());
433 
434  return f.getParent();
435  }
xmipp.jni.MetaData.getFilename
String getFilename()
Definition: MetaData.java:418
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Definition at line 422 of file MetaData.java.

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423  return Filename.getPrefix(filename);
424  }
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static Class xmipp.jni.MetaData.getClassForType (int type)
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Definition at line 261 of file MetaData.java.

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261  {
262  switch (type) {
263  case LABEL_INT:
264  return Integer.class;
265  case LABEL_BOOL:
266  return Boolean.class;
267  case LABEL_DOUBLE:
268  return Double.class;
269  case LABEL_SIZET:
270  return Long.class;
271  case LABEL_STRING:
272  case LABEL_VECTOR_DOUBLE:
273  case LABEL_VECTOR_SIZET:
274  return String.class;
275 
276  }
277  return null;
278  }
xmipp.jni.MetaData.LABEL_VECTOR_DOUBLE
static final int LABEL_VECTOR_DOUBLE
Definition: MetaData.java:49
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xmipp.jni.MetaData.LABEL_DOUBLE
static final int LABEL_DOUBLE
Definition: MetaData.java:47
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xmipp.jni.MetaData.LABEL_STRING
static final int LABEL_STRING
Definition: MetaData.java:48
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xmipp.jni.MetaData.LABEL_BOOL
static final int LABEL_BOOL
Definition: MetaData.java:46
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xmipp.jni.MetaData.LABEL_SIZET
static final int LABEL_SIZET
Definition: MetaData.java:50
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xmipp.jni.MetaData.LABEL_VECTOR_SIZET
static final int LABEL_VECTOR_SIZET
Definition: MetaData.java:51
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static final int LABEL_INT
Definition: MetaData.java:45
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◆ getColumnMin()

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native double xmipp.jni.MetaData.getColumnMin (int column)
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Returns Max and Min values from a column in metadata These functions can only be used for labels of type double

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◆ getColumnValues()

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native double [] xmipp.jni.MetaData.getColumnValues (int label)
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◆ getCTFDescription()

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CTFDescription xmipp.jni.MetaData.getCTFDescription (long id)
- 		-inline
-
- -

Definition at line 641 of file MetaData.java.

-
642  {
643  try {
644  return new CTFDescription(getCTFFile(id));
645  } catch (Exception ex) {
646  Logger.getLogger(MetaData.class.getName()).log(Level.SEVERE, null, ex);
647  throw new IllegalArgumentException(ex);
648  }
649  }
xmipp.jni.MetaData.getCTFFile
String getCTFFile(long id)
Definition: MetaData.java:600
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◆ getCTFFile()

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String xmipp.jni.MetaData.getCTFFile (long id)
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Definition at line 600 of file MetaData.java.

-
601  {
602  return getValueString(MDLabel.MDL_CTF_MODEL, id);
603  }
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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◆ getEllipseCTF() [1/2]

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EllipseCTF xmipp.jni.MetaData.getEllipseCTF (long id)
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- -

Definition at line 605 of file MetaData.java.

-
605  {
606  return getEllipseCTF(id, -1);
607  }
xmipp.jni.MetaData.getEllipseCTF
EllipseCTF getEllipseCTF(long id)
Definition: MetaData.java:605
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EllipseCTF xmipp.jni.MetaData.getEllipseCTF (long id,
int D 
)
- 		-inline
-
- -

Definition at line 609 of file MetaData.java.

-
609  {
610  MetaData md = new MetaData(getCTFFile(id));
611  try {
612  double Q0, Cs, Ts, kV, downsampleFactor, defU, defV, defAngle;
613 
614  Q0 = md.getValueDouble(MDLabel.MDL_CTF_Q0, id);
615  Cs = md.getValueDouble(MDLabel.MDL_CTF_CS, id);
616  downsampleFactor = md.getValueDouble(MDLabel.MDL_CTF_DOWNSAMPLE_PERFORMED, id);
617  Ts = md.getValueDouble(MDLabel.MDL_CTF_SAMPLING_RATE, id) * downsampleFactor;
618  kV = md.getValueDouble(MDLabel.MDL_CTF_VOLTAGE, id);
619 
620  defU = md.getValueDouble(MDLabel.MDL_CTF_DEFOCUSU, id);
621  defV = md.getValueDouble(MDLabel.MDL_CTF_DEFOCUSV, id);
622  defAngle = md.getValueDouble(MDLabel.MDL_CTF_DEFOCUS_ANGLE, id);
623 
624  return new EllipseCTF(id, Q0, Cs, downsampleFactor, Ts, kV, defU, defV, defAngle, D);
625  } catch (Exception ex) {
626  IJ.error(ex.getMessage());
627  throw new IllegalArgumentException(ex);
628  }
629 
630  }
xmipp.jni.MetaData.getCTFFile
String getCTFFile(long id)
Definition: MetaData.java:600
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◆ getEnabled()

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boolean xmipp.jni.MetaData.getEnabled (long objId)
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Definition at line 448 of file MetaData.java.

-
448  {
449  if(!containsLabel(MDLabel.MDL_ENABLED))
450  return true;
451  return getValueInt(MDLabel.MDL_ENABLED, objId) > -1;
452  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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◆ getFilename()

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String xmipp.jni.MetaData.getFilename ()
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Definition at line 418 of file MetaData.java.

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418  {
419  return filename != null ? Filename.getFilename(filename) : "";
420  }
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◆ getLabelClass()

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static Class xmipp.jni.MetaData.getLabelClass (int label)
- 		-inlinestatic
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Definition at line 280 of file MetaData.java.

-
280  {
281  int type = getLabelType(label);
282  return getClassForType(type);
283  }
xmipp.jni.MetaData.getClassForType
static Class getClassForType(int type)
Definition: MetaData.java:261
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xmipp.jni.MetaData.getLabelType
static native int getLabelType(int label)
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◆ getLabelComment()

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static native String xmipp.jni.MetaData.getLabelComment (int label)
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◆ getLabelName()

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static String xmipp.jni.MetaData.getLabelName (int label)
- 		-inlinestatic
-
-

Same of before but handling the exception

- -

Definition at line 247 of file MetaData.java.

-
247  {
248  try {
249  return label2Str(label);
250  } catch (Exception e) {
251  return null;
252  }
253  }
xmipp.jni.MetaData.label2Str
static native String label2Str(int label)
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◆ getLabelType()

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static native int xmipp.jni.MetaData.getLabelType (int label)
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◆ getLabelTypeString()

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static String xmipp.jni.MetaData.getLabelTypeString (int labelType)
- 		-inlinestatic
-
-

Return an String representing the label type

- -

Definition at line 286 of file MetaData.java.

-
286  {
287  switch (labelType) {
288  case LABEL_STRING:
289  return "STRING";
290  case LABEL_DOUBLE:
291  return "DOUBLE";
292  case LABEL_INT:
293  return "INT";
294  case LABEL_BOOL:
295  return "BOOL";
296  case LABEL_VECTOR_DOUBLE:
297  return "VECTOR(DOUBLE)";
298  case LABEL_SIZET:
299  return "SIZE_T";
300  case LABEL_VECTOR_SIZET:
301  return "VECTOR(SIZE_T)";
302  }
303  return "UNKNOWN";
304  }// function getLabelTypeString
xmipp.jni.MetaData.LABEL_VECTOR_DOUBLE
static final int LABEL_VECTOR_DOUBLE
Definition: MetaData.java:49
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xmipp.jni.MetaData.LABEL_DOUBLE
static final int LABEL_DOUBLE
Definition: MetaData.java:47
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xmipp.jni.MetaData.LABEL_STRING
static final int LABEL_STRING
Definition: MetaData.java:48
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xmipp.jni.MetaData.LABEL_BOOL
static final int LABEL_BOOL
Definition: MetaData.java:46
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xmipp.jni.MetaData.LABEL_SIZET
static final int LABEL_SIZET
Definition: MetaData.java:50
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xmipp.jni.MetaData.LABEL_VECTOR_SIZET
static final int LABEL_VECTOR_SIZET
Definition: MetaData.java:51
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xmipp.jni.MetaData.LABEL_INT
static final int LABEL_INT
Definition: MetaData.java:45
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◆ getMetaDataRow()

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MetaData xmipp.jni.MetaData.getMetaDataRow ()
- 		-inline
-
-

Create a metadata row from another metadata Adding the activeLabels and adding an object

- -

Definition at line 384 of file MetaData.java.

-
384  {
385  MetaData md = null;
386  try {
387  md = new MetaData();
388  md.setColumnFormat(false);
389  int[] labels = getActiveLabels();
390  for (int l : labels)
391  md.addLabel(l);
392  md.addObject();
393  } catch (Exception e) {
394  e.printStackTrace();
395  }
396  return md;
397  }
xmipp.jni.MetaData.getActiveLabels
native int [] getActiveLabels()
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◆ getPath()

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String xmipp.jni.MetaData.getPath ()
- 		-inline
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Definition at line 426 of file MetaData.java.

-
426  {
427  return filename;
428  }
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◆ getPCAbasis()

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native void xmipp.jni.MetaData.getPCAbasis (ImageGeneric basis,
int label 
)
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◆ getPSDEnhanced()

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String xmipp.jni.MetaData.getPSDEnhanced (long id)
- 		-inline
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- -

Definition at line 637 of file MetaData.java.

-
637  {
638  return getValueString(MDLabel.MDL_PSD_ENHANCED, id);
639  }
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
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◆ getPSDFile()

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String xmipp.jni.MetaData.getPSDFile (long id)
- 		-inline
-
- -

Definition at line 633 of file MetaData.java.

-
633  {
634  return getValueString(MDLabel.MDL_PSD, id);
635  }
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
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◆ getRow()

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native void xmipp.jni.MetaData.getRow (MDRow mdRow,
long objId 
)
-
-

Return a new metadata containing the values of one row

- -
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◆ getRowValues()

- -
-
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String [] xmipp.jni.MetaData.getRowValues (long objId)
- 		-inline
-
-

Return all values of the row as String[]

-

@

- -

Definition at line 354 of file MetaData.java.

-
354  {
355  String[] values = new String[activeLabels.length];
356  for (int i = 0; i < activeLabels.length; ++i)
357  values[i] = getValueString(activeLabels[i], objId);
358  return values;
359  }
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
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◆ getStatistics()

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native double [] xmipp.jni.MetaData.getStatistics (boolean applyGeo,
int label 
)
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◆ getStatsImages()

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native void xmipp.jni.MetaData.getStatsImages (ImageGeneric imageAvg,
ImageGeneric imageStd,
boolean applyGeo,
boolean wrap,
int label 
)
-
-

Get the average and std images, result is left on input image

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◆ getValueBoolean()

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native boolean xmipp.jni.MetaData.getValueBoolean (int label,
long objId 
)
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◆ getValueDouble()

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native double xmipp.jni.MetaData.getValueDouble (int label,
long objId 
)
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◆ getValueInt()

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native int xmipp.jni.MetaData.getValueInt (int label,
long objId 
)
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◆ getValueLong()

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native long xmipp.jni.MetaData.getValueLong (int label,
long objId 
)
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◆ getValueString() [1/2]

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native String xmipp.jni.MetaData.getValueString (int label,
long objId 
)
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-

Return the value of some label as String

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◆ getValueString() [2/2]

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String xmipp.jni.MetaData.getValueString (int label,
long objId,
boolean fixPaths 
)
- 		-inline
-
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Definition at line 336 of file MetaData.java.

-
336  {
337  String value = getValueString(label, objId);
338 
339 // if(value == null)
340 // DEBUG.printFormat("label: %d, id: %d", label, objId);
341  // Try to fix paths.
342  if (fixPaths && filename != null && isPathField(label)) {
343  value = fixPath(value);
344  }
345 
346  return value;
347  }
-
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
xmipp.jni.MetaData.fixPath
String fixPath(String value)
Definition: MetaData.java:408
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xmipp.jni.MetaData.isPathField
static boolean isPathField(int label)
Definition: MetaData.java:399
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◆ hasRecalculateCTF()

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boolean xmipp.jni.MetaData.hasRecalculateCTF ()
- 		-inline
-
- -

Definition at line 682 of file MetaData.java.

-
682  {
683  return !ctfs.isEmpty();
684  }
xmipp.jni.MetaData.ctfs
HashMap< Long, EllipseCTF > ctfs
Definition: MetaData.java:94
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◆ importObjects()

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native void xmipp.jni.MetaData.importObjects (MetaData from,
long ids[] 
)
-
-

Import objects from other MetaData

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◆ isColumnFormat()

- -
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native boolean xmipp.jni.MetaData.isColumnFormat ()
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◆ isCTFMd()

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boolean xmipp.jni.MetaData.isCTFMd ()
- 		-inline
-
- -

Definition at line 591 of file MetaData.java.

-
591  {
592  try {
593  return containsLabel(MDLabel.MDL_PSD_ENHANCED) && containsLabel(MDLabel.MDL_PSD) && containsLabel(MDLabel.MDL_CTF_MODEL);
594  } catch (Exception e) {
595  e.printStackTrace();
596  }
597  return false;
598  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
-
-
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◆ isCtfParam()

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static native boolean xmipp.jni.MetaData.isCtfParam (int label)
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◆ isImage()

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static native boolean xmipp.jni.MetaData.isImage (int label)
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◆ isMetadata()

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static native boolean xmipp.jni.MetaData.isMetadata (int label)
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◆ isMetadataFile()

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native boolean xmipp.jni.MetaData.isMetadataFile ()
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◆ isMicrograph()

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static native boolean xmipp.jni.MetaData.isMicrograph (int label)
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◆ isPathField()

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static boolean xmipp.jni.MetaData.isPathField (int label)
- 		-inlinestatic
-
- -

Definition at line 399 of file MetaData.java.

-
399  {
400  return isTextFile(label) || isMetadata(label) || isCtfParam(label)
401  || isImage(label) || isStack(label) || isMicrograph(label)
402  || isPSD(label);
403  }
xmipp.jni.MetaData.isMicrograph
static native boolean isMicrograph(int label)
-
xmipp.jni.MetaData.isCtfParam
static native boolean isCtfParam(int label)
-
xmipp.jni.MetaData.isMetadata
static native boolean isMetadata(int label)
-
xmipp.jni.MetaData.isPSD
static native boolean isPSD(int label)
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xmipp.jni.MetaData.isStack
static native boolean isStack(int label)
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xmipp.jni.MetaData.isTextFile
static native boolean isTextFile(int label)
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xmipp.jni.MetaData.isImage
static native boolean isImage(int label)
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◆ isPlainPos()

- -
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static boolean xmipp.jni.MetaData.isPlainPos (String file)
- 		-inlinestatic
-
- -

Definition at line 653 of file MetaData.java.

-
654  {
655  try
656  {
657  InputStream in = new FileInputStream(file);
658  Reader reader = new InputStreamReader(in);
659  // buffer for efficiency
660  BufferedReader buffer = new BufferedReader(reader);
661  String line = buffer.readLine();//dismiss first line
662  if(line == null)
663  return true;//Empty file
664  int count = 0;//small statistics to detect if pos file
665  while ((line = buffer.readLine()) != null) {
666  for(char c: line.toCharArray())
667  if(!(Character.isDigit(c) || Character.isSpaceChar(c)))
668  return false;
669 
670 
671  if(count == 100)
672  break;
673  count ++;
674  }
675  } catch (IOException ex) {
676  return false;
677  }
678  return true;
679  }
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-
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◆ isPSD()

- -
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static native boolean xmipp.jni.MetaData.isPSD (int label)
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◆ isStack()

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static native boolean xmipp.jni.MetaData.isStack (int label)
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◆ isTextFile()

- -
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static native boolean xmipp.jni.MetaData.isTextFile (int label)
- 		-static
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◆ label2Str()

- -
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static native String xmipp.jni.MetaData.label2Str (int label)
- 		-static
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◆ makeAbsPath()

- -
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native void xmipp.jni.MetaData.makeAbsPath (int label)
-
- -
-
- -

◆ operate()

- -
-
- - - - - - - - -
native void xmipp.jni.MetaData.operate (String operateStr)
-
-

Operate directly in metadata

Parameters
- - -
operateStrsql syntanx string of the operation
-
-
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◆ print()

- -
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native void xmipp.jni.MetaData.print ()
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◆ putCTF()

- -
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void xmipp.jni.MetaData.putCTF (long id,
EllipseCTF ellipseCTF 
)
- 		-inline
-
- -

Definition at line 694 of file MetaData.java.

-
694  {
695  ctfs.put(id, ellipseCTF);
696  }
xmipp.jni.MetaData.ctfs
HashMap< Long, EllipseCTF > ctfs
Definition: MetaData.java:94
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◆ read()

- -
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final void xmipp.jni.MetaData.read (String filename)
- 		-inline
-
- -

Definition at line 125 of file MetaData.java.

-
125  {
126  this.filename = filename;
127  read_(filename);
128  activeLabels = getActiveLabels();
129  }
-
xmipp.jni.MetaData.getActiveLabels
native int [] getActiveLabels()
-
xmipp.jni.MetaData.read_
native void read_(String filename)
-
-
-
- -

◆ read_()

- -
-
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native void xmipp.jni.MetaData.read_ (String filename)
-
- -
-
- -

◆ readPlain()

- -
-
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native void xmipp.jni.MetaData.readPlain (String file,
String columns 
)
-
-

Read a metadata from plain textfile.

-
Parameters
- - - -
filefilename from where to read
columnsexpected columns(labels) in file @
-
-
- -
-
- -

◆ removeCTF()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.jni.MetaData.removeCTF (long id)
- 		-inline
-
- -

Definition at line 686 of file MetaData.java.

-
686  {
687  ctfs.remove(id);
688  }
xmipp.jni.MetaData.ctfs
HashMap< Long, EllipseCTF > ctfs
Definition: MetaData.java:94
-
-
-
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◆ removeDisabled()

- -
-
- - - - - - - -
native void xmipp.jni.MetaData.removeDisabled ()
-
-

Remove disabled objects

- -
-
- -

◆ removeLabel()

- -
-
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native boolean xmipp.jni.MetaData.removeLabel (int label)
-
- -
-
- -

◆ removeObject()

- -
-
- - - - - - - - -
native boolean xmipp.jni.MetaData.removeObject (long objId)
-
-

Remove an existing object from metadata

- -
-
- -

◆ renameColumn()

- -
-
- - - - - - - - - - - - - - - - - - -
native void xmipp.jni.MetaData.renameColumn (int oldLabel,
int newLabel 
)
-
-

Rename a MetaData column

- -
-
- -

◆ setColumnFormat()

- -
-
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native void xmipp.jni.MetaData.setColumnFormat (boolean format)
-
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◆ setEnabled()

- -
-
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boolean xmipp.jni.MetaData.setEnabled (boolean value,
long objId 
)
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Definition at line 442 of file MetaData.java.

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442  {
443 
444  return setValueInt(MDLabel.MDL_ENABLED, value ? 1 : -1, objId);
445 
446  }
xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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long objId 
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long objId 
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◆ setValueString()

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boolean ascending 
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Order the metadata by some label. You can order ASCending or DESCending.

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Union of all elements in two Metadata, duplicating common elements. Result in calling metadata object, repetition are allowed

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void xmipp.jni.MetaData.writeWithException (String xmippFilename) throws IOException
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Definition at line 706 of file MetaData.java.

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707 
708  String OSFilename = Filename.getFilename(xmippFilename);
709 
710  File fileObj = new File(OSFilename);
711 
712  boolean exist = fileObj.exists();
713  long fileTs = 0;
714  if (exist) {
715 
716  fileTs = getFileTimeStamp(fileObj);
717 
718  if (!fileObj.canWrite()){
719  throw new IOException("Can't write on " + OSFilename + ". Please check you have permissions to write.");
720  }
721  }
722 
723  this.write(xmippFilename);
724 
725  if (!exist && !fileObj.exists()) {
726 
727  throw new IOException("File: " + OSFilename + " couldn't be created. Check you have permission on the folder.");
728 
729  } else if (fileTs == getFileTimeStamp(fileObj)){
730 
731  throw new IOException("File: " + OSFilename + " couldn't be written. Something went wrong.");
732  }
733 
734 
735  }
xmipp.jni.MetaData.write
native void write(String filename)
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Member Data Documentation

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◆ ctfs

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HashMap<Long, EllipseCTF> xmipp.jni.MetaData.ctfs = new HashMap<Long, EllipseCTF>()
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Definition at line 94 of file MetaData.java.

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Definition at line 87 of file MetaData.java.

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final String xmipp.jni.MetaData.FILL_CONSTANT = "constant"
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Definition at line 53 of file MetaData.java.

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Definition at line 54 of file MetaData.java.

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Definition at line 56 of file MetaData.java.

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Definition at line 55 of file MetaData.java.

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final int xmipp.jni.MetaData.GEOMETRY_LABELS[]
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= { MDLabel.MDL_FLIP,
MDLabel.MDL_ANGLE_PSI, MDLabel.MDL_SHIFT_X, MDLabel.MDL_SHIFT_Y}
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Definition at line 77 of file MetaData.java.

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final int xmipp.jni.MetaData.GEOMETRY_RELION_LABELS[] = { MDLabel.RLN_ORIENT_ORIGIN_X, MDLabel.RLN_ORIENT_ORIGIN_Y, MDLabel.RLN_ORIENT_PSI, MDLabel.RLN_ORIENT_FLIP}
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Definition at line 80 of file MetaData.java.

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Definition at line 46 of file MetaData.java.

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Definition at line 47 of file MetaData.java.

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Definition at line 45 of file MetaData.java.

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final int xmipp.jni.MetaData.LABEL_NOTYPE = -1
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Enum values with Labels possible types

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Definition at line 44 of file MetaData.java.

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Definition at line 50 of file MetaData.java.

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Definition at line 48 of file MetaData.java.

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Definition at line 49 of file MetaData.java.

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Definition at line 51 of file MetaData.java.

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Definition at line 86 of file MetaData.java.

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Definition at line 85 of file MetaData.java.

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final int xmipp.jni.MetaData.MICROGRAPH_BASIC_LABELS[]
- 		-static
-
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= {
MDLabel.MDL_MICROGRAPH, MDLabel.MDL_PSD, MDLabel.MDL_CTF_MODEL }
-

Definition at line 82 of file MetaData.java.

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The documentation for this class was generated from the following file: -
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- - diff --git a/html/classxmipp_1_1jni_1_1MetaData__coll__graph.dot b/html/classxmipp_1_1jni_1_1MetaData__coll__graph.dot deleted file mode 100644 index d88d26da..00000000 --- a/html/classxmipp_1_1jni_1_1MetaData__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.jni.MetaData" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.jni.MetaData",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ctfs" ,fontname="Helvetica"]; - Node3 [label="HashMap\< Long, xmipp.jni.\lEllipseCTF \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1jni_1_1MetaData__coll__graph.md5 b/html/classxmipp_1_1jni_1_1MetaData__coll__graph.md5 deleted file mode 100644 index ae3de799..00000000 --- a/html/classxmipp_1_1jni_1_1MetaData__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -609ba3a73550cded2f02d0f8c599666c \ No newline at end of file diff --git a/html/classxmipp_1_1jni_1_1MetaData__inherit__graph.dot b/html/classxmipp_1_1jni_1_1MetaData__inherit__graph.dot deleted file mode 100644 index 11d60f59..00000000 --- a/html/classxmipp_1_1jni_1_1MetaData__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.jni.MetaData" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.jni.MetaData",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node0 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.scipion.Scipion\lMetaData",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData.html"]; -} diff --git a/html/classxmipp_1_1jni_1_1MetaData__inherit__graph.md5 b/html/classxmipp_1_1jni_1_1MetaData__inherit__graph.md5 deleted file mode 100644 index e75a10c8..00000000 --- a/html/classxmipp_1_1jni_1_1MetaData__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -28c26ab850cca93fdca41b87ccc5dc53 \ No newline at end of file diff --git a/html/classxmipp_1_1jni_1_1Particle-members.html b/html/classxmipp_1_1jni_1_1Particle-members.html deleted file mode 100644 index 2c4f3e32..00000000 --- a/html/classxmipp_1_1jni_1_1Particle-members.html +++ /dev/null @@ -1,98 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.jni.Particle Member List
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This is the complete list of members for xmipp.jni.Particle, including all inherited members.

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compareTo(Particle p)xmipp.jni.Particleinline
contains(int x2, int y2, int size)xmipp.jni.Particleinline
costxmipp.jni.Particleprotected
getCost()xmipp.jni.Particleinline
getPosition()xmipp.jni.Particleinline
getX()xmipp.jni.Particleinline
getY()xmipp.jni.Particleinline
Particle(int x, int y)xmipp.jni.Particleinline
Particle(int x, int y, double cost)xmipp.jni.Particleinline
setCost(double cost)xmipp.jni.Particleinline
setPosition(int x, int y)xmipp.jni.Particleinline
setX(int x)xmipp.jni.Particleinline
setY(int y)xmipp.jni.Particleinline
toString()xmipp.jni.Particleinline
xxmipp.jni.Particleprotected
yxmipp.jni.Particleprotected
- -
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- - diff --git a/html/classxmipp_1_1jni_1_1Particle.html b/html/classxmipp_1_1jni_1_1Particle.html deleted file mode 100644 index 2b265cc4..00000000 --- a/html/classxmipp_1_1jni_1_1Particle.html +++ /dev/null @@ -1,650 +0,0 @@ - - - - - - - -Xmipp: xmipp.jni.Particle Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions

 Particle (int x, int y)
 
 Particle (int x, int y, double cost)
 
int getX ()
 
void setX (int x)
 
int getY ()
 
void setY (int y)
 
double getCost ()
 
void setCost (double cost)
 
boolean contains (int x2, int y2, int size)
 
void setPosition (int x, int y)
 
Point getPosition ()
 
String toString ()
 
int compareTo (Particle p)
 
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-Protected Attributes

int x
 
int y
 
double cost
 
-

Detailed Description

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Definition at line 7 of file Particle.java.

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Constructor & Destructor Documentation

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◆ Particle() [1/2]

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int y 
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Definition at line 12 of file Particle.java.

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13  {
14  this.x = x;
15  this.y = y;
16  }
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Definition at line 18 of file Particle.java.

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19  {
20  this.x = x;
21  this.y = y;
22  this.cost = cost;
23  }
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Member Function Documentation

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◆ compareTo()

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int xmipp.jni.Particle.compareTo (Particle p)
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Definition at line 82 of file Particle.java.

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82  {
83  if(p.x > x)
84  return 1;
85  if(p.x == x)
86  {
87  if(p.y > y)
88  return 1;
89  if(p.y == y)
90  return 0;
91  return -1;
92  }
93  return -1;
94  }
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boolean xmipp.jni.Particle.contains (int x2,
int y2,
int size 
)
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Definition at line 55 of file Particle.java.

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56  {
57  int radius = size/2;
58  if(x2 < x - radius || x2 > x + radius)
59  return false;
60  if(y2 < y - radius || y2 > y + radius)
61  return false;
62  return true;
63  }
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double xmipp.jni.Particle.getCost ()
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Definition at line 42 of file Particle.java.

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43  {
44  return cost;
45  }
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Point xmipp.jni.Particle.getPosition ()
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Definition at line 70 of file Particle.java.

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70  {
71  return new Point(x, y);
72 
73  }
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int xmipp.jni.Particle.getX ()
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Definition at line 26 of file Particle.java.

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26  {
27  return x;
28  }
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int xmipp.jni.Particle.getY ()
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Definition at line 34 of file Particle.java.

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34  {
35  return y;
36  }
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void xmipp.jni.Particle.setCost (double cost)
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Definition at line 47 of file Particle.java.

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48  {
49  this.cost = cost;
50 
51  }
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Definition at line 65 of file Particle.java.

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65  {
66  this.x = x;
67  this.y = y;
68  }
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void xmipp.jni.Particle.setX (int x)
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Definition at line 30 of file Particle.java.

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30  {
31  this.x = x;
32  }
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void xmipp.jni.Particle.setY (int y)
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Definition at line 38 of file Particle.java.

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38  {
39  this.y = y;
40  }
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String xmipp.jni.Particle.toString ()
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Definition at line 75 of file Particle.java.

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76  {
77  return String.format("x = %s; y = %s cost = %.2f", x, y, cost);
78  }
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◆ cost

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double xmipp.jni.Particle.cost
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Definition at line 10 of file Particle.java.

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◆ x

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Definition at line 8 of file Particle.java.

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◆ y

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Definition at line 9 of file Particle.java.

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The documentation for this class was generated from the following file: -
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xmipp.jni.PickingClassifier Member List
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This is the complete list of members for xmipp.jni.PickingClassifier, including all inherited members.

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applyChangesxmipp.jni.Classifierprotected
autopick(String micrograph, int percent)xmipp.jni.PickingClassifier
correct(MDRow[] manualRows, MDRow[] automaticRows)xmipp.jni.PickingClassifier
destroy()xmipp.jni.PickingClassifier
finalize()xmipp.jni.PickingClassifierinlineprotected
getParams()xmipp.jni.Classifierinline
getParticlesThreshold()xmipp.jni.PickingClassifier
getTrainingParticlesMinimum()xmipp.jni.PickingClassifierinline
isApplyChanges()xmipp.jni.Classifierinline
needsTraining()xmipp.jni.PickingClassifierinline
paramsxmipp.jni.Classifierprotected
PickingClassifier(int particlesize, String output, MDRow[] mics)xmipp.jni.PickingClassifierinline
setApplyChanges(boolean applyChanges)xmipp.jni.Classifierinline
setSize(int psize)xmipp.jni.PickingClassifier
train(MDRow[] micrographs, int x, int y, int width, int height)xmipp.jni.PickingClassifier
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-Public Member Functions

 PickingClassifier (int particlesize, String output, MDRow[] mics) throws Exception
 
native void destroy ()
 
synchronized native Particle [] autopick (String micrograph, int percent)
 
synchronized native void correct (MDRow[] manualRows, MDRow[] automaticRows)
 
synchronized native void train (MDRow[] micrographs, int x, int y, int width, int height)
 
synchronized native void setSize (int psize)
 
native int getParticlesThreshold ()
 
boolean needsTraining ()
 
int getTrainingParticlesMinimum ()
 
- Public Member Functions inherited from xmipp.jni.Classifier
abstract int getTrainingParticlesMinimum ()
 
abstract void setSize (int psize)
 
boolean isApplyChanges ()
 
void setApplyChanges (boolean applyChanges)
 
List< Classifier.Parameter > getParams ()
 
abstract boolean needsTraining ()
 
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void finalize () throws Throwable
 
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- Protected Attributes inherited from xmipp.jni.Classifier
List< Classifier.Parameter > params
 
boolean applyChanges
 
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Definition at line 4 of file PickingClassifier.java.

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◆ PickingClassifier()

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xmipp.jni.PickingClassifier.PickingClassifier (int particlesize,
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Definition at line 16 of file PickingClassifier.java.

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16  {
17  create(particlesize, output, mics);
18  }
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◆ autopick()

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synchronized native Particle [] xmipp.jni.PickingClassifier.autopick (String micrograph,
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Definition at line 39 of file PickingClassifier.java.

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40  super.finalize();
41  destroy();
42  }
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Definition at line 51 of file PickingClassifier.java.

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53  // TODO Auto-generated method stub
54  return 15;
55  }
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Definition at line 45 of file PickingClassifier.java.

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47  return true;
48  }
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int x,
int y,
int width,
int height 
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create()xmipp.jni.ProgTomographAlignmentprotected
finalize()xmipp.jni.ProgTomographAlignmentinlineprotected
getIteration()xmipp.jni.ProgTomographAlignment
produceSideInfo()xmipp.jni.ProgTomographAlignment
ProgTomographAlignment()xmipp.jni.ProgTomographAlignmentinline
run()xmipp.jni.ProgTomographAlignment
setInputFilename(String name)xmipp.jni.ProgTomographAlignment
setRoot(String name)xmipp.jni.ProgTomographAlignment
writeTransformations(String name)xmipp.jni.ProgTomographAlignment
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-Public Member Functions

native void setInputFilename (String name)
 
native void setRoot (String name)
 
native void produceSideInfo ()
 
native void run ()
 
native void writeTransformations (String name)
 
native int getIteration ()
 
 ProgTomographAlignment ()
 
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native void create ()
 
void finalize () throws Throwable
 
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Definition at line 3 of file ProgTomographAlignment.java.

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◆ ProgTomographAlignment()

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Definition at line 30 of file ProgTomographAlignment.java.

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Definition at line 37 of file ProgTomographAlignment.java.

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39  super.finalize();
40  destroy();
41  }
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runByName(String progName, String args)xmipp.jni.Programstatic
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static native int runByName (String progName, String args) throws Exception
 
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◆ runByName()

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entropyOtsuSegmentation(ImageGeneric volume, double percentile, boolean binarize)xmipp.jni.Projectionstatic
eulerMatrix2Angles(double matrix[])xmipp.jni.Projectionstatic
projectVolume(ImageGeneric volume, ImageGeneric projection, double matrix[])xmipp.jni.Projectionstatic
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static native void projectVolume (ImageGeneric volume, ImageGeneric projection, double matrix[]) throws Exception
 
static native double entropyOtsuSegmentation (ImageGeneric volume, double percentile, boolean binarize) throws Exception
 
static native double [] eulerMatrix2Angles (double matrix[]) throws Exception
 
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Detailed Description

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Definition at line 3 of file Projection.java.

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Member Function Documentation

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◆ entropyOtsuSegmentation()

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static native double xmipp.jni.Projection.entropyOtsuSegmentation (ImageGeneric volume,
double percentile,
boolean binarize 
) throws Exception
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static native void xmipp.jni.Projection.projectVolume (ImageGeneric volume,
ImageGeneric projection,
double matrix[] 
) throws Exception
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xmipp.jni.TiltPairAligner Member List
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addParticleToAligner(int x1, int y1, int x2, int y2)xmipp.jni.TiltPairAligner
clear()xmipp.jni.TiltPairAligner
computeAngles()xmipp.jni.TiltPairAligner
finalize()xmipp.jni.TiltPairAlignerinlineprotected
getTiltedParticle(int x1, int y1)xmipp.jni.TiltPairAligner
getUntiltedParticle(int x1, int y1)xmipp.jni.TiltPairAligner
TiltPairAligner()xmipp.jni.TiltPairAlignerinline
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-Public Member Functions

native void addParticleToAligner (int x1, int y1, int x2, int y2)
 
native Particle getTiltedParticle (int x1, int y1)
 
native Particle getUntiltedParticle (int x1, int y1)
 
native double [] computeAngles ()
 
native void clear ()
 
 TiltPairAligner ()
 
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-Protected Member Functions

void finalize () throws Throwable
 
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Detailed Description

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Definition at line 3 of file TiltPairAligner.java.

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Constructor & Destructor Documentation

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◆ TiltPairAligner()

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xmipp.jni.TiltPairAligner.TiltPairAligner ()
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Definition at line 35 of file TiltPairAligner.java.

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36  {
37  create();
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Member Function Documentation

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◆ addParticleToAligner()

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native void xmipp.jni.TiltPairAligner.addParticleToAligner (int x1,
int y1,
int x2,
int y2 
)
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◆ clear()

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void xmipp.jni.TiltPairAligner.finalize () throws Throwable
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Definition at line 42 of file TiltPairAligner.java.

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45  destroy();
46  }
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int y1 
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int y1 
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xmipp.jni.XmippError Member List
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This is the complete list of members for xmipp.jni.XmippError, including all inherited members.

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ERR_ARG_BADCMDLINExmipp.jni.XmippErrorstatic
ERR_ARG_DEPENDENCExmipp.jni.XmippErrorstatic
ERR_ARG_INCORRECTxmipp.jni.XmippErrorstatic
ERR_ARG_MISSINGxmipp.jni.XmippErrorstatic
ERR_DEBUG_IMPOSIBLExmipp.jni.XmippErrorstatic
ERR_DEBUG_TESTxmipp.jni.XmippErrorstatic
ERR_DOCFILExmipp.jni.XmippErrorstatic
ERR_FIRST_LABELxmipp.jni.XmippErrorstatic
ERR_GPU_MEMORYxmipp.jni.XmippErrorstatic
ERR_GRIDxmipp.jni.XmippErrorstatic
ERR_GRID_SIZExmipp.jni.XmippErrorstatic
ERR_IMG_NOREADxmipp.jni.XmippErrorstatic
ERR_IMG_NOWRITExmipp.jni.XmippErrorstatic
ERR_IMG_UNKNOWNxmipp.jni.XmippErrorstatic
ERR_INDEX_OUTOFBOUNDSxmipp.jni.XmippErrorstatic
ERR_IOxmipp.jni.XmippErrorstatic
ERR_IO_LOCKEDxmipp.jni.XmippErrorstatic
ERR_IO_NOCLOSEDxmipp.jni.XmippErrorstatic
ERR_IO_NOPATHxmipp.jni.XmippErrorstatic
ERR_IO_NOPERMxmipp.jni.XmippErrorstatic
ERR_IO_NOREADxmipp.jni.XmippErrorstatic
ERR_IO_NOTDIRxmipp.jni.XmippErrorstatic
ERR_IO_NOTEXISTxmipp.jni.XmippErrorstatic
ERR_IO_NOTFILExmipp.jni.XmippErrorstatic
ERR_IO_NOTOPENxmipp.jni.XmippErrorstatic
ERR_IO_NOWRITExmipp.jni.XmippErrorstatic
ERR_IO_SIZExmipp.jni.XmippErrorstatic
ERR_LAST_LABELxmipp.jni.XmippErrorstatic
ERR_LOGIC_ERRORxmipp.jni.XmippErrorstatic
ERR_MATRIXxmipp.jni.XmippErrorstatic
ERR_MATRIX_DIMxmipp.jni.XmippErrorstatic
ERR_MATRIX_EMPTYxmipp.jni.XmippErrorstatic
ERR_MATRIX_SIZExmipp.jni.XmippErrorstatic
ERR_MDxmipp.jni.XmippErrorstatic
ERR_MD_BADBLOCKxmipp.jni.XmippErrorstatic
ERR_MD_BADLABELxmipp.jni.XmippErrorstatic
ERR_MD_BADTYPExmipp.jni.XmippErrorstatic
ERR_MD_MISSINGLABELxmipp.jni.XmippErrorstatic
ERR_MD_NOACTIVExmipp.jni.XmippErrorstatic
ERR_MD_NOOBJxmipp.jni.XmippErrorstatic
ERR_MD_OBJECTNUMBERxmipp.jni.XmippErrorstatic
ERR_MD_SQLxmipp.jni.XmippErrorstatic
ERR_MD_UNDEFINEDxmipp.jni.XmippErrorstatic
ERR_MEM_BADREQUESTxmipp.jni.XmippErrorstatic
ERR_MEM_NOTDEALLOCxmipp.jni.XmippErrorstatic
ERR_MEM_NOTENOUGHxmipp.jni.XmippErrorstatic
ERR_MEM_NULLPOINTERxmipp.jni.XmippErrorstatic
ERR_MMAPxmipp.jni.XmippErrorstatic
ERR_MMAP_NOTADDRxmipp.jni.XmippErrorstatic
ERR_MULTIDIM_DIMxmipp.jni.XmippErrorstatic
ERR_MULTIDIM_EMPTYxmipp.jni.XmippErrorstatic
ERR_MULTIDIM_SIZExmipp.jni.XmippErrorstatic
ERR_NOT_IMPLEMENTEDxmipp.jni.XmippErrorstatic
ERR_NUMERICALxmipp.jni.XmippErrorstatic
ERR_PARAM_INCORRECTxmipp.jni.XmippErrorstatic
ERR_PARAM_MISSINGxmipp.jni.XmippErrorstatic
ERR_PLANS_NOCREATExmipp.jni.XmippErrorstatic
ERR_PROG_NOTDEFxmipp.jni.XmippErrorstatic
ERR_SELFILExmipp.jni.XmippErrorstatic
ERR_THREADS_NOTINITxmipp.jni.XmippErrorstatic
ERR_TYPE_INCORRECTxmipp.jni.XmippErrorstatic
ERR_UNCLASSIFIEDxmipp.jni.XmippErrorstatic
ERR_VALUE_EMPTYxmipp.jni.XmippErrorstatic
ERR_VALUE_INCORRECTxmipp.jni.XmippErrorstatic
ERR_VALUE_NOTSETxmipp.jni.XmippErrorstatic
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xmipp.jni.XmippError Class Reference
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-Static Public Attributes

static final int ERR_FIRST_LABEL = 0
 
static final int ERR_ARG_BADCMDLINE = 1
 
static final int ERR_ARG_INCORRECT = 2
 < Errors on command line parameters. More...
 
static final int ERR_ARG_MISSING = 3
 < Incorrect argument received. More...
 
static final int ERR_ARG_DEPENDENCE = 4
 < Argument missing. More...
 
static final int ERR_PROG_NOTDEF = 5
 < Error with some arguments dependencies More...
 
static final int ERR_DEBUG_TEST = 6
 < Required function not implemented More...
 
static final int ERR_DEBUG_IMPOSIBLE = 7
 < Just an error for debugging purpose. More...
 
static final int ERR_DOCFILE = 8
 < Just for debugging, situation that can't happens More...
 
static final int ERR_GPU_MEMORY = 9
 < Error in docfile format More...
 
static final int ERR_GRID = 10
 < GPU memory related issues More...
 
static final int ERR_GRID_SIZE = 11
 < Grid general error. More...
 
static final int ERR_IMG_NOREAD = 12
 < Incorrect number of GRID volumes or shapes More...
 
static final int ERR_IMG_NOWRITE = 13
 < Cannot read image from file. More...
 
static final int ERR_IMG_UNKNOWN = 14
 < Cannot write image to file. More...
 
static final int ERR_INDEX_OUTOFBOUNDS = 15
 < Unknown image type More...
 
static final int ERR_IO = 16
 < Index out of bounds. More...
 
static final int ERR_IO_NOCLOSED = 17
 < Input/Output general error. More...
 
static final int ERR_IO_NOTEXIST = 18
 < File cannot be closed. More...
 
static final int ERR_IO_NOTOPEN = 19
 < File or directory does not exist. More...
 
static final int ERR_IO_NOPERM = 20
 < File cannot be open. More...
 
static final int ERR_IO_NOREAD = 21
 < Insufficient permissions to perform operation. More...
 
static final int ERR_IO_NOWRITE = 22
 < Couldn't read from file. More...
 
static final int ERR_IO_NOTFILE = 23
 < Couldn't write to file. More...
 
static final int ERR_IO_NOTDIR = 24
 < It is not a file. More...
 
static final int ERR_IO_NOPATH = 25
 < It is not a directory. More...
 
static final int ERR_IO_LOCKED = 26
 < Environment PATH cannot be read. More...
 
static final int ERR_IO_SIZE = 27
 < Error when locking/unloking a file. More...
 
static final int ERR_LOGIC_ERROR = 28
 < Incorrect file size. More...
 
static final int ERR_MATRIX = 29
 < Some logical error in the pipeline More...
 
static final int ERR_MATRIX_DIM = 30
 < Matrix error. More...
 
static final int ERR_MATRIX_EMPTY = 31
 < Problem with matrix dimensions. More...
 
static final int ERR_MATRIX_SIZE = 32
 < The matrix is empty. More...
 
static final int ERR_MD = 33
 < Problem with matrix size. More...
 
static final int ERR_MD_NOACTIVE = 34
 < MetaData error. More...
 
static final int ERR_MD_NOOBJ = 35
 < No active object in MetaData. More...
 
static final int ERR_MD_BADLABEL = 36
 < No exist requested object. More...
 
static final int ERR_MD_MISSINGLABEL = 37
 < Unexpected label. More...
 
static final int ERR_MD_SQL = 38
 < Missing expected label More...
 
static final int ERR_MD_OBJECTNUMBER = 39
 < Error in SQL of MetaData operations. More...
 
static final int ERR_MD_BADTYPE = 40
 < Incorrect number of objects in Metadata More...
 
static final int ERR_MD_UNDEFINED = 41
 < Bad label type. More...
 
static final int ERR_MD_BADBLOCK = 42
 < Undefined label. More...
 
static final int ERR_MEM_BADREQUEST = 43
 < This block does not exist. More...
 
static final int ERR_MEM_NOTENOUGH = 44
 < Bad amount of memory requested. More...
 
static final int ERR_MEM_NOTDEALLOC = 45
 < There is not enough memory for allocation. More...
 
static final int ERR_MEM_NULLPOINTER = 46
 < Memory has not been deallocated. More...
 
static final int ERR_MMAP = 47
 < Null pointer passed as parameter More...
 
static final int ERR_MMAP_NOTADDR = 48
 < Global mmap error. More...
 
static final int ERR_MULTIDIM_DIM = 49
 < Map addressing of file has failed. More...
 
static final int ERR_MULTIDIM_SIZE = 50
 < Incorrect MultidimArray dimensions More...
 
static final int ERR_MULTIDIM_EMPTY = 51
 < Incorrect MultidimArray size More...
 
static final int ERR_NOT_IMPLEMENTED = 52
 < MultidimArray is empty. More...
 
static final int ERR_NUMERICAL = 53
 < Case or algorithm not implemented yet. More...
 
static final int ERR_PARAM_INCORRECT = 54
 < Error related to numerical calculation. More...
 
static final int ERR_PARAM_MISSING = 55
 < Parameter incorrect. More...
 
static final int ERR_PLANS_NOCREATE = 56
 < Parameter missing. More...
 
static final int ERR_SELFILE = 57
 < FFT Plan cannot be created. More...
 
static final int ERR_THREADS_NOTINIT = 58
 < Error in docfile format More...
 
static final int ERR_TYPE_INCORRECT = 59
 < Threads cannot be initiated. More...
 
static final int ERR_UNCLASSIFIED = 60
 < Incorrect type received. More...
 
static final int ERR_VALUE_EMPTY = 61
 < Just to locate unclassified errors. More...
 
static final int ERR_VALUE_INCORRECT = 62
 < Empty value. More...
 
static final int ERR_VALUE_NOTSET = 63
 < Incorrect value received. More...
 
static final int ERR_LAST_LABEL = 64
 < Value has not been set. More...
 
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Definition at line 3 of file XmippError.java.

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Member Data Documentation

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< Argument missing.

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< Just an error for debugging purpose.

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Definition at line 11 of file XmippError.java.

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< Required function not implemented

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Definition at line 10 of file XmippError.java.

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Definition at line 12 of file XmippError.java.

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Definition at line 13 of file XmippError.java.

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< GPU memory related issues

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Definition at line 14 of file XmippError.java.

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< Grid general error.

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Definition at line 15 of file XmippError.java.

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◆ ERR_IMG_NOREAD

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< Incorrect number of GRID volumes or shapes

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Definition at line 16 of file XmippError.java.

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◆ ERR_IMG_NOWRITE

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< Cannot read image from file.

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Definition at line 17 of file XmippError.java.

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◆ ERR_IMG_UNKNOWN

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< Cannot write image to file.

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Definition at line 18 of file XmippError.java.

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◆ ERR_INDEX_OUTOFBOUNDS

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< Unknown image type

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Definition at line 19 of file XmippError.java.

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< Index out of bounds.

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Definition at line 20 of file XmippError.java.

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◆ ERR_IO_LOCKED

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final int xmipp.jni.XmippError.ERR_IO_LOCKED = 26
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< Environment PATH cannot be read.

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Definition at line 30 of file XmippError.java.

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◆ ERR_IO_NOCLOSED

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< Input/Output general error.

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Definition at line 21 of file XmippError.java.

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◆ ERR_IO_NOPATH

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final int xmipp.jni.XmippError.ERR_IO_NOPATH = 25
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< It is not a directory.

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Definition at line 29 of file XmippError.java.

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◆ ERR_IO_NOPERM

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final int xmipp.jni.XmippError.ERR_IO_NOPERM = 20
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< File cannot be open.

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Definition at line 24 of file XmippError.java.

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◆ ERR_IO_NOREAD

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final int xmipp.jni.XmippError.ERR_IO_NOREAD = 21
- 		-static
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< Insufficient permissions to perform operation.

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Definition at line 25 of file XmippError.java.

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◆ ERR_IO_NOTDIR

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final int xmipp.jni.XmippError.ERR_IO_NOTDIR = 24
- 		-static
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- -

< It is not a file.

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Definition at line 28 of file XmippError.java.

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◆ ERR_IO_NOTEXIST

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final int xmipp.jni.XmippError.ERR_IO_NOTEXIST = 18
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< File cannot be closed.

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Definition at line 22 of file XmippError.java.

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◆ ERR_IO_NOTFILE

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- 		-static
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< Couldn't write to file.

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Definition at line 27 of file XmippError.java.

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◆ ERR_IO_NOTOPEN

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< File or directory does not exist.

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Definition at line 23 of file XmippError.java.

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Definition at line 26 of file XmippError.java.

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< Error when locking/unloking a file.

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Definition at line 31 of file XmippError.java.

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< Value has not been set.

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Definition at line 68 of file XmippError.java.

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< Incorrect file size.

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Definition at line 32 of file XmippError.java.

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< Some logical error in the pipeline

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Definition at line 33 of file XmippError.java.

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< Matrix error.

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Definition at line 34 of file XmippError.java.

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Definition at line 35 of file XmippError.java.

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Definition at line 36 of file XmippError.java.

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< Problem with matrix size.

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Definition at line 37 of file XmippError.java.

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◆ ERR_MD_BADBLOCK

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< Undefined label.

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Definition at line 46 of file XmippError.java.

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< No exist requested object.

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Definition at line 40 of file XmippError.java.

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◆ ERR_MD_BADTYPE

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final int xmipp.jni.XmippError.ERR_MD_BADTYPE = 40
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< Incorrect number of objects in Metadata

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Definition at line 44 of file XmippError.java.

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◆ ERR_MD_MISSINGLABEL

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Definition at line 41 of file XmippError.java.

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final int xmipp.jni.XmippError.ERR_MD_NOACTIVE = 34
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< MetaData error.

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Definition at line 38 of file XmippError.java.

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◆ ERR_MD_NOOBJ

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Definition at line 39 of file XmippError.java.

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< Error in SQL of MetaData operations.

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Definition at line 43 of file XmippError.java.

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Definition at line 42 of file XmippError.java.

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Definition at line 45 of file XmippError.java.

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◆ ERR_MEM_BADREQUEST

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< This block does not exist.

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Definition at line 47 of file XmippError.java.

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Definition at line 49 of file XmippError.java.

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< Bad amount of memory requested.

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Definition at line 48 of file XmippError.java.

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◆ ERR_MEM_NULLPOINTER

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< Memory has not been deallocated.

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Definition at line 50 of file XmippError.java.

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< Null pointer passed as parameter

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Definition at line 51 of file XmippError.java.

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◆ ERR_MMAP_NOTADDR

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final int xmipp.jni.XmippError.ERR_MMAP_NOTADDR = 48
- 		-static
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< Global mmap error.

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Definition at line 52 of file XmippError.java.

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◆ ERR_MULTIDIM_DIM

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final int xmipp.jni.XmippError.ERR_MULTIDIM_DIM = 49
- 		-static
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< Map addressing of file has failed.

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Definition at line 53 of file XmippError.java.

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◆ ERR_MULTIDIM_EMPTY

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final int xmipp.jni.XmippError.ERR_MULTIDIM_EMPTY = 51
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Definition at line 55 of file XmippError.java.

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◆ ERR_MULTIDIM_SIZE

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final int xmipp.jni.XmippError.ERR_MULTIDIM_SIZE = 50
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< Incorrect MultidimArray dimensions

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Definition at line 54 of file XmippError.java.

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◆ ERR_NOT_IMPLEMENTED

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final int xmipp.jni.XmippError.ERR_NOT_IMPLEMENTED = 52
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< MultidimArray is empty.

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Definition at line 56 of file XmippError.java.

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◆ ERR_NUMERICAL

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final int xmipp.jni.XmippError.ERR_NUMERICAL = 53
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< Case or algorithm not implemented yet.

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Definition at line 57 of file XmippError.java.

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◆ ERR_PARAM_INCORRECT

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< Error related to numerical calculation.

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Definition at line 58 of file XmippError.java.

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◆ ERR_PARAM_MISSING

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< Parameter incorrect.

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Definition at line 59 of file XmippError.java.

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< Parameter missing.

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Definition at line 60 of file XmippError.java.

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< Error with some arguments dependencies

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Definition at line 9 of file XmippError.java.

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◆ ERR_SELFILE

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< FFT Plan cannot be created.

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Definition at line 61 of file XmippError.java.

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◆ ERR_THREADS_NOTINIT

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< Error in docfile format

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Definition at line 62 of file XmippError.java.

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final int xmipp.jni.XmippError.ERR_TYPE_INCORRECT = 59
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< Threads cannot be initiated.

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Definition at line 63 of file XmippError.java.

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final int xmipp.jni.XmippError.ERR_UNCLASSIFIED = 60
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< Incorrect type received.

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Definition at line 64 of file XmippError.java.

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◆ ERR_VALUE_EMPTY

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final int xmipp.jni.XmippError.ERR_VALUE_EMPTY = 61
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< Just to locate unclassified errors.

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Definition at line 65 of file XmippError.java.

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◆ ERR_VALUE_INCORRECT

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final int xmipp.jni.XmippError.ERR_VALUE_INCORRECT = 62
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< Empty value.

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Definition at line 66 of file XmippError.java.

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◆ ERR_VALUE_NOTSET

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< Incorrect value received.

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Definition at line 67 of file XmippError.java.

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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1test_1_1FilenameTest-members.html b/html/classxmipp_1_1test_1_1FilenameTest-members.html deleted file mode 100644 index 4ed13f8e..00000000 --- a/html/classxmipp_1_1test_1_1FilenameTest-members.html +++ /dev/null @@ -1,87 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.test.FilenameTest Member List
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This is the complete list of members for xmipp.test.FilenameTest, including all inherited members.

- - - - - - -
setUp()xmipp.test.FilenameTestinline
setUpClass()xmipp.test.FilenameTestinlinestatic
tearDown()xmipp.test.FilenameTestinline
tearDownClass()xmipp.test.FilenameTestinlinestatic
testGetXmippPath()xmipp.test.FilenameTestinline
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- - diff --git a/html/classxmipp_1_1test_1_1FilenameTest.html b/html/classxmipp_1_1test_1_1FilenameTest.html deleted file mode 100644 index 4ca32ade..00000000 --- a/html/classxmipp_1_1test_1_1FilenameTest.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - - -Xmipp: xmipp.test.FilenameTest Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.test.FilenameTest Class Reference
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-Public Member Functions

void setUp ()
 
void tearDown ()
 
void testGetXmippPath ()
 
- - - - - -

-Static Public Member Functions

static void setUpClass () throws Exception
 
static void tearDownClass () throws Exception
 
-

Detailed Description

-
-

Definition at line 33 of file FilenameTest.java.

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Member Function Documentation

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◆ setUp()

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void xmipp.test.FilenameTest.setUp ()
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Definition at line 51 of file FilenameTest.java.

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◆ setUpClass()

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static void xmipp.test.FilenameTest.setUpClass () throws Exception
- 		-inlinestatic
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Definition at line 43 of file FilenameTest.java.

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43  {
44  }
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◆ tearDown()

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Definition at line 56 of file FilenameTest.java.

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56  {
57  }
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- 		-inlinestatic
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Definition at line 47 of file FilenameTest.java.

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47  {
48  }
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◆ testGetXmippPath()

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void xmipp.test.FilenameTest.testGetXmippPath ()
- 		-inline
-
-

Test of getFilename method, of class ImageGeneric.

- -

Definition at line 63 of file FilenameTest.java.

-
63  {
64  try {
65  String xmipp_home = Filename.getXmippPath();
66  String xmipp_home2 = System.getenv("XMIPP_HOME");
67  assertEquals(xmipp_home, xmipp_home2);
68  } catch (Exception ex) {
69  fail("testGetFilename");
70  }
71  }//function testGetXmippPath
-
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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1test_1_1ImageGenericTest-members.html b/html/classxmipp_1_1test_1_1ImageGenericTest-members.html deleted file mode 100644 index fe878088..00000000 --- a/html/classxmipp_1_1test_1_1ImageGenericTest-members.html +++ /dev/null @@ -1,96 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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This is the complete list of members for xmipp.test.ImageGenericTest, including all inherited members.

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ImageGenericTest()xmipp.test.ImageGenericTestinline
setUp()xmipp.test.ImageGenericTestinline
setUpClass()xmipp.test.ImageGenericTestinlinestatic
tearDown()xmipp.test.ImageGenericTestinline
tearDownClass()xmipp.test.ImageGenericTestinlinestatic
testEqual()xmipp.test.ImageGenericTestinline
testGetArrayFloat()xmipp.test.ImageGenericTestinline
testGetDataType()xmipp.test.ImageGenericTestinline
testGetDimensions()xmipp.test.ImageGenericTestinline
testGetFilename()xmipp.test.ImageGenericTestinline
testGetStatistics()xmipp.test.ImageGenericTestinline
testSetArrayFloat()xmipp.test.ImageGenericTestinline
testSubtract()xmipp.test.ImageGenericTestinline
testWhatIs()xmipp.test.ImageGenericTestinline
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- - diff --git a/html/classxmipp_1_1test_1_1ImageGenericTest.html b/html/classxmipp_1_1test_1_1ImageGenericTest.html deleted file mode 100644 index d80d6a5b..00000000 --- a/html/classxmipp_1_1test_1_1ImageGenericTest.html +++ /dev/null @@ -1,514 +0,0 @@ - - - - - - - -Xmipp: xmipp.test.ImageGenericTest Class Reference - - - - - - - - - -
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xmipp.test.ImageGenericTest Class Reference
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-Public Member Functions

 ImageGenericTest ()
 
void setUp ()
 
void tearDown ()
 
void testGetFilename () throws Exception
 
void testGetDimensions () throws Exception
 
void testGetDataType () throws Exception
 
void testGetArrayFloat () throws Exception
 
void testEqual () throws Exception
 
void testSubtract () throws Exception
 
void testGetStatistics () throws Exception
 
void testSetArrayFloat () throws Exception
 
void testWhatIs () throws Exception
 
- - - - - -

-Static Public Member Functions

static void setUpClass () throws Exception
 
static void tearDownClass () throws Exception
 
-

Detailed Description

-
Author
Juanjo Vega
- -

Definition at line 52 of file ImageGenericTest.java.

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Constructor & Destructor Documentation

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◆ ImageGenericTest()

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xmipp.test.ImageGenericTest.ImageGenericTest ()
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Definition at line 75 of file ImageGenericTest.java.

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75  {
76 
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Member Function Documentation

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Definition at line 88 of file ImageGenericTest.java.

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◆ setUpClass()

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Definition at line 80 of file ImageGenericTest.java.

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◆ tearDown()

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Definition at line 92 of file ImageGenericTest.java.

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◆ tearDownClass()

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Definition at line 84 of file ImageGenericTest.java.

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◆ testEqual()

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void xmipp.test.ImageGenericTest.testEqual () throws Exception
- 		-inline
-
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Test of getDataType method, of class ImageGeneric.

- -

Definition at line 142 of file ImageGenericTest.java.

-
142  {
143  ImageGeneric image = XmippTest.getImageGeneric(filename);
144  ImageGeneric image2 = XmippTest.getImageGeneric(filename2);
145 
146  assertTrue(image.equal(image, XmippTest.EQUAL_ACCURACY));
147  assertFalse(image.equal(image2, XmippTest.EQUAL_ACCURACY));
148  }
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void xmipp.test.ImageGenericTest.testGetArrayFloat () throws Exception
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Test of getArrayFloat method, of class ImageGeneric.

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Definition at line 130 of file ImageGenericTest.java.

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130  {
131  ImageGeneric image = XmippTest.getImageGeneric(filename);
132 
133  float[] result = image.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE);
134  for (int i = 0; i < imagePixels.length; i++)
135  assertEquals(imagePixels[i], result[i], XmippTest.EQUAL_ACCURACY);
136  }
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Definition at line 121 of file ImageGenericTest.java.

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121  {
122  ImageGeneric image = new ImageGeneric(filename);
123  assertEquals(imageDatatype, image.getDataType());
124  }
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Test of getXDim method, of class ImageGeneric.

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Definition at line 109 of file ImageGenericTest.java.

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109  {
110  ImageGeneric image = new ImageGeneric(filename);
111  assertEquals(xdim, image.getXDim());
112  assertEquals(ydim, image.getYDim());
113  assertEquals(zdim, image.getZDim());
114  assertEquals(ndim, image.getNDim());
115  }
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Definition at line 99 of file ImageGenericTest.java.

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99  {
100  ImageGeneric image = new ImageGeneric(filename);
101  String imageFn = image.getFilename();
102  assertEquals(filename, imageFn);
103  }
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Definition at line 169 of file ImageGenericTest.java.

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169  {
170  ImageGeneric image = XmippTest.getImageGeneric(filename);
171  double[] stats = image.getStatistics();
172  for (int i = 0; i < stats.length; i++) {
173  assertEquals(imageStats[i], stats[i], XmippTest.EQUAL_ACCURACY);
174  }
175  }
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Definition at line 181 of file ImageGenericTest.java.

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181  {
182  //PENDING TO CHANGE IMAGE GENERIC TO ALLOW WRITE MODE ON MEMORY MAPPED TO DISK
183  System.out.println("TestSetArrayFloat");
184  int size = 100;
185  String templatesfile = "imagegeneric.stk";
186  ImageGeneric templates = new ImageGeneric(templatesfile);
187  XmippImageConverter.readToImagePlus(templates);//to load templates on memory
188 
189 
190  String micrographfile = XmippTest.getTestFilename("BPV_1386.mrc");
191  ImagePlus mimage = new ImagePlus(micrographfile);
192  Rectangle r = new Rectangle(0, 0, size, size);
193  mimage.setRoi(r);
194  ImageProcessor processor = mimage.getProcessor().crop();
195  ImagePlus particleimg = new ImagePlus("particle", processor);
196  //new FileSaver(particleimg).save();
197  ImageGeneric particleig = XmippImageConverter.convertToImageGeneric(particleimg);
198  float[] matrix = particleig.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.ALL_SLICES);
199  templates.setArrayFloat(matrix, ImageGeneric.FIRST_IMAGE, ImageGeneric.ALL_SLICES);
200  templates.write(templatesfile);
201  }
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Definition at line 154 of file ImageGenericTest.java.

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154  {
155  ImageGeneric image = XmippTest.getImageGeneric(filename);
156  ImageGeneric image2 = XmippTest.getImageGeneric(filename2);
157  ImageGeneric image3 = new ImageGeneric();
158  image2.subtract(image,image3);
159  float[] result = image3.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE);
160  for (int i = 0; i < imagePixels.length -1; i++)
161  assertEquals(result[i],0., XmippTest.EQUAL_ACCURACY);
162  assertEquals(result[8],27.0, XmippTest.EQUAL_ACCURACY);
163  }
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Test of isPSD method, of class ImageGeneric.

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Definition at line 207 of file ImageGenericTest.java.

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207  {
208  ImageGeneric image = new ImageGeneric(filename);
209  assertTrue(image.isSingleImage());
210  assertFalse(image.isStackOrVolume());
211  assertFalse(image.isPSD());
212  }
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- - diff --git a/html/classxmipp_1_1test_1_1MetadataTest-members.html b/html/classxmipp_1_1test_1_1MetadataTest-members.html deleted file mode 100644 index 719198f7..00000000 --- a/html/classxmipp_1_1test_1_1MetadataTest-members.html +++ /dev/null @@ -1,96 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.test.MetadataTest Member List
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This is the complete list of members for xmipp.test.MetadataTest, including all inherited members.

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readRuntimeMd()xmipp.test.MetadataTestinline
setUp()xmipp.test.MetadataTestinline
setUpClass()xmipp.test.MetadataTestinlinestatic
tearDown()xmipp.test.MetadataTestinline
tearDownClass()xmipp.test.MetadataTestinlinestatic
testFill()xmipp.test.MetadataTestinline
testLabelType()xmipp.test.MetadataTestinline
testMakeAbsPath()xmipp.test.MetadataTestinline
testOperate()xmipp.test.MetadataTestinline
testRead()xmipp.test.MetadataTestinline
testReadQuotedString()xmipp.test.MetadataTestinline
testRemoveObject()xmipp.test.MetadataTestinline
testSort()xmipp.test.MetadataTestinline
updateMetaDataRowWithRow()xmipp.test.MetadataTestinline
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xmipp.test.MetadataTest Class Reference
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-Classes

class  Worker
 
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-Public Member Functions

void setUp ()
 
void tearDown ()
 
void testRead () throws Exception
 
void testLabelType () throws Exception
 
void testSort () throws Exception
 
void testMakeAbsPath () throws Exception
 
void testFill () throws Exception
 
void testRemoveObject () throws Exception
 
void testReadQuotedString () throws Exception
 
void readRuntimeMd () throws Exception
 
void updateMetaDataRowWithRow () throws Exception
 
void testOperate () throws Exception
 
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-Static Public Member Functions

static void setUpClass () throws Exception
 
static void tearDownClass () throws Exception
 
-

Detailed Description

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Test metadata

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sample metadata:

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data_ loop_ _image _enabled _shiftX _ref 00000.nosp@m.1@tu.nosp@m.x.stk 1 0.000000 3 00000.nosp@m.2@tu.nosp@m.x.stk 1 1.404060 4 00000.nosp@m.3@tu.nosp@m.x.stk 1 1.715445 1 00000.nosp@m.4@tu.nosp@m.x.stk 1 1.266333 2

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Definition at line 57 of file MetadataTest.java.

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Member Function Documentation

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◆ readRuntimeMd()

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void xmipp.test.MetadataTest.readRuntimeMd () throws Exception
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Definition at line 331 of file MetadataTest.java.

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332  {
333  try
334  {
335  System.out.println("read runtime md...");
336 
337  MetaData md = new MetaData(XmippTest.getTestFilename("images.stk"));
338  MetaData imagesmd = new MetaData();
339  String imagepath;
340  int idlabel = MDLabel.MDL_IMAGE;
341 
342 
343 
344  Worker w = new Worker(md, imagesmd);
345  //w.run();
346 
347  Thread th = new Thread(w);
348  th.start();
349 
350  md.destroy();
351 
352  System.out.println("read runtime md ended...");
353  }
354  catch (Exception ex)
355  {
356  ex.printStackTrace();
357  }
358  }
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void xmipp.test.MetadataTest.setUp ()
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Definition at line 79 of file MetadataTest.java.

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80  {
81  }
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static void xmipp.test.MetadataTest.setUpClass () throws Exception
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Definition at line 69 of file MetadataTest.java.

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70  {
71  }
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◆ tearDown()

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void xmipp.test.MetadataTest.tearDown ()
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Definition at line 84 of file MetadataTest.java.

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85  {
86  }
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Definition at line 74 of file MetadataTest.java.

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75  {
76  }
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◆ testFill()

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void xmipp.test.MetadataTest.testFill () throws Exception
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Definition at line 160 of file MetadataTest.java.

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161  {
162  // Test fillConstant
163  String imagePath = "resources/test/singleImage.img";
164  MetaData md = new MetaData(mdFn);
165  md.fillConstant(MDLabel.MDL_IMAGE1, imagePath);
166  long[] ids = md.findObjects();
167  for (int i = 0; i < ids.length; ++i)
168  assertEquals(imagePath, md.getValueString(MDLabel.MDL_IMAGE1, ids[i]));
169 
170  // Test fillLinear
171  md.fillLinear(MDLabel.MDL_SHIFT_Y, 0.0, 0.5);
172  double value = 0.0;
173  for (int i = 0; i < ids.length; ++i)
174  {
175  assertEquals(value, md.getValueDouble(MDLabel.MDL_SHIFT_Y, ids[i]), XmippTest.EQUAL_ACCURACY);
176  value += 0.5;
177  }
178  // md.print();
179 
180  // Test fillRandom
181  // md.fillRandom(MDLabel.MDL_SHIFT_Y, "uniform", 2.0, 3.0);
182  // md.print();
183  md.destroy();
184  }// function testFill
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◆ testLabelType()

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void xmipp.test.MetadataTest.testLabelType () throws Exception
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Definition at line 113 of file MetadataTest.java.

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114  {
115  int type = MetaData.getLabelType(MDLabel.MDL_IMAGE);
116  assertEquals(MetaData.LABEL_STRING, type);
117  }// function testLabelType
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void xmipp.test.MetadataTest.testMakeAbsPath () throws Exception
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Definition at line 137 of file MetadataTest.java.

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138  {
139  MetaData md = new MetaData(mdFn), md2 = new MetaData(mdFn);
140  md2.makeAbsPath(MDLabel.MDL_IMAGE);
141  long[] ids = md.findObjects();
142  long[] ids2 = md2.findObjects();
143 
144  for (int i = 0; i < ids.length; ++i)
145  {
146  String path = md.getValueString(MDLabel.MDL_IMAGE, ids[i]);
147  File f = new File(Filename.getFilename(path));
148  path = md2.getValueString(MDLabel.MDL_IMAGE, ids2[i]);
149  assertEquals(Filename.getFilename(path), f.getAbsolutePath());
150  }
151  //md.print();
152  //md2.print();
153 
154  md.destroy();
155  md2.destroy();
156 
157  }// function testSort
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Definition at line 446 of file MetadataTest.java.

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447  {
448  MetaData md = new MetaData(mdFn);
449  md.operate("shiftX=2*shiftX, ref=ref+10");
450  long[] ids = md.findObjects();
451  long id;
452  for (int i = 0; i < ids.length; ++i)
453  {
454  id = ids[i];
455  assertEquals(shiftXValues[i] * 2, md.getValueDouble(MDLabel.MDL_SHIFT_X, id), XmippTest.EQUAL_ACCURACY);
456  assertEquals(refValues[i] + 10, md.getValueInt(MDLabel.MDL_REF, id));
457  }
458  }// function testRead
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Definition at line 89 of file MetadataTest.java.

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90  {
91  MetaData md = new MetaData(mdFn);
92  MDRow row = new MDRow();
93 
94  long[] ids = md.findObjects();
95  long id;
96  for (int i = 0; i < ids.length; ++i)
97  {
98  id = ids[i];
99  assertEquals(imageValues[i], md.getValueString(MDLabel.MDL_IMAGE, id));
100  assertEquals(shiftXValues[i], md.getValueDouble(MDLabel.MDL_SHIFT_X, id), XmippTest.EQUAL_ACCURACY);
101  assertEquals(refValues[i], md.getValueInt(MDLabel.MDL_REF, id));
102 
103  //Test MDRow
104  md.getRow(row, id);
105  assertEquals(imageValues[i], row.getValueString(MDLabel.MDL_IMAGE));
106  assertEquals(shiftXValues[i], row.getValueDouble(MDLabel.MDL_SHIFT_X), XmippTest.EQUAL_ACCURACY);
107  assertEquals(refValues[i], row.getValueInt(MDLabel.MDL_REF));
108  }
109  md.destroy();
110  }// function testRead
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Definition at line 203 of file MetadataTest.java.

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204  {
205  // MetaData md = new MetaData("kk.xmd");
206  // long[] ids = md.findObjects();
207  // md.print();
208  // System.out.println("------------------------------------");
209  // for (int i=0; i < ids.length; ++i){
210  // System.out.println(md.getValueString(MDLabel.MDL_IMAGE, ids[i]));
211  // System.out.println(md.getValueString(MDLabel.MDL_ANGLE_DIFF,
212  // ids[i]));
213  // }
214  // md.print();
215  }
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Definition at line 187 of file MetadataTest.java.

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188  {
189  double[] localShiftXValues = { shiftXValues[1], shiftXValues[3] };
190  MetaData md = new MetaData(mdFn);
191  long[] ids = md.findObjects();
192  md.removeObject(ids[0]);
193  md.removeObject(ids[2]);
194  assertEquals(2, md.size());
195  ids = md.findObjects();
196  for (int i = 0; i < ids.length; ++i)
197  assertEquals(localShiftXValues[i], md.getValueDouble(MDLabel.MDL_SHIFT_X, ids[i]), XmippTest.EQUAL_ACCURACY);
198  // md.print();
199  md.destroy();
200  }
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Definition at line 120 of file MetadataTest.java.

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121  {
122  MetaData md = new MetaData(mdFn);
123  // Sort by MDL_SHIFT_X ascending
124  md.sort(MDLabel.MDL_SHIFT_X, true);
125  long[] ids = md.findObjects();
126  for (int i = 0; i < ids.length; ++i)
127  assertEquals(shiftXSorted[i], md.getValueDouble(MDLabel.MDL_SHIFT_X, ids[i]), XmippTest.EQUAL_ACCURACY);
128  // Sort by MDL_REF descending
129  md.sort(MDLabel.MDL_REF, false);
130  ids = md.findObjects();
131  for (int i = 0; i < ids.length; ++i)
132  assertEquals(refSorted[i], md.getValueInt(MDLabel.MDL_REF, ids[i]));
133  md.destroy();
134  }// function testSort
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Definition at line 361 of file MetadataTest.java.

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362  {
363  try
364  {
365  System.out.println("updateMetaDataRowWithRow");
366 
367  MetaData md = new MetaData(XmippTest.getTestFilename("images.stk"));
368  MetaData imagesmd = new MetaData();
369  String imagepath;
370  int idlabel = MDLabel.MDL_IMAGE;
371  MDRow mdRow = new MDRow();
372  long[] ids = md.findObjects();
373 
374  long id2;
375  for (long id: ids)
376  {
377  imagepath = md.getValueString(idlabel, id, true);
378  if (imagepath != null && ImageGeneric.exists(imagepath))
379  {
380  id2 = imagesmd.addObject();
381  md.getRow(mdRow, id);
382  mdRow.setValueString(idlabel, imagepath);
383  imagesmd.setRow(mdRow, id2);
384  }
385  }
386 
387  long[] ids2 = imagesmd.findObjects();
388  for (int i=0; i < ids.length; i++)
389  {
390  assertEquals(md.getValueString(idlabel, ids[i]),
391  imagesmd.getValueString(idlabel, ids2[i]));
392  }
393 
394  //imagesmd.print();
395 
396  imagesmd.destroy();
397  md.destroy();
398  mdRow.destroy();
399 
400  System.out.println("updateMetaDataRowWithRow ended...");
401  }
402  catch (Exception ex)
403  {
404  ex.printStackTrace();
405  }
406  }
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run()xmipp.test.MetadataTest.Workerinline
Worker(MetaData md, MetaData imagesmd)xmipp.test.MetadataTest.Workerinline
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 Worker (MetaData md, MetaData imagesmd)
 
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Definition at line 294 of file MetadataTest.java.

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Constructor & Destructor Documentation

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◆ Worker()

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Definition at line 299 of file MetadataTest.java.

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300  {
301  this.imagesmd = imagesmd;
302  this.md = md;
303  }
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Definition at line 305 of file MetadataTest.java.

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306  {
307  String imagepath;
308  int idlabel = MDLabel.MDL_IMAGE;
309 
310  long id2;
311  for (long id : md.findObjects())
312  {
313  imagepath = md.getValueString(idlabel, id, true);
314  if (imagepath != null && ImageGeneric.exists(imagepath))
315  {
316  id2 = imagesmd.addObject();
317  imagesmd.setValueString(idlabel, imagepath, id2);
318  }
319  }
320 
321  for (long id : imagesmd.findObjects())
322  {
323  imagepath = imagesmd.getValueString(idlabel, id, true);
324  System.out.printf("%d %s\n", id, imagepath);
325  }
326 
327  imagesmd.destroy();
328  }
xmipp.jni.MetaData.addObject
native long addObject()
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getImageGeneric(String filename)xmipp.test.XmippTestinlinestatic
getTestFilename(String file)xmipp.test.XmippTestinlinestatic
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static String getTestFilename (String file)
 
static ImageGeneric getImageGeneric (String filename) throws Exception
 
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Class to group common utilities for Java tests

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Definition at line 33 of file XmippTest.java.

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◆ getImageGeneric()

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static ImageGeneric xmipp.test.XmippTest.getImageGeneric (String filename) throws Exception
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Create and read the image generic

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45  {
46  ImageGeneric image = new ImageGeneric(filename);
47  image.read(ImageGeneric.FIRST_SLICE);
48  return image;
49  }
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Return the filename relative to tests folder

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40  {
41  return TESTS_PATH + file;
42  }
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eq(Matrix B)xmipp.tomography.alignment.Matrixinline
identity(int N)xmipp.tomography.alignment.Matrixinlinestatic
main(String[] args)xmipp.tomography.alignment.Matrixinlinestatic
Matrix(int M, int N)xmipp.tomography.alignment.Matrixinline
Matrix(double[][] data)xmipp.tomography.alignment.Matrixinline
minus(Matrix B)xmipp.tomography.alignment.Matrixinline
plus(Matrix B)xmipp.tomography.alignment.Matrixinline
random(int M, int N)xmipp.tomography.alignment.Matrixinlinestatic
show()xmipp.tomography.alignment.Matrixinline
solve(Matrix rhs)xmipp.tomography.alignment.Matrixinline
times(Matrix B)xmipp.tomography.alignment.Matrixinline
transpose()xmipp.tomography.alignment.Matrixinline
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xmipp.tomography.alignment.Matrix Class Reference
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 Matrix (int M, int N)
 
 Matrix (double[][] data)
 
Matrix transpose ()
 
Matrix plus (Matrix B)
 
Matrix minus (Matrix B)
 
boolean eq (Matrix B)
 
Matrix times (Matrix B)
 
Matrix solve (Matrix rhs)
 
void show ()
 
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static Matrix random (int M, int N)
 
static Matrix identity (int N)
 
static void main (String[] args)
 
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Definition at line 5 of file Matrix.java.

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◆ Matrix() [1/2]

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Definition at line 11 of file Matrix.java.

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11  {
12  this.M = M;
13  this.N = N;
14  data = new double[M][N];
15  }
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Definition at line 18 of file Matrix.java.

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18  {
19  M = data.length;
20  N = data[0].length;
21  this.data = new double[M][N];
22  for (int i = 0; i < M; i++)
23  for (int j = 0; j < N; j++)
24  this.data[i][j] = data[i][j];
25  }
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Definition at line 87 of file Matrix.java.

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87  {
88  Matrix A = this;
89  if (B.M != A.M || B.N != A.N) throw new RuntimeException("Illegal matrix dimensions.");
90  for (int i = 0; i < M; i++)
91  for (int j = 0; j < N; j++)
92  if (A.data[i][j] != B.data[i][j]) return false;
93  return true;
94  }
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Definition at line 40 of file Matrix.java.

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40  {
41  Matrix I = new Matrix(N, N);
42  for (int i = 0; i < N; i++)
43  I.data[i][i] = 1;
44  return I;
45  }
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Definition at line 170 of file Matrix.java.

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170  {
171  double[][] d = { { 1, 2, 3 }, { 4, 5, 6 }, { 9, 1, 3} };
172  Matrix D = new Matrix(d);
173  D.show();
174  System.out.println();
175 
176  Matrix A = Matrix.random(5, 5);
177  A.show();
178  System.out.println();
179 
180  A.swap(1, 2);
181  A.show();
182  System.out.println();
183 
184  Matrix B = A.transpose();
185  B.show();
186  System.out.println();
187 
188  Matrix C = Matrix.identity(5);
189  C.show();
190  System.out.println();
191 
192  A.plus(B).show();
193  System.out.println();
194 
195  B.times(A).show();
196  System.out.println();
197 
198  // shouldn't be equal since AB != BA in general
199  System.out.println(A.times(B).eq(B.times(A)));
200  System.out.println();
201 
202  Matrix b = Matrix.random(5, 1);
203  b.show();
204  System.out.println();
205 
206  Matrix x = A.solve(b);
207  x.show();
208  System.out.println();
209 
210  A.times(x).show();
211 
212  }
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Definition at line 76 of file Matrix.java.

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76  {
77  Matrix A = this;
78  if (B.M != A.M || B.N != A.N) throw new RuntimeException("Illegal matrix dimensions.");
79  Matrix C = new Matrix(M, N);
80  for (int i = 0; i < M; i++)
81  for (int j = 0; j < N; j++)
82  C.data[i][j] = A.data[i][j] - B.data[i][j];
83  return C;
84  }
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Definition at line 64 of file Matrix.java.

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64  {
65  Matrix A = this;
66  if (B.M != A.M || B.N != A.N) throw new RuntimeException("Illegal matrix dimensions.");
67  Matrix C = new Matrix(M, N);
68  for (int i = 0; i < M; i++)
69  for (int j = 0; j < N; j++)
70  C.data[i][j] = A.data[i][j] + B.data[i][j];
71  return C;
72  }
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Definition at line 31 of file Matrix.java.

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31  {
32  Matrix A = new Matrix(M, N);
33  for (int i = 0; i < M; i++)
34  for (int j = 0; j < N; j++)
35  A.data[i][j] = Math.random();
36  return A;
37  }
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Definition at line 159 of file Matrix.java.

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159  {
160  for (int i = 0; i < M; i++) {
161  for (int j = 0; j < N; j++)
162  System.out.printf("%9.4f ", data[i][j]);
163  System.out.println();
164  }
165  }
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Definition at line 110 of file Matrix.java.

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110  {
111  if (M != N || rhs.M != N || rhs.N != 1)
112  throw new RuntimeException("Illegal matrix dimensions.");
113 
114  // create copies of the data
115  Matrix A = new Matrix(this);
116  Matrix b = new Matrix(rhs);
117 
118  // Gaussian elimination with partial pivoting
119  for (int i = 0; i < N; i++) {
120 
121  // find pivot row and swap
122  int max = i;
123  for (int j = i + 1; j < N; j++)
124  if (Math.abs(A.data[j][i]) > Math.abs(A.data[max][i]))
125  max = j;
126  A.swap(i, max);
127  b.swap(i, max);
128 
129  // singular
130  if (A.data[i][i] == 0.0) throw new RuntimeException("Matrix is singular.");
131 
132  // pivot within b
133  for (int j = i + 1; j < N; j++)
134  b.data[j][0] -= b.data[i][0] * A.data[j][i] / A.data[i][i];
135 
136  // pivot within A
137  for (int j = i + 1; j < N; j++) {
138  double m = A.data[j][i] / A.data[i][i];
139  for (int k = i+1; k < N; k++) {
140  A.data[j][k] -= A.data[i][k] * m;
141  }
142  A.data[j][i] = 0.0;
143  }
144  }
145 
146  // back substitution
147  Matrix x = new Matrix(N, 1);
148  for (int j = N - 1; j >= 0; j--) {
149  double t = 0.0;
150  for (int k = j + 1; k < N; k++)
151  t += A.data[j][k] * x.data[k][0];
152  x.data[j][0] = (b.data[j][0] - t) / A.data[j][j];
153  }
154  return x;
155 
156  }
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97  {
98  Matrix A = this;
99  if (A.N != B.M) throw new RuntimeException("Illegal matrix dimensions.");
100  Matrix C = new Matrix(A.M, B.N);
101  for (int i = 0; i < C.M; i++)
102  for (int j = 0; j < C.N; j++)
103  for (int k = 0; k < A.N; k++)
104  C.data[i][j] += (A.data[i][k] * B.data[k][j]);
105  return C;
106  }
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55  {
56  Matrix A = new Matrix(N, M);
57  for (int i = 0; i < M; i++)
58  for (int j = 0; j < N; j++)
59  A.data[j][i] = this.data[i][j];
60  return A;
61  }
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- - diff --git a/html/classxmipp_1_1tomography_1_1alignment_1_1TomoSerieAligner-members.html b/html/classxmipp_1_1tomography_1_1alignment_1_1TomoSerieAligner-members.html deleted file mode 100644 index 826085e9..00000000 --- a/html/classxmipp_1_1tomography_1_1alignment_1_1TomoSerieAligner-members.html +++ /dev/null @@ -1,89 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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alignTomographies()xmipp.tomography.alignment.TomoSerieAlignerinline
getDmax()xmipp.tomography.alignment.TomoSerieAlignerinline
getDmin()xmipp.tomography.alignment.TomoSerieAlignerinline
getLogger()xmipp.tomography.alignment.TomoSerieAlignerinlinestatic
getTomographies()xmipp.tomography.alignment.TomoSerieAlignerinline
main(String[] args)xmipp.tomography.alignment.TomoSerieAlignerinlinestatic
TomoSerieAligner(String tomoseriefile, String outputdir, int dmin, int dmax)xmipp.tomography.alignment.TomoSerieAlignerinline
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-Public Member Functions

 TomoSerieAligner (String tomoseriefile, String outputdir, int dmin, int dmax)
 
int getDmin ()
 
int getDmax ()
 
List< Tomography > getTomographies ()
 
ImageStack alignTomographies ()
 
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static void main (String[] args)
 
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Definition at line 20 of file TomoSerieAligner.java.

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Definition at line 57 of file TomoSerieAligner.java.

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58  {
59  this.tomoseriefile = tomoseriefile;
60  this.outputdir = outputdir;
61  this.dmin = dmin;
62  this.dmax = dmax;
63  loadTomographies();
64  }
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Definition at line 117 of file TomoSerieAligner.java.

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118  {
119  System.out.println(new Date());
120  for(Tomography t: tomographies)
121  {
122  if(t.getPrevious() != null)
123  {
124  t.computeAffineTransform();
125  }
126  }
127  System.out.println(new Date());
128  return null;
129  }
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Definition at line 72 of file TomoSerieAligner.java.

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72  {
73  return dmax;
74  }
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Definition at line 66 of file TomoSerieAligner.java.

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67  return dmin;
68  }
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Definition at line 28 of file TomoSerieAligner.java.

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29  {
30  try
31  {
32  if (logger == null)
33  {
34  FileHandler fh = new FileHandler("TomoSerieAligner.log", true);
35  fh.setFormatter(new SimpleFormatter());
36  logger = Logger.getLogger("TomoSerieAlignerLogger");
37  logger.addHandler(fh);
38  }
39  return logger;
40  }
41  catch (Exception e)
42  {
43  // TODO Auto-generated catch block
44  e.printStackTrace();
45  }
46  return null;
47  }
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Definition at line 112 of file TomoSerieAligner.java.

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113  {
114  return tomographies;
115  }
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Definition at line 22 of file TomoSerieAligner.java.

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23  {
24  TomoSerieAligner aligner = new TomoSerieAligner(args[0], args[1], 50, 45);
25  aligner.alignTomographies();
26  }
xmipp.tomography.alignment.TomoSerieAligner.TomoSerieAligner
TomoSerieAligner(String tomoseriefile, String outputdir, int dmin, int dmax)
Definition: TomoSerieAligner.java:57
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computeAffineTransform()xmipp.tomography.alignment.Tomographyinline
detectAndDescribeInterestPoints(IntegralImage intImg, Params p)xmipp.tomography.alignment.Tomographyinlinestatic
getAffineTransform()xmipp.tomography.alignment.Tomographyinline
getCommonPointsMapping()xmipp.tomography.alignment.Tomographyinline
getImagePlus()xmipp.tomography.alignment.Tomographyinline
getIntegralImage()xmipp.tomography.alignment.Tomographyinline
getNext()xmipp.tomography.alignment.Tomographyinline
getOverlappedArea()xmipp.tomography.alignment.Tomographyinline
getPrevious()xmipp.tomography.alignment.Tomographyinline
setNext(Tomography next)xmipp.tomography.alignment.Tomographyinline
setPrevious(Tomography previous)xmipp.tomography.alignment.Tomographyinline
Tomography(String tomofile, int tiltangle)xmipp.tomography.alignment.Tomographyinline
Tomography(String tomofile, int tiltangle, Tomography previous)xmipp.tomography.alignment.Tomographyinline
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-Public Member Functions

 Tomography (String tomofile, int tiltangle)
 
 Tomography (String tomofile, int tiltangle, Tomography previous)
 
void setPrevious (Tomography previous)
 
void setNext (Tomography next)
 
Tomography getPrevious ()
 
Tomography getNext ()
 
void computeAffineTransform ()
 
Map< InterestPoint, InterestPoint > getCommonPointsMapping ()
 
Matrix getAffineTransform ()
 
Rectangle getOverlappedArea ()
 
ImagePlus getImagePlus ()
 
IntegralImage getIntegralImage ()
 
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-Static Public Member Functions

static List< InterestPoint > detectAndDescribeInterestPoints (IntegralImage intImg, Params p)
 
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Definition at line 22 of file Tomography.java.

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Definition at line 32 of file Tomography.java.

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33  {
34  this.tomofile = tomofile;
35  this.tiltangle = tiltangle;
36  }
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Definition at line 38 of file Tomography.java.

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38  {
39  this(tomofile, tiltangle);
40  setPrevious(previous);
41  }
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void setPrevious(Tomography previous)
Definition: Tomography.java:44
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Definition at line 65 of file Tomography.java.

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66  {
67 
68  Map<InterestPoint, InterestPoint> cpm = getCommonPointsMapping();
69  if (cpm == null || cpm.isEmpty())
70  return;//no affine transform
71  System.out.println("Computing affine transform on " + tomofile + " and " + getPrevious().getTomofile());
72 
73  System.out.println(cpm.size());
74  }
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Map< InterestPoint, InterestPoint > getCommonPointsMapping()
Definition: Tomography.java:81
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Definition at line 107 of file Tomography.java.

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107  {
108 
109  List<InterestPoint> ipts = Detector.fastHessian(intImg, p);
110 
111 
112  // Describe interest points with SURF-descriptor
113  if (!p.isUpright())
114  for (InterestPoint ipt: ipts)
115  Descriptor.computeAndSetOrientation(ipt, intImg);
116  for (InterestPoint ipt: ipts)
117  Descriptor.computeAndSetDescriptor(ipt, intImg, p);
118 
119  return ipts;
120  }
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Definition at line 122 of file Tomography.java.

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123  {
124  return atmatrix;
125  }
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Definition at line 81 of file Tomography.java.

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82  {
83  if(previous == null)
84  return null;
85 
86  Params pparams = new Params(4, 4, 0.0001f, 2, false, false, false, 1, false);//octaves, layers, threshold, initialStep, upright, ...
87  Params params = new Params(pparams);
88 
89 
90  List<InterestPoint> pipoints = detectAndDescribeInterestPoints(previous.getIntegralImage(), pparams);
91  List<InterestPoint> ipoints = detectAndDescribeInterestPoints(getIntegralImage(), params);
92 
93 
94  Map<InterestPoint, InterestPoint> matchedpoints = Matcher.findMathes(pipoints, ipoints);
95  Map<InterestPoint, InterestPoint> revmatchedpoints = Matcher.findMathes(ipoints, pipoints);
96  // take only those points that matched in the reverse comparison too
97  Map<InterestPoint, InterestPoint> commonpoints = new HashMap<InterestPoint, InterestPoint>();
98  for (InterestPoint ppoint : matchedpoints.keySet()) {
99  InterestPoint point = matchedpoints.get(ppoint);
100  if (ppoint == revmatchedpoints.get(point))
101  commonpoints.put(ppoint, point);
102  }
103 
104  return commonpoints;
105  }
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Definition: Tomography.java:107
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Definition at line 132 of file Tomography.java.

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133  {
134  if(imp == null)
135  imp = XmippUtil.getImagePlus(tomofile);
136  return imp;
137  }
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Definition at line 139 of file Tomography.java.

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140  {
141  if(intimg == null)
142  intimg = new IntegralImage(getImagePlus().getProcessor(), true);
143  return intimg;
144  }
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Definition at line 60 of file Tomography.java.

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61  {
62  return next;
63  }
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Definition at line 127 of file Tomography.java.

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128  {
129  return null;
130  }
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Definition at line 55 of file Tomography.java.

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56  {
57  return previous;
58  }
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Definition at line 49 of file Tomography.java.

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51  this.next = next;
52  }
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Definition at line 44 of file Tomography.java.

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45  {
46  this.previous = previous;
47  }
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27  {
28  super(limit + 1);
29 
30  this.limit = limit;
31  }
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68  {
69  T object = super.get((K) key);
70 
71  if (object != null) { // Object has been referenced, so place it at higher position.
72  remove((K) key);
73  put((K) key, (T) object);
74  }
75 
76  return object;
77  }
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Definition at line 33 of file Cache.java.

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34  {
35  int imageSize = thumb_height * thumb_width * Cache.MAXPXSIZE;
36  int elements = imageSize > 0 ? Cache.MEMORY_SIZE / imageSize : 1;
37  if(elements > 512)//Too many elements cause memory issues
38  elements = 512;
39  return elements;
40  }
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81  {
82  return size() > limit;
83  }
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43  {
44  // If new limit is lower than previous, remaining items are removed.
45  DEBUG.printMessage(" *** Cache: resizing to: [" + limit + "] elements");
46  //DEBUG.printMessage(" *** this.limit: [" + this.limit + "] / limit: [" + limit + "]");
47 
48  if (this.limit > limit && limit < size()) {
49  Iterator iter = keySet().iterator();
50  int items2remove = size() - limit;
51  ArrayList toRemove = new ArrayList(items2remove);
52 
53  // To avoid synchronizing problems, store items in a temporary array...
54  while (items2remove-- > 0) {
55  toRemove.add(iter.next());
56  }
57 
58  // ...and remove them later.
59  for (Object o : toRemove) {
60  remove(o);
61  }
62  }
63 
64  this.limit = limit;
65  }
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Definition at line 20 of file Cache.java.

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Definition at line 19 of file Cache.java.

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xmipp.utils.ColorEditor Class Reference
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-Public Member Functions

 ColorEditor ()
 
 ColorEditor (float position)
 
void actionPerformed (ActionEvent e)
 
Object getCellEditorValue ()
 
Component getTableCellEditorComponent (JTable table, Object value, boolean isSelected, int row, int column)
 
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-Static Public Member Functions

static Color stringToColor (String input)
 
static String colorToString (Color c)
 
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-Static Protected Attributes

static final String EDIT = "edit"
 
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Detailed Description

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Definition at line 52 of file ColorEditor.java.

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◆ ColorEditor() [1/2]

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Definition at line 59 of file ColorEditor.java.

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59  {
60  this(0.0f);
61  }
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Definition at line 63 of file ColorEditor.java.

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63  {
64  this.position = position;
65 
66  // Set up the editor (from the table's point of view),
67  // which is a button.
68  // This button brings up the color chooser dialog,
69  // which is the editor from the user's point of view.
70  button = new JButton();
71  button.addActionListener(this);
72  button.setBorderPainted(false);
73  }
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◆ actionPerformed()

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void xmipp.utils.ColorEditor.actionPerformed (ActionEvent e)
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Handles events from the editor button and from the dialog's OK button.

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Definition at line 78 of file ColorEditor.java.

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78  {
79  button.setBackground(currentColor);
80  Color c = JColorChooser
81  .showDialog(button, "Pick a Color", currentColor);
82  if (c != null)
83  currentColor = c;
84  fireEditingStopped();
85  }
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Definition at line 109 of file ColorEditor.java.

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109  {
110  if (c == null)
111  return null;
112  String rgb = Integer.toHexString(c.getRGB());
113  return rgb.substring(2, rgb.length());
114  }
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Definition at line 88 of file ColorEditor.java.

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88  {
89  return currentColor;
90  }
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Definition at line 93 of file ColorEditor.java.

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94  {
95  currentColor = (Color) value;
96  return button;
97  }
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◆ stringToColor()

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Definition at line 99 of file ColorEditor.java.

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99  {
100  try {
101  return Color.decode("0x" + input);
102  }
103  catch (Exception ex){
104  ex.printStackTrace();
105  return null;
106  }
107  }
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◆ EDIT

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final String xmipp.utils.ColorEditor.EDIT = "edit"
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Definition at line 56 of file ColorEditor.java.

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ColorIcon(Color c)xmipp.utils.ColorIconinline
ColorIcon(Color c, int w, int h)xmipp.utils.ColorIconinline
ColorIcon(Color c, int w, int h, int g, boolean isRounded, boolean withborder)xmipp.utils.ColorIconinline
getColor()xmipp.utils.ColorIconinline
getGap()xmipp.utils.ColorIconinline
getIconHeight()xmipp.utils.ColorIconinline
getIconWidth()xmipp.utils.ColorIconinline
paintIcon(Component c, Graphics g, int x, int y)xmipp.utils.ColorIconinline
setColor(Color value)xmipp.utils.ColorIconinline
setGap(int g)xmipp.utils.ColorIconinline
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-Public Member Functions

 ColorIcon (Color c)
 
 ColorIcon (Color c, int w, int h)
 
 ColorIcon (Color c, int w, int h, int g, boolean isRounded, boolean withborder)
 
int getIconWidth ()
 
int getIconHeight ()
 
Color getColor ()
 
void setColor (Color value)
 
int getGap ()
 
void setGap (int g)
 
void paintIcon (Component c, Graphics g, int x, int y)
 
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Detailed Description

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The ColoredRectangleIcon will paint a simple rectagle icon. The icon will ve painted with a specified color.

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Definition at line 14 of file ColorIcon.java.

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◆ ColorIcon() [1/3]

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Definition at line 23 of file ColorIcon.java.

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24  {
25  this(c, 16, 16);
26  }
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Definition at line 28 of file ColorIcon.java.

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29  {
30  this(c, w, h, 0, true, true);
31  }
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Definition at line 33 of file ColorIcon.java.

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34  {
35  color = c;
36  width = w;
37  height = h;
38  gap = g;
39  rounded = isRounded;
40  this.withborder = withborder;
41 
42  }// Constructor
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◆ getColor()

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Definition at line 67 of file ColorIcon.java.

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68  {
69  return color;
70  }
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Definition at line 77 of file ColorIcon.java.

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78  {
79  return gap;
80  }
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Gets the height of this icon.

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Definition at line 62 of file ColorIcon.java.

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63  {
64  return height;
65  }
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Definition at line 51 of file ColorIcon.java.

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52  {
53  return width;
54  }
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Paint the icons of this compound icon at the specified location

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xthe X coordinate of the icon's top-left corner
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Definition at line 100 of file ColorIcon.java.

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101  {
102  x += gap;
103  y += gap;
104  int w = width - 2 * gap;
105  int h = height - 2 * gap;
106  g.setColor(color);
107  if (rounded)
108  g.fillRoundRect(x, y, w, h, ROUND_WIDTH, ROUND_WIDTH);
109  else
110  g.fillRect(x, y, w, h);
111  if (withborder)
112  {
113  g.setColor(Color.black);
114  if (rounded)
115  g.drawRoundRect(x, y, w, h, ROUND_WIDTH, ROUND_WIDTH);
116  else
117  g.drawRect(x, y, w, h);
118  }
119  }
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Definition at line 72 of file ColorIcon.java.

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73  {
74  color = value;
75  }
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Definition at line 82 of file ColorIcon.java.

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83  {
84  gap = g;
85  }
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ColorRenderer()xmipp.utils.ColorRendererinline
getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)xmipp.utils.ColorRendererinline
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 ColorRenderer ()
 
Component getTableCellRendererComponent (JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)
 
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Detailed Description

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Used by CLegendJDialog to display colors on legend.

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Author
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Definition at line 42 of file ColorRenderer.java.

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◆ ColorRenderer()

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Definition at line 46 of file ColorRenderer.java.

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46  {
47  setOpaque(true); //MUST do this for background to show up.
48  setHorizontalAlignment(JLabel.CENTER);
49  }
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◆ getTableCellRendererComponent()

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Definition at line 52 of file ColorRenderer.java.

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54  {
55  color = (Color)value;
56  setIcon(new ColorIcon(color));
57  return this;
58  }
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xmipp.utils.CompoundIcon Member List
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This is the complete list of members for xmipp.utils.CompoundIcon, including all inherited members.

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BOTTOMxmipp.utils.CompoundIconstatic
CENTERxmipp.utils.CompoundIconstatic
CompoundIcon(Icon... icons)xmipp.utils.CompoundIconinline
CompoundIcon(Axis axis, Icon... icons)xmipp.utils.CompoundIconinline
CompoundIcon(Axis axis, int gap, Icon... icons)xmipp.utils.CompoundIconinline
CompoundIcon(Axis axis, int gap, float alignmentX, float alignmentY, Icon... icons)xmipp.utils.CompoundIconinline
getAlignmentX()xmipp.utils.CompoundIconinline
getAlignmentY()xmipp.utils.CompoundIconinline
getAxis()xmipp.utils.CompoundIconinline
getGap()xmipp.utils.CompoundIconinline
getIcon(int index)xmipp.utils.CompoundIconinline
getIconCount()xmipp.utils.CompoundIconinline
getIconHeight()xmipp.utils.CompoundIconinline
getIconWidth()xmipp.utils.CompoundIconinline
LEFTxmipp.utils.CompoundIconstatic
paintIcon(Component c, Graphics g, int x, int y)xmipp.utils.CompoundIconinline
RIGHTxmipp.utils.CompoundIconstatic
TOPxmipp.utils.CompoundIconstatic
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xmipp.utils.CompoundIcon Class Reference
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-Classes

enum  Axis
 
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-Public Member Functions

 CompoundIcon (Icon... icons)
 
 CompoundIcon (Axis axis, Icon... icons)
 
 CompoundIcon (Axis axis, int gap, Icon... icons)
 
 CompoundIcon (Axis axis, int gap, float alignmentX, float alignmentY, Icon... icons)
 
Axis getAxis ()
 
int getGap ()
 
float getAlignmentX ()
 
float getAlignmentY ()
 
int getIconCount ()
 
Icon getIcon (int index)
 
int getIconWidth ()
 
int getIconHeight ()
 
void paintIcon (Component c, Graphics g, int x, int y)
 
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-Static Public Attributes

static final float TOP = 0.0f
 
static final float LEFT = 0.0f
 
static final float CENTER = 0.5f
 
static final float BOTTOM = 1.0f
 
static final float RIGHT = 1.0f
 
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Detailed Description

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The CompoundIcon will paint two, or more, Icons as a single Icon. The Icons are painted in the order in which they are added.

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The Icons are laid out on the specified axis:

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Definition at line 21 of file CompoundIcon.java.

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◆ CompoundIcon() [1/4]

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xmipp.utils.CompoundIcon.CompoundIcon (Icon... icons)
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Convenience contructor for creating a CompoundIcon where the icons are laid out on on the X-AXIS, the gap is 0 and the X/Y alignments will default to CENTER.

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iconsthe Icons to be painted as part of the CompoundIcon
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Definition at line 52 of file CompoundIcon.java.

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53  {
54  this(Axis.X_AXIS, icons);
55  }
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Convenience contructor for creating a CompoundIcon where the gap is 0 and the X/Y alignments will default to CENTER.

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axisthe axis used to lay out the icons for painting. Must be one of the Axis enums: X_AXIS, Y_AXIS, Z_Axis.
iconsthe Icons to be painted as part of the CompoundIcon
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Definition at line 65 of file CompoundIcon.java.

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66  {
67  this(axis, 0, icons);
68  }
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xmipp.utils.CompoundIcon.CompoundIcon (Axis axis,
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Convenience contructor for creating a CompoundIcon where the X/Y alignments will default to CENTER.

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axisthe axis used to lay out the icons for painting Must be one of the Axis enums: X_AXIS, Y_AXIS, Z_Axis.
gapthe gap between the icons
iconsthe Icons to be painted as part of the CompoundIcon
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Definition at line 79 of file CompoundIcon.java.

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80  {
81  this(axis, gap, CENTER, CENTER, icons);
82  }
xmipp.utils.CompoundIcon.CENTER
static final float CENTER
Definition: CompoundIcon.java:32
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xmipp.utils.CompoundIcon.CompoundIcon (Axis axis,
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Create a CompoundIcon specifying all the properties.

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axisthe axis used to lay out the icons for painting Must be one of the Axis enums: X_AXIS, Y_AXIS, Z_Axis.
gapthe gap between the icons
alignmentXthe X alignment of the icons. Common values are LEFT, CENTER, RIGHT. Can be any value between 0.0 and 1.0
alignmentYthe Y alignment of the icons. Common values are TOP, CENTER, BOTTOM. Can be any value between 0.0 and 1.0
iconsthe Icons to be painted as part of the CompoundIcon
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Definition at line 96 of file CompoundIcon.java.

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97  {
98  this.axis = axis;
99  this.gap = gap;
100  this.alignmentX = alignmentX > 1.0f ? 1.0f : alignmentX < 0.0f ? 0.0f : alignmentX;
101  this.alignmentY = alignmentY > 1.0f ? 1.0f : alignmentY < 0.0f ? 0.0f : alignmentY;
102 
103  for (int i = 0; i < icons.length; i++)
104  {
105  if (icons[i] == null)
106  {
107  String message = "Icon (" + i + ") cannot be null";
108  throw new IllegalArgumentException( message );
109  }
110  }
111 
112  this.icons = icons;
113  }
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◆ getAlignmentX()

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float xmipp.utils.CompoundIcon.getAlignmentX ()
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Get the alignment of the icon on the x-axis

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Definition at line 140 of file CompoundIcon.java.

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141  {
142  return alignmentX;
143  }
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Get the alignment of the icon on the y-axis

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Definition at line 150 of file CompoundIcon.java.

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151  {
152  return alignmentY;
153  }
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Get the Axis along which each icon is painted.

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Definition at line 120 of file CompoundIcon.java.

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121  {
122  return axis;
123  }
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Get the gap between each icon

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Definition at line 130 of file CompoundIcon.java.

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131  {
132  return gap;
133  }
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Get the Icon at the specified index.

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Definition at line 172 of file CompoundIcon.java.

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173  {
174  return icons[ index ];
175  }
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Get the number of Icons contained in this CompoundIcon.

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Definition at line 160 of file CompoundIcon.java.

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161  {
162  return icons.length;
163  }
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Gets the height of this icon.

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Definition at line 213 of file CompoundIcon.java.

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214  {
215  int height = 0;
216 
217  // Add the height of all Icons while also including the gap
218 
219  if (axis == Axis.Y_AXIS)
220  {
221  height += (icons.length - 1) * gap;
222 
223  for (Icon icon : icons)
224  height += icon.getIconHeight();
225  }
226  else // Just find the maximum height
227  {
228  for (Icon icon : icons)
229  height = Math.max(height, icon.getIconHeight());
230  }
231 
232  return height;
233  }
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Gets the width of this icon.

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Definition at line 185 of file CompoundIcon.java.

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186  {
187  int width = 0;
188 
189  // Add the width of all Icons while also including the gap
190 
191  if (axis == Axis.X_AXIS)
192  {
193  width += (icons.length - 1) * gap;
194 
195  for (Icon icon : icons)
196  width += icon.getIconWidth();
197  }
198  else // Just find the maximum width
199  {
200  for (Icon icon : icons)
201  width = Math.max(width, icon.getIconWidth());
202  }
203 
204  return width;
205  }
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Paint the icons of this compound icon at the specified location

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gthe graphics context
xthe X coordinate of the icon's top-left corner
ythe Y coordinate of the icon's top-left corner
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Definition at line 244 of file CompoundIcon.java.

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245  {
246  if (axis == Axis.X_AXIS)
247  {
248  int height = getIconHeight();
249 
250  for (Icon icon : icons)
251  {
252  int iconY = getOffset(height, icon.getIconHeight(), alignmentY);
253  icon.paintIcon(c, g, x, y + iconY);
254  x += icon.getIconWidth() + gap;
255  }
256  }
257  else if (axis == Axis.Y_AXIS)
258  {
259  int width = getIconWidth();
260 
261  for (Icon icon : icons)
262  {
263  int iconX = getOffset(width, icon.getIconWidth(), alignmentX);
264  icon.paintIcon(c, g, x + iconX, y);
265  y += icon.getIconHeight() + gap;
266  }
267  }
268  else // must be Z_AXIS
269  {
270  int width = getIconWidth();
271  int height = getIconHeight();
272 
273  for (Icon icon : icons)
274  {
275  int iconX = getOffset(width, icon.getIconWidth(), alignmentX);
276  int iconY = getOffset(height, icon.getIconHeight(), alignmentY);
277  icon.paintIcon(c, g, x + iconX, y + iconY);
278  }
279  }
280  }
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Definition at line 33 of file CompoundIcon.java.

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Definition at line 32 of file CompoundIcon.java.

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Definition at line 31 of file CompoundIcon.java.

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Definition at line 34 of file CompoundIcon.java.

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Definition at line 30 of file CompoundIcon.java.

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enableDebug(boolean enable)xmipp.utils.DEBUGinlinestatic
hasScipionDebug()xmipp.utils.DEBUGinlinestatic
millisecsxmipp.utils.DEBUGstatic
printException(Exception ex)xmipp.utils.DEBUGinlinestatic
printFormat(String format, Object...objects)xmipp.utils.DEBUGinlinestatic
printMessage(String message)xmipp.utils.DEBUGinlinestatic
printStackTrace()xmipp.utils.DEBUGinlinestatic
tic()xmipp.utils.DEBUGinlinestatic
toc()xmipp.utils.DEBUGinlinestatic
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static void enableDebug (boolean enable)
 
static void printMessage (String message)
 
static void printFormat (String format, Object...objects)
 
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static void printStackTrace ()
 
static boolean hasScipionDebug ()
 
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static long millisecs
 
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Author
Juanjo Vega
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Definition at line 10 of file DEBUG.java.

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◆ enableDebug()

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15  DEBUG = enable;
16  }
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44  String debug = System.getenv("SCIPION_DEBUG");
45  return (debug != null && debug.equals("1"));
46  }
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26  System.out.format(format+"\n", objects);
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37  if (DEBUG){
38  Exception ex = new Exception();
39  ex.printStackTrace();
40  }
41  }
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51  {
52  millisecs = System.currentTimeMillis();
53  return millisecs;
54  }
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56  {
57  long current = System.currentTimeMillis();
58  long result = current - millisecs;
59  millisecs = current;
60  System.out.format("took: %d milliseconds %n", result);
61  return result;
62  }
xmipp.utils.DEBUG.millisecs
static long millisecs
Definition: DEBUG.java:49
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getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)xmipp.utils.ImageRendererinline
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-Public Member Functions

Component getTableCellRendererComponent (JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)
 
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Detailed Description

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Author
airen
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Definition at line 20 of file ImageRenderer.java.

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Member Function Documentation

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◆ getTableCellRendererComponent()

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)
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Definition at line 25 of file ImageRenderer.java.

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26  {
27  lbl.setIcon((ImageIcon)value);
28  return lbl;
29  }
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alphaLevelxmipp.utils.InfiniteProgressPanelprotected
animationxmipp.utils.InfiniteProgressPanelprotected
barsCountxmipp.utils.InfiniteProgressPanelprotected
fpsxmipp.utils.InfiniteProgressPanelprotected
getText()xmipp.utils.InfiniteProgressPanelinline
hintsxmipp.utils.InfiniteProgressPanelprotected
InfiniteProgressPanel()xmipp.utils.InfiniteProgressPanelinline
InfiniteProgressPanel(String text)xmipp.utils.InfiniteProgressPanelinline
InfiniteProgressPanel(Window window, String text)xmipp.utils.InfiniteProgressPanelinline
InfiniteProgressPanel(String text, int barsCount)xmipp.utils.InfiniteProgressPanelinline
InfiniteProgressPanel(String text, int barsCount, float shield)xmipp.utils.InfiniteProgressPanelinline
InfiniteProgressPanel(String text, int barsCount, float shield, float fps)xmipp.utils.InfiniteProgressPanelinline
InfiniteProgressPanel(String text, int barsCount, float shield, float fps, int rampDelay)xmipp.utils.InfiniteProgressPanelinline
interrupt()xmipp.utils.InfiniteProgressPanelinline
mouseClicked(MouseEvent e)xmipp.utils.InfiniteProgressPanelinline
mouseEntered(MouseEvent e)xmipp.utils.InfiniteProgressPanelinline
mouseExited(MouseEvent e)xmipp.utils.InfiniteProgressPanelinline
mousePressed(MouseEvent e)xmipp.utils.InfiniteProgressPanelinline
mouseReleased(MouseEvent e)xmipp.utils.InfiniteProgressPanelinline
paintComponent(Graphics g)xmipp.utils.InfiniteProgressPanelinline
rampDelayxmipp.utils.InfiniteProgressPanelprotected
setText(String text)xmipp.utils.InfiniteProgressPanelinline
shieldxmipp.utils.InfiniteProgressPanelprotected
start()xmipp.utils.InfiniteProgressPanelinline
startedxmipp.utils.InfiniteProgressPanelprotected
stop()xmipp.utils.InfiniteProgressPanelinline
textxmipp.utils.InfiniteProgressPanelprotected
tickerxmipp.utils.InfiniteProgressPanelprotected
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-Public Member Functions

 InfiniteProgressPanel ()
 
 InfiniteProgressPanel (String text)
 
 InfiniteProgressPanel (Window window, String text)
 
 InfiniteProgressPanel (String text, int barsCount)
 
 InfiniteProgressPanel (String text, int barsCount, float shield)
 
 InfiniteProgressPanel (String text, int barsCount, float shield, float fps)
 
 InfiniteProgressPanel (String text, int barsCount, float shield, float fps, int rampDelay)
 
void setText (String text)
 
String getText ()
 
void start ()
 
void stop ()
 
void interrupt ()
 
void paintComponent (Graphics g)
 
void mouseClicked (MouseEvent e)
 
void mousePressed (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
void mouseEntered (MouseEvent e)
 
void mouseExited (MouseEvent e)
 
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-Protected Attributes

Area [] ticker = null
 
Thread animation = null
 
boolean started = false
 
int alphaLevel = 0
 
int rampDelay = 300
 
float shield = 0.70f
 
String text = ""
 
int barsCount = 14
 
float fps = 15.0f
 
RenderingHints hints = null
 
-

Detailed Description

-

An infinite progress panel displays a rotating figure and a message to notice the user of a long, duration unknown task. The shape and the text are drawn upon a white veil which alpha level (or shield value) lets the underlying component shine through. This panel is meant to be used asa glass pane in the window performing the long operation.
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- On the contrary to regular glass panes, you don't need to set it visible or not by yourself. Once you've started the animation all the mouse events are intercepted by this panel, preventing them from being forwared to the underlying components.
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InfiniteProgressPanel pane = new InfiniteProgressPanel();
-frame.setGlassPane(pane);
-pane.start()


-
- Several properties can be configured at creation time. The message and its font can be changed at runtime. Changing the font can be done using setFont() and setForeground().

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Author
Romain Guy
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Version
1.0
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Definition at line 58 of file InfiniteProgressPanel.java.

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Creates a new progress panel with default values:
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Definition at line 92 of file InfiniteProgressPanel.java.

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92  {
93  this("");
94  }
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Creates a new progress panel with default values:
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textThe message to be displayed. Can be null or empty.
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Definition at line 106 of file InfiniteProgressPanel.java.

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106  {
107  this(text, 14);
108  }
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Definition at line 110 of file InfiniteProgressPanel.java.

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110  {
111 
112  this(text, 14);
113  this.window = window;
114  }
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Creates a new progress panel with default values:
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textThe message to be displayed. Can be null or empty.
barsCountThe amount of bars composing the circular shape
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Definition at line 126 of file InfiniteProgressPanel.java.

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126  {
127  this(text, barsCount, 0.70f);
128  }
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Creates a new progress panel with default values:
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textThe message to be displayed. Can be null or empty.
barsCountThe amount of bars composing the circular shape.
shieldThe alpha level between 0.0 and 1.0 of the colored shield (or veil).
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Definition at line 141 of file InfiniteProgressPanel.java.

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141  {
142  this(text, barsCount, shield, 15.0f);
143  }
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Creates a new progress panel with default values:
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textThe message to be displayed. Can be null or empty.
barsCountThe amount of bars composing the circular shape.
shieldThe alpha level between 0.0 and 1.0 of the colored shield (or veil).
fpsThe number of frames per second. Lower this value to decrease CPU usage.
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Definition at line 157 of file InfiniteProgressPanel.java.

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157  {
158  this(text, barsCount, shield, fps, 300);
159  }
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Creates a new progress panel.

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textThe message to be displayed. Can be null or empty.
barsCountThe amount of bars composing the circular shape.
shieldThe alpha level between 0.0 and 1.0 of the colored shield (or veil).
fpsThe number of frames per second. Lower this value to decrease CPU usage.
rampDelayThe duration, in milli seconds, of the fade in and the fade out of the veil.
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Definition at line 172 of file InfiniteProgressPanel.java.

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172  {
173  this.text = text;
174  this.rampDelay = rampDelay >= 0 ? rampDelay : 0;
175  this.shield = shield >= 0.0f ? shield : 0.0f;
176  this.fps = fps > 0.0f ? fps : 15.0f;
177  this.barsCount = barsCount > 0 ? barsCount : 14;
178 
179  this.hints = new RenderingHints(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY);
180  this.hints.put(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
181  this.hints.put(RenderingHints.KEY_FRACTIONALMETRICS, RenderingHints.VALUE_FRACTIONALMETRICS_ON);
182  }
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Definition at line 197 of file InfiniteProgressPanel.java.

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197  {
198  return text;
199  }
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Interrupts the animation, whatever its state is. You can use it when you need to stop the animation without running the fade out phase. This methods sets the panel invisible at the end.

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Definition at line 234 of file InfiniteProgressPanel.java.

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234  {
235  if (animation != null) {
236  animation.interrupt();
237  animation = null;
238 
239  removeMouseListener(this);
240  setVisible(false);
241  }
242  }
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Definition at line 404 of file InfiniteProgressPanel.java.

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Definition at line 413 of file InfiniteProgressPanel.java.

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Definition at line 416 of file InfiniteProgressPanel.java.

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Definition at line 407 of file InfiniteProgressPanel.java.

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Definition at line 410 of file InfiniteProgressPanel.java.

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Definition at line 247 of file InfiniteProgressPanel.java.

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247  {
248  if (started) {
249  int width = (window != null)? window.getWidth(): getWidth();
250  int height = (window != null)? window.getHeight(): getHeight();
251  double maxY = 0.0;
252 
253  Graphics2D g2 = (Graphics2D) g;
254  g2.setRenderingHints(hints);
255 
256  g2.setColor(new Color(255, 255, 255, (int) (alphaLevel * shield)));
257  g2.fillRect(0, 0, width, height);
258 
259  AffineTransform oCenterT = AffineTransform.getTranslateInstance(
260  (double) width / 2.,
261  (double) height / 2.);
262 
263  g2.transform(oCenterT);
264 
265  for (int i = 0; i < ticker.length; i++) {
266  int channel = 224 - 128 / (i + 1);
267  g2.setColor(new Color(channel, channel, channel, alphaLevel));
268  g2.fill(ticker[i]);
269 
270  Rectangle2D bounds = ticker[i].getBounds2D();
271  if (bounds.getMaxY() > maxY) {
272  maxY = bounds.getMaxY();
273  }
274  }
275 
276  try {
277  g2.transform(oCenterT.createInverse());
278  } catch (Exception e) {
279  }
280 
281  if (text != null && text.length() > 0) {
282  FontRenderContext context = g2.getFontRenderContext();
283  TextLayout layout = new TextLayout(text, getFont(), context);
284  Rectangle2D bounds = layout.getBounds();
285  g2.setColor(getForeground());
286  layout.draw(g2, (float) (width - bounds.getWidth()) / 2,
287  (float) (maxY + layout.getLeading() + 2 * layout.getAscent()));
288  }
289  }
290  }
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Changes the displayed message at runtime.

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Definition at line 189 of file InfiniteProgressPanel.java.

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189  {
190  this.text = text;
191  repaint();
192  }
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Starts the waiting animation by fading the veil in, then rotating the shapes. This method handles the visibility of the glass pane.

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Definition at line 206 of file InfiniteProgressPanel.java.

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206  {
207  addMouseListener(this);
208  setVisible(true);
209  ticker = buildTicker();
210  animation = new Thread(new Animator(true),"Progress panel");
211  animation.start();
212  }
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Stops the waiting animation by stopping the rotation of the circular shape and then by fading out the veil. This methods sets the panel invisible at the end.

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Definition at line 219 of file InfiniteProgressPanel.java.

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219  {
220  if (animation != null) {
221  animation.interrupt();
222  animation = null;
223  animation = new Thread(new Animator(false));
224  animation.start();
225  }
226  }
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int xmipp.utils.InfiniteProgressPanel.alphaLevel = 0
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Alpha level of the veil, used for fade in/out.

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Definition at line 67 of file InfiniteProgressPanel.java.

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The animation thread is responsible for fade in/out and rotation.

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Definition at line 63 of file InfiniteProgressPanel.java.

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Amount of bars composing the circular shape.

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Definition at line 75 of file InfiniteProgressPanel.java.

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Amount of frames per seconde. Lowers this to save CPU.

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Definition at line 77 of file InfiniteProgressPanel.java.

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Rendering hints to set anti aliasing.

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Definition at line 79 of file InfiniteProgressPanel.java.

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Duration of the veil's fade in/out.

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Definition at line 69 of file InfiniteProgressPanel.java.

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Alpha level of the veil.

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Definition at line 71 of file InfiniteProgressPanel.java.

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Notifies whether the animation is running or not.

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Message displayed below the circular shape.

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Definition at line 73 of file InfiniteProgressPanel.java.

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Contains the bars composing the circular shape.

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Definition at line 61 of file InfiniteProgressPanel.java.

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- - diff --git a/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__coll__graph.dot b/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__coll__graph.dot deleted file mode 100644 index 859c6957..00000000 --- a/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__coll__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.utils.InfiniteProgressPanel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="xmipp.utils.InfiniteProgress\lPanel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="JComponent",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="MouseListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" hints" ,fontname="Helvetica"]; - Node6 [label="RenderingHints",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ticker" ,fontname="Helvetica"]; - Node7 [label="Area",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__coll__graph.md5 b/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__coll__graph.md5 deleted file mode 100644 index 6a54999e..00000000 --- a/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -73d3d94735cd94f1c49bef62bf59d067 \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__inherit__graph.dot b/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__inherit__graph.dot deleted file mode 100644 index 16a1502f..00000000 --- a/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.utils.InfiniteProgressPanel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.utils.InfiniteProgress\lPanel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JComponent",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="MouseListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__inherit__graph.md5 b/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__inherit__graph.md5 deleted file mode 100644 index 1f7bdeb4..00000000 --- a/html/classxmipp_1_1utils_1_1InfiniteProgressPanel__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -a15840a76b3d4b74e2e232c3f3e5f3f1 \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1MultilineCellRenderer-members.html b/html/classxmipp_1_1utils_1_1MultilineCellRenderer-members.html deleted file mode 100644 index c21c302b..00000000 --- a/html/classxmipp_1_1utils_1_1MultilineCellRenderer-members.html +++ /dev/null @@ -1,84 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.utils.MultilineCellRenderer Member List
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This is the complete list of members for xmipp.utils.MultilineCellRenderer, including all inherited members.

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getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)xmipp.utils.MultilineCellRendererinline
MultilineCellRenderer()xmipp.utils.MultilineCellRendererinline
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- - diff --git a/html/classxmipp_1_1utils_1_1MultilineCellRenderer.html b/html/classxmipp_1_1utils_1_1MultilineCellRenderer.html deleted file mode 100644 index dcfa13d9..00000000 --- a/html/classxmipp_1_1utils_1_1MultilineCellRenderer.html +++ /dev/null @@ -1,202 +0,0 @@ - - - - - - - -Xmipp: xmipp.utils.MultilineCellRenderer Class Reference - - - - - - - - - -
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-Public Member Functions

 MultilineCellRenderer ()
 
Component getTableCellRendererComponent (JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column)
 
-

Detailed Description

-
Version
1.0 11/09/98
- -

Definition at line 12 of file MultilineCellRenderer.java.

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Constructor & Destructor Documentation

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◆ MultilineCellRenderer()

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xmipp.utils.MultilineCellRenderer.MultilineCellRenderer ()
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Definition at line 14 of file MultilineCellRenderer.java.

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14  {
15  setLineWrap(true);
16  setWrapStyleWord(true);
17  setOpaque(true);
18  }
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Member Function Documentation

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◆ getTableCellRendererComponent()

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Component xmipp.utils.MultilineCellRenderer.getTableCellRendererComponent (JTable table,
Object value,
boolean isSelected,
boolean hasFocus,
int row,
int column 
)
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Definition at line 20 of file MultilineCellRenderer.java.

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21  {
22  if (isSelected) {
23  setForeground(table.getSelectionForeground());
24  setBackground(table.getSelectionBackground());
25  } else {
26  setForeground(table.getForeground());
27  setBackground(table.getBackground());
28  }
29  setFont(table.getFont());
30  if (hasFocus) {
31  setBorder( UIManager.getBorder("Table.focusCellHighlightBorder") );
32  if (table.isCellEditable(row, column)) {
33  setForeground( UIManager.getColor("Table.focusCellForeground") );
34  setBackground( UIManager.getColor("Table.focusCellBackground") );
35  }
36  } else {
37  setBorder(new EmptyBorder(1, 2, 1, 2));
38  }
39  setText((value == null) ? "" : value.toString());
40  return this;
41  }
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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1utils_1_1MultilineCellRenderer__coll__graph.dot b/html/classxmipp_1_1utils_1_1MultilineCellRenderer__coll__graph.dot deleted file mode 100644 index 5cc13476..00000000 --- a/html/classxmipp_1_1utils_1_1MultilineCellRenderer__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.utils.MultilineCellRenderer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="xmipp.utils.MultilineCell\lRenderer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="JTextArea",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="TableCellRenderer",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1MultilineCellRenderer__coll__graph.md5 b/html/classxmipp_1_1utils_1_1MultilineCellRenderer__coll__graph.md5 deleted file mode 100644 index e55e072c..00000000 --- a/html/classxmipp_1_1utils_1_1MultilineCellRenderer__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -b2180e4e06761dd8c23e4ddb0c2b474c \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1MultilineCellRenderer__inherit__graph.dot b/html/classxmipp_1_1utils_1_1MultilineCellRenderer__inherit__graph.dot deleted file mode 100644 index 29953dfa..00000000 --- a/html/classxmipp_1_1utils_1_1MultilineCellRenderer__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.utils.MultilineCellRenderer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.utils.MultilineCell\lRenderer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JTextArea",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="TableCellRenderer",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1MultilineCellRenderer__inherit__graph.md5 b/html/classxmipp_1_1utils_1_1MultilineCellRenderer__inherit__graph.md5 deleted file mode 100644 index 19b1d4c0..00000000 --- a/html/classxmipp_1_1utils_1_1MultilineCellRenderer__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -1ce57446a17bfb7724a013bbcfdb79b9 \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1Params-members.html b/html/classxmipp_1_1utils_1_1Params-members.html deleted file mode 100644 index c8e31629..00000000 --- a/html/classxmipp_1_1utils_1_1Params-members.html +++ /dev/null @@ -1,166 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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This is the complete list of members for xmipp.utils.Params, including all inherited members.

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BAD_PIXELS_FACTORxmipp.utils.Paramsstatic
bad_pixels_factorxmipp.utils.Params
CHIMERAPORTxmipp.utils.Paramsstatic
chimeraPortxmipp.utils.Params
classesFilenamexmipp.utils.Params
cmdLinexmipp.utils.Paramsprotected
dataFilenamexmipp.utils.Params
DEBUGxmipp.utils.Paramsstatic
debugxmipp.utils.Params
defineArgs()xmipp.utils.Paramsinline
directoryxmipp.utils.Params
DIRECTORYxmipp.utils.Paramsstatic
DISPLAY_LABELSxmipp.utils.Paramsstatic
displayLabelsxmipp.utils.Params
DOWNSAMPLINGxmipp.utils.Paramsstatic
downsamplingxmipp.utils.Params
FILExmipp.utils.Paramsstatic
filesxmipp.utils.Params
FILTERxmipp.utils.Paramsstatic
FILTERS_SEPARATORxmipp.utils.Paramsstatic
getBlock()xmipp.utils.Paramsinline
getChimeraPort()xmipp.utils.Paramsinline
getDisplayLabels()xmipp.utils.Paramsinline
getRenderLabel()xmipp.utils.Paramsinline
getSamplingRate()xmipp.utils.Paramsinline
INPUT_CLASSESFILExmipp.utils.Paramsstatic
INPUT_DATAFILExmipp.utils.Paramsstatic
INPUT_VECTORSFILExmipp.utils.Paramsstatic
INVERTYxmipp.utils.Paramsstatic
invertyxmipp.utils.Params
isMask()xmipp.utils.Paramsinline
MASKxmipp.utils.Paramsstatic
mask_toolbarxmipp.utils.Params
maskFilenamexmipp.utils.Params
MASKTOOLBARxmipp.utils.Paramsstatic
modexmipp.utils.Params
NO_GEOxmipp.utils.Paramsstatic
NO_WRAPxmipp.utils.Paramsstatic
OBJECT_CMDSxmipp.utils.Paramsstatic
objectCommandsxmipp.utils.Params
OPENING_MODExmipp.utils.Paramsstatic
OPENING_MODE_DEFAULTxmipp.utils.Paramsstatic
OPENING_MODE_GALLERYxmipp.utils.Paramsstatic
OPENING_MODE_IMAGExmipp.utils.Paramsstatic
OPENING_MODE_METADATAxmipp.utils.Paramsstatic
optionsxmipp.utils.Paramsprotected
ORDER_LABELSxmipp.utils.Paramsstatic
orderLabelsxmipp.utils.Params
Params()xmipp.utils.Paramsinline
Params(String args[])xmipp.utils.Paramsinline
pollxmipp.utils.Params
POLLxmipp.utils.Paramsstatic
PORTxmipp.utils.Paramsstatic
portxmipp.utils.Params
processArgs(String args[])xmipp.utils.Paramsinline
RAISED_Wxmipp.utils.Paramsstatic
raised_wxmipp.utils.Params
recalculateCTFxmipp.utils.Params
RENDER_IMAGESxmipp.utils.Paramsstatic
renderImagesxmipp.utils.Params
renderLabelxmipp.utils.Params
renderLabelsxmipp.utils.Params
resliceViewxmipp.utils.Params
rowsxmipp.utils.Params
SAMPLINGRATExmipp.utils.Paramsstatic
setBlock(String block)xmipp.utils.Paramsinline
setChimeraPort(int i)xmipp.utils.Paramsinline
singleSelectionxmipp.utils.Params
sortbyxmipp.utils.Params
SORTBY_LABELxmipp.utils.Paramsstatic
TABLE_COLUMNSxmipp.utils.Paramsstatic
TABLE_ROWSxmipp.utils.Paramsstatic
useGeoxmipp.utils.Params
vectorsFilenamexmipp.utils.Params
VIEWxmipp.utils.Paramsstatic
VISIBLE_LABELSxmipp.utils.Paramsstatic
visibleLabelsxmipp.utils.Params
w1xmipp.utils.Params
W1xmipp.utils.Paramsstatic
w2xmipp.utils.Params
W2xmipp.utils.Paramsstatic
wrapxmipp.utils.Params
ZOOMxmipp.utils.Paramsstatic
zoomxmipp.utils.Params
- -
-Generated by   -doxygen - 1.8.13 -
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-Public Member Functions

 Params ()
 
 Params (String args[])
 
void defineArgs ()
 
void processArgs (String args[])
 
String getRenderLabel ()
 
String [] getDisplayLabels ()
 
void setBlock (String block)
 
String getBlock ()
 
boolean isMask ()
 
Float getSamplingRate ()
 
Integer getChimeraPort ()
 
void setChimeraPort (int i)
 
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-Public Attributes

String directory
 
String files []
 
Integer port
 
boolean singleSelection
 
String mode = OPENING_MODE_DEFAULT
 
boolean poll
 
Integer zoom
 
String [] renderLabels = new String[]{"first"}
 
String renderLabel
 
String [] displayLabels
 
boolean debug = false
 
boolean mask_toolbar = false
 
int rows = -1
 
double bad_pixels_factor
 
double w1
 
double w2
 
double raised_w
 
double downsampling
 
String maskFilename
 
String vectorsFilename
 
String classesFilename
 
String dataFilename
 
int resliceView = ImageGeneric.Z_NEG
 
boolean useGeo = true
 
boolean wrap = true
 
String [] visibleLabels
 
String [] orderLabels
 
String [] sortby
 
String [] objectCommands
 
Integer chimeraPort
 
boolean inverty
 
boolean renderImages = true
 
boolean recalculateCTF = true
 
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-Static Public Attributes

static final String FILE = "i"
 
static final String DIRECTORY = "dir"
 
static final String INPUT_VECTORSFILE = "vectors"
 
static final String INPUT_CLASSESFILE = "classes"
 
static final String INPUT_DATAFILE = "data"
 
static final String POLL = "poll"
 
static final String TABLE_ROWS = "rows"
 
static final String TABLE_COLUMNS = "columns"
 
static final String ZOOM = "zoom"
 
static final String OPENING_MODE = "mode"
 
static final String OPENING_MODE_DEFAULT = "default"
 
static final String OPENING_MODE_IMAGE = "image"
 
static final String OPENING_MODE_GALLERY = "gallery"
 
static final String OPENING_MODE_METADATA = "metadata"
 
static final String RENDER_IMAGES = "render"
 
static final String VISIBLE_LABELS = "visible"
 
static final String ORDER_LABELS = "order"
 
static final String SORTBY_LABEL = "sortby"
 
static final String DISPLAY_LABELS = "labels"
 
static final String FILTER = "filter"
 
static final String FILTERS_SEPARATOR = ","
 
static final String PORT = "port"
 
static final String DOWNSAMPLING = "downsampling"
 
static final String BAD_PIXELS_FACTOR = "factor"
 
static final String W1 = "w1"
 
static final String W2 = "w2"
 
static final String RAISED_W = "raised_w"
 
static final String MASK = "mask"
 
static final String DEBUG = "debug"
 
static final String MASKTOOLBAR = "mask_toolbar"
 
static final String VIEW = "view"
 
static final String NO_GEO = "dont_apply_geo"
 
static final String NO_WRAP = "dont_wrap"
 
static final String OBJECT_CMDS = "object_commands"
 
static final String SAMPLINGRATE = "sampling_rate"
 
static final String CHIMERAPORT = "chimera_port"
 
static final String INVERTY = "inverty"
 
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Definition at line 14 of file Params.java.

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Definition at line 96 of file Params.java.

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97  }
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Definition at line 99 of file Params.java.

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99  {
100  options = new Options();
101  defineArgs();
102  processArgs(args);
103  }
xmipp.utils.Params.options
Options options
Definition: Params.java:82
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xmipp.utils.Params.processArgs
void processArgs(String args[])
Definition: Params.java:169
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void xmipp.utils.Params.defineArgs ()
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Definition at line 105 of file Params.java.

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106  {
107  options.addOption(FILE, true, "");
108  // It should be able to handle multiple files.
109  options.getOption(FILE).setOptionalArg(true);
110  options.getOption(FILE).setArgs(Integer.MAX_VALUE);
111 
112  options.addOption(DIRECTORY, true, "");
113  options.addOption(PORT, true, "");
114 
115  options.addOption(OPENING_MODE, true, "");
116  options.addOption(POLL, false, "");
117  options.addOption(ZOOM, true, "");
118  Option opt = new Option(RENDER_IMAGES, true, "");
119  opt.setArgs(Integer.MAX_VALUE);
120  options.addOption(opt);
121  opt = new Option(VISIBLE_LABELS, "");
122  opt.setArgs(Integer.MAX_VALUE);
123  options.addOption(opt);
124  opt = new Option(ORDER_LABELS, "");
125  opt.setArgs(Integer.MAX_VALUE);
126  options.addOption(opt);
127 
128  opt = new Option(SORTBY_LABEL, "");
129  opt.setArgs(2);
130  options.addOption(opt);
131 
132  opt = new Option(DISPLAY_LABELS, "");
133  opt.setArgs(Integer.MAX_VALUE);
134  options.addOption(opt);
135  options.addOption(DEBUG, false, "");
136  options.addOption(MASKTOOLBAR, false, "");
137  options.addOption(TABLE_ROWS, true, "");
138  options.addOption(TABLE_COLUMNS, true, "");
139 
140  options.addOption(BAD_PIXELS_FACTOR, true, "");
141 
142  options.addOption(W1, true, "");
143  options.addOption(W2, true, "");
144  options.addOption(RAISED_W, true, "");
145 
146  options.addOption(DOWNSAMPLING, true, "");
147 
148  options.addOption(MASK, false, "");
149 
150  options.addOption(INPUT_VECTORSFILE, true, "");
151  options.addOption(INPUT_CLASSESFILE, true, "");
152  options.addOption(INPUT_DATAFILE, true, "");
153  options.addOption(VIEW, true, "z");
154  options.addOption(NO_GEO, false, "");
155  options.addOption(NO_WRAP, false, "");
156  opt = new Option(OBJECT_CMDS, "");
157  opt.setArgs(Integer.MAX_VALUE);
158  options.addOption(opt);
159  options.addOption(SAMPLINGRATE, true, "");
160  options.addOption(CHIMERAPORT, true, "");
161  options.addOption(INVERTY, false, "");
162  // Do not offer to recalculate CFT if true
163  options.addOption(NO_RECALCULATE_CTF, false, "");
164 
165 
166  }
xmipp.utils.Params.DIRECTORY
static final String DIRECTORY
Definition: Params.java:18
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xmipp.utils.Params.TABLE_COLUMNS
static final String TABLE_COLUMNS
Definition: Params.java:24
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xmipp.utils.Params.options
Options options
Definition: Params.java:82
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xmipp.utils.Params.W1
static final String W1
Definition: Params.java:41
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xmipp.utils.Params.MASKTOOLBAR
static final String MASKTOOLBAR
Definition: Params.java:46
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xmipp.utils.Params.FILE
static final String FILE
Definition: Params.java:17
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xmipp.utils.Params.PORT
static final String PORT
Definition: Params.java:38
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xmipp.utils.Params.W2
static final String W2
Definition: Params.java:42
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xmipp.utils.Params.NO_GEO
static final String NO_GEO
Definition: Params.java:48
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xmipp.utils.Params.DISPLAY_LABELS
static final String DISPLAY_LABELS
Definition: Params.java:35
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xmipp.utils.Params.ORDER_LABELS
static final String ORDER_LABELS
Definition: Params.java:33
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xmipp.utils.Params.OPENING_MODE
static final String OPENING_MODE
Definition: Params.java:26
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xmipp.utils.Params.VIEW
static final String VIEW
Definition: Params.java:47
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xmipp.utils.Params.NO_WRAP
static final String NO_WRAP
Definition: Params.java:49
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xmipp.utils.Params.TABLE_ROWS
static final String TABLE_ROWS
Definition: Params.java:23
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xmipp.utils.Params.RENDER_IMAGES
static final String RENDER_IMAGES
Definition: Params.java:31
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xmipp.utils.Params.INPUT_VECTORSFILE
static final String INPUT_VECTORSFILE
Definition: Params.java:19
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xmipp.utils.Params.ZOOM
static final String ZOOM
Definition: Params.java:25
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xmipp.utils.Params.POLL
static final String POLL
Definition: Params.java:22
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xmipp.utils.Params.DEBUG
static final String DEBUG
Definition: Params.java:45
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xmipp.utils.Params.BAD_PIXELS_FACTOR
static final String BAD_PIXELS_FACTOR
Definition: Params.java:40
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xmipp.utils.Params.INPUT_CLASSESFILE
static final String INPUT_CLASSESFILE
Definition: Params.java:20
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xmipp.utils.Params.INVERTY
static final String INVERTY
Definition: Params.java:53
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xmipp.utils.Params.CHIMERAPORT
static final String CHIMERAPORT
Definition: Params.java:52
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xmipp.utils.Params.SAMPLINGRATE
static final String SAMPLINGRATE
Definition: Params.java:51
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xmipp.utils.Params.INPUT_DATAFILE
static final String INPUT_DATAFILE
Definition: Params.java:21
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xmipp.utils.Params.RAISED_W
static final String RAISED_W
Definition: Params.java:43
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xmipp.utils.Params.DOWNSAMPLING
static final String DOWNSAMPLING
Definition: Params.java:39
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xmipp.utils.Params.OBJECT_CMDS
static final String OBJECT_CMDS
Definition: Params.java:50
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xmipp.utils.Params.MASK
static final String MASK
Definition: Params.java:44
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xmipp.utils.Params.SORTBY_LABEL
static final String SORTBY_LABEL
Definition: Params.java:34
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xmipp.utils.Params.VISIBLE_LABELS
static final String VISIBLE_LABELS
Definition: Params.java:32
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Definition at line 323 of file Params.java.

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324  {
325  return block;
326  }
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Definition at line 339 of file Params.java.

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340  {
341  return chimeraPort;
342  }
xmipp.utils.Params.chimeraPort
Integer chimeraPort
Definition: Params.java:90
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Definition at line 313 of file Params.java.

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314  {
315  return displayLabels;
316  }
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String [] displayLabels
Definition: Params.java:66
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Definition at line 308 of file Params.java.

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309  {
310  return renderLabels[0];
311  }
xmipp.utils.Params.renderLabels
String [] renderLabels
Definition: Params.java:64
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Definition at line 334 of file Params.java.

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335  {
336  return samplingRate;
337  }
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Definition at line 328 of file Params.java.

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328  {
329  if(cmdLine == null)
330  return false;
331  return cmdLine.hasOption("mask");
332  }
xmipp.utils.Params.cmdLine
CommandLine cmdLine
Definition: Params.java:83
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Definition at line 169 of file Params.java.

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169  {
170 
171 
172  try {
173  BasicParser parser = new BasicParser();
174  cmdLine = parser.parse(options, args);
175 
176  if (cmdLine.hasOption(FILE)) {
177  files = cmdLine.getOptionValues(FILE);
178  }
179 
180  if (cmdLine.hasOption(DIRECTORY)) {
181  directory = cmdLine.getOptionValue(DIRECTORY);
182  }
183 
184  if (cmdLine.hasOption(PORT)) {
185  port = Integer.parseInt(cmdLine.getOptionValue(PORT));
186  }
187 
188  if (cmdLine.hasOption(OPENING_MODE)) {
189  mode = cmdLine.getOptionValue(OPENING_MODE);
190  } else {
191  mode = OPENING_MODE_DEFAULT;
192  }
193 
194  poll = cmdLine.hasOption(POLL);
195 
196  if (cmdLine.hasOption(ZOOM)) {
197  zoom = Integer.parseInt(cmdLine.getOptionValue(ZOOM));
198  }
199 
200  if(cmdLine.hasOption(RENDER_IMAGES))
201  {
202  renderLabels = cmdLine.getOptionValues(RENDER_IMAGES);
203  renderImages = !(renderLabels.length == 1 && renderLabels[0].equalsIgnoreCase("no"));
204 
205  }
206  if(cmdLine.hasOption(VISIBLE_LABELS))
207  {
208  visibleLabels = cmdLine.getOptionValues(VISIBLE_LABELS);
209  }
210  if(cmdLine.hasOption(ORDER_LABELS))
211  {
212  orderLabels = cmdLine.getOptionValues(ORDER_LABELS);
213  }
214  if(cmdLine.hasOption(SORTBY_LABEL))
215  {
216 
217  sortby = cmdLine.getOptionValues(SORTBY_LABEL);
218 
219  }
220  if(cmdLine.hasOption(DISPLAY_LABELS))
221  displayLabels = cmdLine.getOptionValues(DISPLAY_LABELS);
222 
223  debug = cmdLine.hasOption(DEBUG);
224  mask_toolbar = cmdLine.hasOption(MASKTOOLBAR);
225 
226  if (cmdLine.hasOption(TABLE_ROWS)) {
227  rows = Integer.parseInt(cmdLine.getOptionValue(TABLE_ROWS));
228  }
229 
230  if (cmdLine.hasOption(TABLE_COLUMNS)) {
231  columns = Integer.parseInt(cmdLine.getOptionValue(TABLE_COLUMNS));
232  }
233 
234  if (cmdLine.hasOption(BAD_PIXELS_FACTOR)) {
235  bad_pixels_factor = Double.parseDouble(cmdLine.getOptionValue(BAD_PIXELS_FACTOR));
236  System.out.println("bad_pixels.-.. "+bad_pixels_factor);
237  }
238 
239  if (cmdLine.hasOption(W1)) {
240  w1 = Double.parseDouble(cmdLine.getOptionValue(W1));
241  }
242 
243  if (cmdLine.hasOption(W2)) {
244  w2 = Double.parseDouble(cmdLine.getOptionValue(W2));
245  }
246 
247  if (cmdLine.hasOption(RAISED_W)) {
248  raised_w = Double.parseDouble(cmdLine.getOptionValue(RAISED_W));
249  }
250 
251  if (cmdLine.hasOption(DOWNSAMPLING)) {
252  downsampling = Double.parseDouble(cmdLine.getOptionValue(DOWNSAMPLING));
253  }
254 
255 
256 
257  if (cmdLine.hasOption(INPUT_VECTORSFILE)) {
258  vectorsFilename = cmdLine.getOptionValue(INPUT_VECTORSFILE);
259  }
260 
261  if (cmdLine.hasOption(INPUT_CLASSESFILE)) {
262  classesFilename = cmdLine.getOptionValue(INPUT_CLASSESFILE);
263  }
264 
265  if (cmdLine.hasOption(INPUT_DATAFILE)) {
266  dataFilename = cmdLine.getOptionValue(INPUT_DATAFILE);
267  }
268 
269 
270  useGeo = !cmdLine.hasOption(NO_GEO);
271  wrap = !cmdLine.hasOption(NO_WRAP);
272  recalculateCTF = !cmdLine.hasOption(NO_RECALCULATE_CTF);
273 
274  if (cmdLine.hasOption(VIEW)){
275  String view = cmdLine.getOptionValue(VIEW);
276  if (view.equals("z"))
277  resliceView = ImageGeneric.Z_NEG;
278  else if (view.equals("y"))
279  resliceView = ImageGeneric.Y_NEG;
280  else if (view.equals("x"))
281  resliceView = ImageGeneric.X_NEG;
282  else if (view.equals("z_pos"))
283  resliceView = ImageGeneric.Z_POS;
284  else if (view.equals("y_pos"))
285  resliceView = ImageGeneric.Y_POS;
286  else if (view.equals("x_pos"))
287  resliceView = ImageGeneric.X_POS;
288  }
289 
290  if(cmdLine.hasOption(OBJECT_CMDS))
291  objectCommands = cmdLine.getOptionValues(OBJECT_CMDS);
292 
293  if (cmdLine.hasOption(SAMPLINGRATE)) {
294  samplingRate = Float.parseFloat(cmdLine.getOptionValue(SAMPLINGRATE));
295  }
296  if (cmdLine.hasOption(CHIMERAPORT)) {
297  chimeraPort = Integer.parseInt(cmdLine.getOptionValue(CHIMERAPORT));
298  }
299  inverty = cmdLine.hasOption(INVERTY);
300 
301 
302 
303  } catch (Exception ex) {
304  ex.printStackTrace();
305  }
306  }
xmipp.utils.Params.displayLabels
String [] displayLabels
Definition: Params.java:66
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xmipp.utils.Params.DIRECTORY
static final String DIRECTORY
Definition: Params.java:18
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Definition: Params.java:24
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boolean useGeo
Definition: Params.java:80
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xmipp.utils.Params.chimeraPort
Integer chimeraPort
Definition: Params.java:90
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xmipp.utils.Params.options
Options options
Definition: Params.java:82
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xmipp.utils.Params.sortby
String [] sortby
Definition: Params.java:86
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xmipp.utils.Params.cmdLine
CommandLine cmdLine
Definition: Params.java:83
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xmipp.utils.Params.W1
static final String W1
Definition: Params.java:41
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xmipp.utils.Params.MASKTOOLBAR
static final String MASKTOOLBAR
Definition: Params.java:46
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static final String FILE
Definition: Params.java:17
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xmipp.utils.Params.PORT
static final String PORT
Definition: Params.java:38
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xmipp.utils.Params.W2
static final String W2
Definition: Params.java:42
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xmipp.utils.Params.downsampling
double downsampling
Definition: Params.java:74
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xmipp.utils.Params.NO_GEO
static final String NO_GEO
Definition: Params.java:48
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xmipp.utils.Params.bad_pixels_factor
double bad_pixels_factor
Definition: Params.java:70
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xmipp.utils.Params.mask_toolbar
boolean mask_toolbar
Definition: Params.java:68
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Definition: Params.java:35
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xmipp.utils.Params.ORDER_LABELS
static final String ORDER_LABELS
Definition: Params.java:33
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xmipp.utils.Params.vectorsFilename
String vectorsFilename
Definition: Params.java:76
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xmipp.utils.Params.OPENING_MODE
static final String OPENING_MODE
Definition: Params.java:26
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xmipp.utils.Params.VIEW
static final String VIEW
Definition: Params.java:47
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xmipp.utils.Params.NO_WRAP
static final String NO_WRAP
Definition: Params.java:49
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xmipp.utils.Params.TABLE_ROWS
static final String TABLE_ROWS
Definition: Params.java:23
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xmipp.utils.Params.orderLabels
String [] orderLabels
Definition: Params.java:85
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xmipp.utils.Params.renderImages
boolean renderImages
Definition: Params.java:92
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xmipp.utils.Params.OPENING_MODE_DEFAULT
static final String OPENING_MODE_DEFAULT
Definition: Params.java:27
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xmipp.utils.Params.RENDER_IMAGES
static final String RENDER_IMAGES
Definition: Params.java:31
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xmipp.utils.Params.dataFilename
String dataFilename
Definition: Params.java:78
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xmipp.utils.Params.INPUT_VECTORSFILE
static final String INPUT_VECTORSFILE
Definition: Params.java:19
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xmipp.utils.Params.ZOOM
static final String ZOOM
Definition: Params.java:25
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xmipp.utils.Params.recalculateCTF
boolean recalculateCTF
Definition: Params.java:93
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xmipp.utils.Params.directory
String directory
Definition: Params.java:57
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xmipp.utils.Params.classesFilename
String classesFilename
Definition: Params.java:77
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xmipp.utils.Params.objectCommands
String [] objectCommands
Definition: Params.java:88
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xmipp.utils.Params.POLL
static final String POLL
Definition: Params.java:22
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static final String DEBUG
Definition: Params.java:45
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xmipp.utils.Params.BAD_PIXELS_FACTOR
static final String BAD_PIXELS_FACTOR
Definition: Params.java:40
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xmipp.utils.Params.INPUT_CLASSESFILE
static final String INPUT_CLASSESFILE
Definition: Params.java:20
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xmipp.utils.Params.INVERTY
static final String INVERTY
Definition: Params.java:53
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xmipp.utils.Params.CHIMERAPORT
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Definition: Params.java:52
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xmipp.utils.Params.SAMPLINGRATE
static final String SAMPLINGRATE
Definition: Params.java:51
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xmipp.utils.Params.INPUT_DATAFILE
static final String INPUT_DATAFILE
Definition: Params.java:21
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xmipp.utils.Params.RAISED_W
static final String RAISED_W
Definition: Params.java:43
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xmipp.utils.Params.files
String files[]
Definition: Params.java:58
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xmipp.utils.Params.DOWNSAMPLING
static final String DOWNSAMPLING
Definition: Params.java:39
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xmipp.utils.Params.OBJECT_CMDS
static final String OBJECT_CMDS
Definition: Params.java:50
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xmipp.utils.Params.SORTBY_LABEL
static final String SORTBY_LABEL
Definition: Params.java:34
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xmipp.utils.Params.renderLabels
String [] renderLabels
Definition: Params.java:64
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xmipp.utils.Params.inverty
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Definition: Params.java:91
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Definition: Params.java:32
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Definition: Params.java:84
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Definition at line 318 of file Params.java.

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319  {
320  this.block = block;
321  }
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Definition at line 344 of file Params.java.

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344  {
345  chimeraPort = i;
346  }
xmipp.utils.Params.chimeraPort
Integer chimeraPort
Definition: Params.java:90
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Definition at line 40 of file Params.java.

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Definition at line 70 of file Params.java.

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Definition at line 52 of file Params.java.

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Definition at line 90 of file Params.java.

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Definition at line 83 of file Params.java.

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Definition at line 45 of file Params.java.

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Definition at line 18 of file Params.java.

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Definition at line 57 of file Params.java.

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Definition at line 37 of file Params.java.

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Definition at line 20 of file Params.java.

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Definition at line 76 of file Params.java.

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Definition at line 84 of file Params.java.

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Definition at line 81 of file Params.java.

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editmapxmipp.utils.QuickHelpJDialogprotected
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QuickHelpJDialog(Frame window, boolean modal, String helptitle, Map< Object, Object > map)xmipp.utils.QuickHelpJDialoginline
QuickHelpJDialog(Frame window, boolean modal, String helptitle, Map< Object, Object > map, boolean editmap)xmipp.utils.QuickHelpJDialoginline
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-Public Member Functions

 QuickHelpJDialog (Frame window, boolean modal, String helptitle, Map< Object, Object > map)
 
 QuickHelpJDialog (Frame window, boolean modal, String helptitle, Map< Object, Object > map, boolean editmap)
 
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-Protected Attributes

JButton okbt
 
QuickHelpPane helppn
 
String helptitle
 
Map< Object, Object > helpmap
 
final boolean editmap
 
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Definition at line 17 of file QuickHelpJDialog.java.

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◆ QuickHelpJDialog() [1/2]

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xmipp.utils.QuickHelpJDialog.QuickHelpJDialog (Frame window,
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String helptitle,
Map< Object, Object > map 
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Definition at line 26 of file QuickHelpJDialog.java.

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xmipp.utils.QuickHelpJDialog.QuickHelpJDialog (Frame window,
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Definition at line 31 of file QuickHelpJDialog.java.

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32  {
33  super(window, modal);
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37  initComponents();
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Definition: QuickHelpJDialog.java:23
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Definition at line 24 of file QuickHelpJDialog.java.

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Definition at line 23 of file QuickHelpJDialog.java.

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Definition at line 21 of file QuickHelpJDialog.java.

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Definition at line 22 of file QuickHelpJDialog.java.

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Definition at line 20 of file QuickHelpJDialog.java.

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This is the complete list of members for xmipp.utils.QuickHelpPane, including all inherited members.

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buttonspnxmipp.utils.QuickHelpPaneprotected
editmapxmipp.utils.QuickHelpPaneprotected
helpmapxmipp.utils.QuickHelpPaneprotected
helptbxmipp.utils.QuickHelpPaneprotected
initComponents()xmipp.utils.QuickHelpPaneinlineprotected
initHelpTable()xmipp.utils.QuickHelpPaneinlineprotected
keysxmipp.utils.QuickHelpPaneprotected
QuickHelpPane(String title, Map< Object, Object > helpmap)xmipp.utils.QuickHelpPaneinline
QuickHelpPane(String title, Map< Object, Object > helpmap, boolean editmap)xmipp.utils.QuickHelpPaneinline
titlexmipp.utils.QuickHelpPaneprotected
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-Public Member Functions

 QuickHelpPane (String title, Map< Object, Object > helpmap)
 
 QuickHelpPane (String title, Map< Object, Object > helpmap, boolean editmap)
 
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-Protected Member Functions

void initComponents ()
 
void initHelpTable ()
 
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-Protected Attributes

JPanel buttonspn
 
String title
 
JTable helptb
 
Map< Object, Object > helpmap
 
Object [] keys
 
final boolean editmap
 
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Detailed Description

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Definition at line 17 of file QuickHelpPane.java.

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Constructor & Destructor Documentation

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◆ QuickHelpPane() [1/2]

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xmipp.utils.QuickHelpPane.QuickHelpPane (String title,
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Definition at line 26 of file QuickHelpPane.java.

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27  {
28  this(title, helpmap, false);
29  }
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Map< Object, Object > helpmap
Definition: QuickHelpPane.java:22
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xmipp.utils.QuickHelpPane.QuickHelpPane (String title,
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Definition at line 31 of file QuickHelpPane.java.

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32  {
33 
34  this.helpmap = helpmap;
35  this.editmap = editmap;
36  if(helpmap.size() == 0)
37  throw new IllegalArgumentException("There is no help information available");
38  keys = helpmap.keySet().toArray();
39  this.title = title;
40  initComponents();
41  }
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Map< Object, Object > helpmap
Definition: QuickHelpPane.java:22
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◆ initComponents()

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Definition at line 43 of file QuickHelpPane.java.

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44  {
45 // setBorder(BorderFactory.createTitledBorder(title));
46 
47  JScrollPane sp = new JScrollPane();
48  add(sp);
49  sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
50  sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
51  initHelpTable();
52  sp.setViewportView(helptb);
53  int height = Math.min(600, helptb.getRowHeight() * helpmap.size() + 5);
54  sp.setPreferredSize(new Dimension(800, height));
55  setVisible(true);
56  }
xmipp.utils.QuickHelpPane.helpmap
Map< Object, Object > helpmap
Definition: QuickHelpPane.java:22
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Definition at line 58 of file QuickHelpPane.java.

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59  {
60  helptb = new JTable();
61  helptb.setShowHorizontalLines(false);
62  helptb.setTableHeader(null);
63 // int lines = 2;
64 // helptb.setRowHeight( helptb.getRowHeight() * lines);
65  helptb.setModel(new AbstractTableModel()
66  {
67 
68  @Override
69  public Object getValueAt(int row, int column)
70  {
71  Object key = keys[row];
72  if(column == 0)
73  return key;
74  return helpmap.get(key);
75 
76  }
77 
78  @Override
79  public boolean isCellEditable(int row, int column)
80  {
81  if(column == 0)
82  return false;
83  return editmap;
84  }
85 
86  @Override
87  public Class getColumnClass(int column)
88  {
89  return String.class;
90  }
91 
92  @Override
93  public int getRowCount()
94  {
95  return helpmap.size();
96  }
97 
98  @Override
99  public int getColumnCount()
100  {
101  return 2;
102  }
103 
104  @Override
105  public void setValueAt(Object value, int row, int column)
106  {
107  helpmap.put(keys[row], value);
108  }
109 
110 
111  });
112  helptb.setDefaultRenderer(String.class, new MultilineCellRenderer());
113  helptb.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
114  helptb.getColumnModel().getColumn(0).setPreferredWidth(250);
115  helptb.getColumnModel().getColumn(1).setPreferredWidth(550);
116 
117  }
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xmipp.utils.QuickHelpPane.helpmap
Map< Object, Object > helpmap
Definition: QuickHelpPane.java:22
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◆ buttonspn

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Definition at line 19 of file QuickHelpPane.java.

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Definition at line 24 of file QuickHelpPane.java.

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Definition at line 22 of file QuickHelpPane.java.

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Definition at line 21 of file QuickHelpPane.java.

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Definition at line 23 of file QuickHelpPane.java.

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Definition at line 20 of file QuickHelpPane.java.

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BAD_PIXELS_FACTORxmipp.utils.Paramsstatic
bad_pixels_factorxmipp.utils.Params
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getScipionParams()xmipp.utils.ScipionParamsinline
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INPUT_DATAFILExmipp.utils.Paramsstatic
INPUT_VECTORSFILExmipp.utils.Paramsstatic
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maskFilenamexmipp.utils.Params
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OPENING_MODE_GALLERYxmipp.utils.Paramsstatic
OPENING_MODE_IMAGExmipp.utils.Paramsstatic
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 ScipionParams (String args[])
 
 ScipionParams ()
 
 ScipionParams (Integer port, String inputid, String other)
 
boolean isScipion ()
 
void defineArgs ()
 
void processArgs (String args[])
 
ScipionParams getScipionParams ()
 
- Public Member Functions inherited from xmipp.utils.Params
 Params ()
 
 Params (String args[])
 
void defineArgs ()
 
void processArgs (String args[])
 
String getRenderLabel ()
 
String [] getDisplayLabels ()
 
void setBlock (String block)
 
String getBlock ()
 
boolean isMask ()
 
Float getSamplingRate ()
 
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void setChimeraPort (int i)
 
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String inputid
 
String other
 
- Public Attributes inherited from xmipp.utils.Params
String directory
 
String files []
 
Integer port
 
boolean singleSelection
 
String mode = OPENING_MODE_DEFAULT
 
boolean poll
 
Integer zoom
 
String [] renderLabels = new String[]{"first"}
 
String renderLabel
 
String [] displayLabels
 
boolean debug = false
 
boolean mask_toolbar = false
 
int rows = -1
 
double bad_pixels_factor
 
double w1
 
double w2
 
double raised_w
 
double downsampling
 
String maskFilename
 
String vectorsFilename
 
String classesFilename
 
String dataFilename
 
int resliceView = ImageGeneric.Z_NEG
 
boolean useGeo = true
 
boolean wrap = true
 
String [] visibleLabels
 
String [] orderLabels
 
String [] sortby
 
String [] objectCommands
 
Integer chimeraPort
 
boolean inverty
 
boolean renderImages = true
 
boolean recalculateCTF = true
 
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-Static Public Attributes

static final String SCIPION = "scipion"
 
- Static Public Attributes inherited from xmipp.utils.Params
static final String FILE = "i"
 
static final String DIRECTORY = "dir"
 
static final String INPUT_VECTORSFILE = "vectors"
 
static final String INPUT_CLASSESFILE = "classes"
 
static final String INPUT_DATAFILE = "data"
 
static final String POLL = "poll"
 
static final String TABLE_ROWS = "rows"
 
static final String TABLE_COLUMNS = "columns"
 
static final String ZOOM = "zoom"
 
static final String OPENING_MODE = "mode"
 
static final String OPENING_MODE_DEFAULT = "default"
 
static final String OPENING_MODE_IMAGE = "image"
 
static final String OPENING_MODE_GALLERY = "gallery"
 
static final String OPENING_MODE_METADATA = "metadata"
 
static final String RENDER_IMAGES = "render"
 
static final String VISIBLE_LABELS = "visible"
 
static final String ORDER_LABELS = "order"
 
static final String SORTBY_LABEL = "sortby"
 
static final String DISPLAY_LABELS = "labels"
 
static final String FILTER = "filter"
 
static final String FILTERS_SEPARATOR = ","
 
static final String PORT = "port"
 
static final String DOWNSAMPLING = "downsampling"
 
static final String BAD_PIXELS_FACTOR = "factor"
 
static final String W1 = "w1"
 
static final String W2 = "w2"
 
static final String RAISED_W = "raised_w"
 
static final String MASK = "mask"
 
static final String DEBUG = "debug"
 
static final String MASKTOOLBAR = "mask_toolbar"
 
static final String VIEW = "view"
 
static final String NO_GEO = "dont_apply_geo"
 
static final String NO_WRAP = "dont_wrap"
 
static final String OBJECT_CMDS = "object_commands"
 
static final String SAMPLINGRATE = "sampling_rate"
 
static final String CHIMERAPORT = "chimera_port"
 
static final String INVERTY = "inverty"
 
- - - - - - -

-Additional Inherited Members

- Protected Attributes inherited from xmipp.utils.Params
Options options
 
CommandLine cmdLine
 
-

Detailed Description

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Author
airen
- -

Definition at line 16 of file ScipionParams.java.

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◆ ScipionParams() [1/3]

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Definition at line 26 of file ScipionParams.java.

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27  super(args);
28  }
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Definition at line 30 of file ScipionParams.java.

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31  super();
32  }
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xmipp.utils.ScipionParams.ScipionParams (Integer port,
String inputid,
String other 
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Definition at line 34 of file ScipionParams.java.

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34  {
35  this.port = port;
36  this.inputid = inputid;
37  this.other = other;
38  }
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Definition at line 45 of file ScipionParams.java.

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45  {
46  super.defineArgs();
47  Option opt = new Option(SCIPION, "");
48  opt.setArgs(3);
49  options.addOption(opt);
50  opt = new Option(OBJECT_CMDS, "");
51  opt.setArgs(Integer.MAX_VALUE);
52  options.addOption(opt);
53  }
xmipp.utils.Params.options
Options options
Definition: Params.java:82
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xmipp.utils.Params.OBJECT_CMDS
static final String OBJECT_CMDS
Definition: Params.java:50
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static final String SCIPION
Definition: ScipionParams.java:23
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Definition at line 69 of file ScipionParams.java.

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70  {
71  return new ScipionParams(port, inputid, other);
72  }
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Definition at line 40 of file ScipionParams.java.

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41  {
42  return cmdLine.hasOption(SCIPION);
43  }
xmipp.utils.Params.cmdLine
CommandLine cmdLine
Definition: Params.java:83
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static final String SCIPION
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Definition at line 56 of file ScipionParams.java.

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56  {
57  super.processArgs(args);
58 
59  if (cmdLine.hasOption(SCIPION)) {
60 
61  String[] cmdargs = cmdLine.getOptionValues(SCIPION);
62  port = Integer.parseInt(cmdargs[0]);
63  inputid = cmdargs[1];
64  other = (cmdargs.length == 3)? cmdargs[2]: "";
65  }
66 
67  }
xmipp.utils.Params.cmdLine
CommandLine cmdLine
Definition: Params.java:83
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xmipp.utils.ScipionParams.SCIPION
static final String SCIPION
Definition: ScipionParams.java:23
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◆ inputid

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Definition at line 20 of file ScipionParams.java.

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Definition at line 21 of file ScipionParams.java.

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Definition at line 23 of file ScipionParams.java.

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This is the complete list of members for xmipp.utils.SpringUtilities, including all inherited members.

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makeCompactGrid(Container parent, int rows, int cols, int initialX, int initialY, int xPad, int yPad)xmipp.utils.SpringUtilitiesinlinestatic
makeGrid(Container parent, int rows, int cols, int initialX, int initialY, int xPad, int yPad)xmipp.utils.SpringUtilitiesinlinestatic
printSizes(Component c)xmipp.utils.SpringUtilitiesinlinestatic
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xmipp.utils.SpringUtilities Class Reference
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-Static Public Member Functions

static void printSizes (Component c)
 
static void makeGrid (Container parent, int rows, int cols, int initialX, int initialY, int xPad, int yPad)
 
static void makeCompactGrid (Container parent, int rows, int cols, int initialX, int initialY, int xPad, int yPad)
 
-

Detailed Description

-

A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout. These utilities are used by several programs, such as SpringBox and SpringCompactGrid.

- -

Definition at line 14 of file SpringUtilities.java.

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Member Function Documentation

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◆ makeCompactGrid()

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static void xmipp.utils.SpringUtilities.makeCompactGrid (Container parent,
int rows,
int cols,
int initialX,
int initialY,
int xPad,
int yPad 
)
- 		-inlinestatic
-
-

Aligns the first rows * cols components of parent in a grid. Each component in a column is as wide as the maximum preferred width of the components in that column; height is similarly determined for each row. The parent is made just big enough to fit them all.

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rowsnumber of rows
colsnumber of columns
initialXx location to start the grid at
initialYy location to start the grid at
xPadx padding between cells
yPady padding between cells
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Definition at line 143 of file SpringUtilities.java.

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146  {
147  SpringLayout layout;
148  try {
149  layout = (SpringLayout) parent.getLayout();
150  } catch (ClassCastException exc) {
151  System.err.println("The first argument to makeCompactGrid must use SpringLayout.");
152  return;
153  }
154 
155  //Align all cells in each column and make them the same width.
156  Spring x = Spring.constant(initialX);
157  for (int c = 0; c < cols; c++) {
158  Spring width = Spring.constant(0);
159  for (int r = 0; r < rows; r++) {
160  width = Spring.max(width,
161  getConstraintsForCell(r, c, parent, cols).
162  getWidth());
163  }
164  for (int r = 0; r < rows; r++) {
165  SpringLayout.Constraints constraints =
166  getConstraintsForCell(r, c, parent, cols);
167  constraints.setX(x);
168  constraints.setWidth(width);
169  }
170  x = Spring.sum(x, Spring.sum(width, Spring.constant(xPad)));
171  }
172 
173  //Align all cells in each row and make them the same height.
174  Spring y = Spring.constant(initialY);
175  for (int r = 0; r < rows; r++) {
176  Spring height = Spring.constant(0);
177  for (int c = 0; c < cols; c++) {
178  height = Spring.max(height,
179  getConstraintsForCell(r, c, parent, cols).
180  getHeight());
181  }
182  for (int c = 0; c < cols; c++) {
183  SpringLayout.Constraints constraints =
184  getConstraintsForCell(r, c, parent, cols);
185  constraints.setY(y);
186  constraints.setHeight(height);
187  }
188  y = Spring.sum(y, Spring.sum(height, Spring.constant(yPad)));
189  }
190 
191  //Set the parent's size.
192  SpringLayout.Constraints pCons = layout.getConstraints(parent);
193  pCons.setConstraint(SpringLayout.SOUTH, y);
194  pCons.setConstraint(SpringLayout.EAST, x);
195  }
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static void xmipp.utils.SpringUtilities.makeGrid (Container parent,
int rows,
int cols,
int initialX,
int initialY,
int xPad,
int yPad 
)
- 		-inlinestatic
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Aligns the first rows * cols components of parent in a grid. Each component is as big as the maximum preferred width and height of the components. The parent is made just big enough to fit them all.

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colsnumber of columns
initialXx location to start the grid at
initialYy location to start the grid at
xPadx padding between cells
yPady padding between cells
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Definition at line 40 of file SpringUtilities.java.

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43  {
44  SpringLayout layout;
45  try {
46  layout = (SpringLayout) parent.getLayout();
47  } catch (ClassCastException exc) {
48  System.err.println("The first argument to makeGrid must use SpringLayout.");
49  return;
50  }
51 
52  Spring xPadSpring = Spring.constant(xPad);
53  Spring yPadSpring = Spring.constant(yPad);
54  Spring initialXSpring = Spring.constant(initialX);
55  Spring initialYSpring = Spring.constant(initialY);
56  int max = rows * cols;
57 
58  //Calculate Springs that are the max of the width/height so that all
59  //cells have the same size.
60  Spring maxWidthSpring = layout.getConstraints(parent.getComponent(0)).
61  getWidth();
62  Spring maxHeightSpring = layout.getConstraints(parent.getComponent(0)).
63  getWidth();
64  for (int i = 1; i < max; i++) {
65  SpringLayout.Constraints cons = layout.getConstraints(
66  parent.getComponent(i));
67 
68  maxWidthSpring = Spring.max(maxWidthSpring, cons.getWidth());
69  maxHeightSpring = Spring.max(maxHeightSpring, cons.getHeight());
70  }
71 
72  //Apply the new width/height Spring. This forces all the
73  //components to have the same size.
74  for (int i = 0; i < max; i++) {
75  SpringLayout.Constraints cons = layout.getConstraints(
76  parent.getComponent(i));
77 
78  cons.setWidth(maxWidthSpring);
79  cons.setHeight(maxHeightSpring);
80  }
81 
82  //Then adjust the x/y constraints of all the cells so that they
83  //are aligned in a grid.
84  SpringLayout.Constraints lastCons = null;
85  SpringLayout.Constraints lastRowCons = null;
86  for (int i = 0; i < max; i++) {
87  SpringLayout.Constraints cons = layout.getConstraints(
88  parent.getComponent(i));
89  if (i % cols == 0) { //start of new row
90  lastRowCons = lastCons;
91  cons.setX(initialXSpring);
92  } else { //x position depends on previous component
93  cons.setX(Spring.sum(lastCons.getConstraint(SpringLayout.EAST),
94  xPadSpring));
95  }
96 
97  if (i / cols == 0) { //first row
98  cons.setY(initialYSpring);
99  } else { //y position depends on previous row
100  cons.setY(Spring.sum(lastRowCons.getConstraint(SpringLayout.SOUTH),
101  yPadSpring));
102  }
103  lastCons = cons;
104  }
105 
106  //Set the parent's size.
107  SpringLayout.Constraints pCons = layout.getConstraints(parent);
108  pCons.setConstraint(SpringLayout.SOUTH,
109  Spring.sum(
110  Spring.constant(yPad),
111  lastCons.getConstraint(SpringLayout.SOUTH)));
112  pCons.setConstraint(SpringLayout.EAST,
113  Spring.sum(
114  Spring.constant(xPad),
115  lastCons.getConstraint(SpringLayout.EAST)));
116  }
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A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.

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20  {
21  System.out.println("minimumSize = " + c.getMinimumSize());
22  System.out.println("preferredSize = " + c.getPreferredSize());
23  System.out.println("maximumSize = " + c.getMaximumSize());
24  }
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getElapsedTime()xmipp.utils.StopWatchinline
getInstance()xmipp.utils.StopWatchinlinestatic
printElapsedTime(String comment)xmipp.utils.StopWatchinline
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xmipp.utils.StopWatch Class Reference
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double getElapsedTime ()
 
void printElapsedTime (String comment)
 
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static StopWatch getInstance ()
 
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Definition at line 13 of file StopWatch.java.

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38  {
39  long endTime = System.currentTimeMillis();
40  return (double) (endTime - startTime) / (1000);
41  }
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27  {
28  if(stopwatch == null)
29  stopwatch = new StopWatch();
30  return stopwatch;
31  }
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43  {
44 // double time = getElapsedTime();
45 // if(comment != null)
46 // System.out.printf("%.2f %s\n", time, comment);
47 // else
48 // System.out.println(time);
49  }
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Definition at line 51 of file StopWatch.java.

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52  {
53  startTime = System.currentTimeMillis();
54  }
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xmipp.utils.TaskTimer Member List
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actionPerformed(ActionEvent e)xmipp.utils.TaskTimerinline
isRunning()xmipp.utils.TaskTimerinline
start()xmipp.utils.TaskTimerinline
TaskTimer(Runnable runnable)xmipp.utils.TaskTimerinline
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-Public Member Functions

 TaskTimer (Runnable runnable)
 
void start ()
 
boolean isRunning ()
 
void actionPerformed (ActionEvent e)
 
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Detailed Description

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Author
Juanjo Vega
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Definition at line 15 of file TaskTimer.java.

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◆ TaskTimer()

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xmipp.utils.TaskTimer.TaskTimer (Runnable runnable)
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Definition at line 20 of file TaskTimer.java.

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20  {
21  this.runnable = runnable;
22  timer = new Timer(500, this);
23  timer.setRepeats(false); // Repeats only once.
24  }
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◆ actionPerformed()

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Definition at line 38 of file TaskTimer.java.

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38  {
39  runnable.run();
40  }
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Definition at line 34 of file TaskTimer.java.

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34  {
35  return timer.isRunning();
36  }
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Definition at line 26 of file TaskTimer.java.

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26  {
27  if (timer.isRunning()) {
28  timer.restart();
29  } else {
30  timer.start();
31  }
32  }
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- - diff --git a/html/classxmipp_1_1utils_1_1TaskTimer__coll__graph.dot b/html/classxmipp_1_1utils_1_1TaskTimer__coll__graph.dot deleted file mode 100644 index 601006f0..00000000 --- a/html/classxmipp_1_1utils_1_1TaskTimer__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.utils.TaskTimer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.utils.TaskTimer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node4 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" timer" ,fontname="Helvetica"]; - Node4 [label="Timer",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1TaskTimer__coll__graph.md5 b/html/classxmipp_1_1utils_1_1TaskTimer__coll__graph.md5 deleted file mode 100644 index d5e12950..00000000 --- a/html/classxmipp_1_1utils_1_1TaskTimer__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -4e8f045876c7a3939aa79f351c5e4d10 \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1TaskTimer__inherit__graph.dot b/html/classxmipp_1_1utils_1_1TaskTimer__inherit__graph.dot deleted file mode 100644 index e3025981..00000000 --- a/html/classxmipp_1_1utils_1_1TaskTimer__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.utils.TaskTimer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.utils.TaskTimer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1TaskTimer__inherit__graph.md5 b/html/classxmipp_1_1utils_1_1TaskTimer__inherit__graph.md5 deleted file mode 100644 index 67392e7a..00000000 --- a/html/classxmipp_1_1utils_1_1TaskTimer__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -2bf76dd4f7d9eb598237bd332de47a5f \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1XmippDialog-members.html b/html/classxmipp_1_1utils_1_1XmippDialog-members.html deleted file mode 100644 index 55d65c36..00000000 --- a/html/classxmipp_1_1utils_1_1XmippDialog-members.html +++ /dev/null @@ -1,122 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.utils.XmippDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
handleActionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
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-Protected Member Functions

void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Protected Attributes

Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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Detailed Description

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This class serve as a simple JDialog extension. The Ok and Cancel buttons are added and the dispose of the dialog is set. After constructing a dialog the show function should be called. It will return true if OK is pressed and false if Cancel.

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Definition at line 45 of file XmippDialog.java.

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Definition at line 61 of file XmippDialog.java.

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61  {
62  super(parent, title, modal);
63  this.parent = parent;
64  }
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Definition at line 66 of file XmippDialog.java.

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66  {
67  super(parent, title, modal);
68  this.parent = parent;
69  }
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Definition at line 163 of file XmippDialog.java.

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163  {
164  Object obj = evt.getSource();
165  if (obj == btnOk) {
166  close(true);
167  } else if (obj == btnCancel) {
168  close(false);
169  } else
170  handleActionPerformed(evt);
171  }
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Definition: XmippDialog.java:144
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Definition at line 105 of file XmippDialog.java.

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105  {
106  return addButton(text, 0);
107  }
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JButton addButton(String text)
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Definition at line 108 of file XmippDialog.java.

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108  {
109  JButton btn = XmippWindowUtil.getTextButton(text, this);
110  panelBtn.add(btn);
111 
112  if (keyStroke != 0){
113  registerHotKeys(btn, keyStroke);
114  }
115  return btn;
116  }
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Definition: XmippDialog.java:91
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Definition at line 174 of file XmippDialog.java.

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174  {
175  if (result)
176  handleOk();
177  else
178  handleCancel();
179 
180  if (closeOnAction) {
181  this.result = result;
182  setVisible(false);
183  if (disposeOnClose)
184  dispose();
185  }
186  }// function close
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118  {
119  // Create panel for Ok and Cancel buttons
120  panelBtn = new JPanel(new FlowLayout(FlowLayout.TRAILING));
121  btnOk = addButton(btnOkText, KeyEvent.VK_ENTER);
122  if (btnCancelDisplay)
123  btnCancel = addButton(btnCancelText, KeyEvent.VK_ESCAPE);
124  }
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Definition at line 75 of file XmippDialog.java.

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75  {
76  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
77  Container content = getContentPane();
78  panel = new JPanel();
79  createContent(panel);
80  content.add(panel, BorderLayout.CENTER);
81  createButtons();
82  content.add(panelBtn, BorderLayout.PAGE_END);
83 
84  pack();
85  if (parent != null)
86  XmippWindowUtil.centerWindows(this, parent);
87  else
88  XmippWindowUtil.centerWindows(this);
89  }
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Definition at line 91 of file XmippDialog.java.

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91  {
92  // Associate the escape with cancel
93  KeyStroke stroke = KeyStroke.getKeyStroke(keyStroke, 0);
94 
95  panel.registerKeyboardAction(
96  new ActionListener() {
97  @Override
98  public void actionPerformed(ActionEvent e) {
99  btn.doClick();
100  }
101  }, stroke, JComponent.WHEN_IN_FOCUSED_WINDOW);
102 
103  }
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Definition at line 280 of file XmippDialog.java.

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280  {
281  if (message == null)
282  return null;
283  String redPrefix = String.format("%c[%d;%dm", 0x1B, 1, 31);
284  String redSuffix = String.format("%c[0m", 0x1B);
285  return message.replace(redPrefix, "").replace(redSuffix, "");
286  }
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194  {
195  closeOnAction = value;
196  }
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189  {
190  disposeOnClose = value;
191  }
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127  {
128  setVisible(true);
129 
130  return result;
131  }
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Definition at line 211 of file XmippDialog.java.

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211  {
212  XmippMessageDialog dlg = new XmippMessageDialog(this, "ERROR", message,
213  "error.gif");
214  return dlg.showDialog();
215  }
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Definition at line 240 of file XmippDialog.java.

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240  {
241  if(message == null || message.isEmpty())
242  message = XmippMessage.getUnexpectedErrorMsg();
243  XmippMessageDialog dlg = new XmippMessageDialog(parent, "ERROR",
244  message, "error.gif");
245  dlg.btnCancel.setVisible(false);
246  return dlg.showDialog();
247  }
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Definition at line 217 of file XmippDialog.java.

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217  {
218  XmippMessageDialog dlg = new XmippMessageDialog(this, "ERROR",
219  e.getMessage(), "error.gif");
220  // TODO: Integrate the stack trace into the dialog
221  e.printStackTrace();
222  return dlg.showDialog();
223  }
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249  {
250  XmippMessageDialog dlg = new XmippMessageDialog(parent, "ERROR",
251  e.getMessage(), "error.gif");
252  dlg.btnCancel.setVisible(false);
253  // TODO: Integrate the stack trace into the dialog
254  e.printStackTrace();
255  return dlg.showDialog();
256  }
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199  {
200  XmippMessageDialog dlg = new XmippMessageDialog(this, "INFO", message,
201  "info.gif");
202  return dlg.showDialog();
203  }
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226  {
227  XmippMessageDialog dlg = new XmippMessageDialog(parent, "INFO",
228  message, "info.gif");
229  dlg.btnCancel.setVisible(false);
230  return dlg.showDialog();
231  }
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258  {
259  XmippMessageDialog dlg = new XmippQuestionDialog(parent, message);
260  return dlg.showDialog();
261  }
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269  {
270  XmippMessageDialog dlg = new XmippQuestionDialog(parent, message);
271  return dlg.showDialog();
272  }
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274  {
275  XmippQuestionDialog dlg = new XmippQuestionDialog(parent, message);
276  dlg.setVisible(true);
277  return dlg.getOption();
278  }
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205  {
206  XmippMessageDialog dlg = new XmippMessageDialog(this, "WARNING",
207  message, "warning.gif");
208  return dlg.showDialog();
209  }
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233  {
234  XmippMessageDialog dlg = new XmippMessageDialog(parent, "WARNING",
235  message, "warning.gif");
236  dlg.btnCancel.setVisible(false);
237  return dlg.showDialog();
238  }
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263  {
264  XmippMessageDialog dlg = new XmippQuestionDialog(parent, message, false);
265  return dlg.showDialog();
266  }
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Definition at line 48 of file XmippDialog.java.

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This is the complete list of members for xmipp.utils.XmippFileChooser, including all inherited members.

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getSelectedPath()xmipp.utils.XmippFileChooserinline
XmippFileChooser()xmipp.utils.XmippFileChooserinline
XmippFileChooser(File f)xmipp.utils.XmippFileChooserinline
XmippFileChooser(String path)xmipp.utils.XmippFileChooserinline
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-Public Member Functions

 XmippFileChooser ()
 
 XmippFileChooser (File f)
 
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Xmipp customization of the default XmippFileChooser

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Definition at line 36 of file XmippFileChooser.java.

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Definition at line 39 of file XmippFileChooser.java.

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39  {
40  this(new File(Filename.getCurrentDir()));
41  }
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43  {
44  super(f);
45  init();
46  }
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48  {
49  this(new File(path));
50  }
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62  {
63  return getSelectedFile().getPath();
64  }
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loadImage()xmipp.utils.XmippFilePreviewinline
paintComponent(Graphics g)xmipp.utils.XmippFilePreviewinlineprotected
propertyChange(PropertyChangeEvent e)xmipp.utils.XmippFilePreviewinline
XmippFilePreview(XmippFileChooser fc)xmipp.utils.XmippFilePreviewinline
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-Public Member Functions

 XmippFilePreview (XmippFileChooser fc)
 
void loadImage ()
 
void propertyChange (PropertyChangeEvent e)
 
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void paintComponent (Graphics g)
 
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Definition at line 43 of file XmippFilePreview.java.

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◆ XmippFilePreview()

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xmipp.utils.XmippFilePreview.XmippFilePreview (XmippFileChooser fc)
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Definition at line 48 of file XmippFilePreview.java.

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48  {
49  setPreferredSize(new Dimension(128, 128));
50  fc.addPropertyChangeListener(this);
51  }
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◆ loadImage()

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void xmipp.utils.XmippFilePreview.loadImage ()
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Definition at line 69 of file XmippFilePreview.java.

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69  {
70  if (file == null) {
71  thumbnail = null;
72  return;
73  }
74 
75  try {
76  String filename = file.getPath();
77  if (!file.exists() || file.isDirectory()){
78  thumbnail = null;
79  return;
80  }
81  if(filename.endsWith(".pos"))
82  return;// no image on it
83  if (Filename.isSingleImageExt(filename) ||
84  Filename.isStackExt(filename) ||
85  Filename.isVolumeExt(filename))
86  loadImage(filename);
87  else if (Filename.isMetadataExt(filename)){
88  MetaData md = new MetaData(filename);
89  int[] labels = md.getActiveLabels();
90  for (int l: labels)
91  if (MetaData.isImage(l))
92  loadImage(md.getValueString(l, md.firstObject()));
93  md.destroy();
94  }
95 
96 
97  } catch (Exception e) {
98  // TODO Auto-generated catch block
99  e.printStackTrace();
100  }
101  }
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Definition at line 128 of file XmippFilePreview.java.

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128  {
129  if (thumbnail == null) {
130  loadImage();
131  }
132  if (thumbnail != null) {
133  int x = getWidth() / 2 - thumbnail.getIconWidth() / 2;
134  int y = getHeight() / 2 - thumbnail.getIconHeight() / 2;
135 
136  if (y < 0) {
137  y = 0;
138  }
139 
140  if (x < 5) {
141  x = 5;
142  }
143  thumbnail.paintIcon(this, g, x, y);
144  }
145  }
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Definition at line 103 of file XmippFilePreview.java.

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103  {
104  boolean update = false;
105  String prop = e.getPropertyName();
106 
107  // If the directory changed, don't show an image.
108  if (XmippFileChooser.DIRECTORY_CHANGED_PROPERTY.equals(prop)) {
109  file = null;
110  update = true;
111 
112  // If a file became selected, find out which one.
113  } else if (XmippFileChooser.SELECTED_FILE_CHANGED_PROPERTY.equals(prop)) {
114  file = (File) e.getNewValue();
115  update = true;
116  }
117 
118  // Update the preview accordingly.
119  if (update) {
120  thumbnail = null;
121  if (isShowing()) {
122  loadImage();
123  repaint();
124  }
125  }
126  }
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getDescription(File f)xmipp.utils.XmippFileViewinline
getIcon(File f)xmipp.utils.XmippFileViewinline
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getTypeDescription(File f)xmipp.utils.XmippFileViewinline
isTraversable(File f)xmipp.utils.XmippFileViewinline
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-Public Member Functions

String getName (File f)
 
String getDescription (File f)
 
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String getTypeDescription (File f)
 
Icon getIcon (File f)
 
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Definition at line 37 of file XmippFileView.java.

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Definition at line 43 of file XmippFileView.java.

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43  {
44  try {
45  if (!f.isDirectory()) {
46  String filename = f.getPath();
47  if (Filename.isSingleImageExt(filename)
48  || Filename.isStackExt(filename)
49  || Filename.isVolumeExt(filename)) {
50  ImageGeneric image = new ImageGeneric(filename);
51  String desc = String.format("<Image dimensions: %d x %d",
52  image.getXDim(), image.getYDim());
53  return desc;
54  }
55  }
56  } catch (Exception e) {
57  e.printStackTrace();
58  }
59  return null; // let the L&F FileView figure this out
60  }
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Definition at line 71 of file XmippFileView.java.

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71  {
72  Icon icon = null;
73  try {
74  String filename = f.getPath();
75  // if (Filename.exists(filename))
76  {
77  String iconString = "generic_file.gif";
78  if (f.isDirectory())
79  iconString = "folderopen.gif";
80  else if (Filename.isSingleImageExt(filename))
81  iconString = "image.gif";
82  else if (Filename.isMetadataExt(filename))
83  iconString = "md.gif";
84  else if (Filename.isVolumeExt(filename))
85  iconString = "vol.gif";
86  else if (Filename.isStackExt(filename))
87  iconString = "stack.gif";
88  else if (filename.endsWith(Filename.EXT_ERR))
89  iconString = "err.gif";
90  else if (filename.endsWith(Filename.EXT_OUT))
91  iconString = "out.gif";
92  else if (filename.endsWith(Filename.EXT_LOG))
93  iconString = "log.gif";
94  else if (filename.endsWith(Filename.EXT_PY))
95  iconString = "python_file.gif";
96  return XmippResource.getIcon(iconString);
97  }
98  } catch (Exception e) {
99  e.printStackTrace();
100  }
101  return icon;
102  }
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Definition at line 39 of file XmippFileView.java.

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39  {
40  return null; // let the L&F FileView figure this out
41  }
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66  {
67  String type = null;
68  return type;
69  }
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Definition at line 62 of file XmippFileView.java.

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62  {
63  return null; // let the L&F FileView figure this out
64  }
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MSG_APPLY_GEOxmipp.utils.XmippLabelstatic
MSG_NO_ITEMS_SELECTEDxmipp.utils.XmippLabelstatic
MSG_NORMALIZExmipp.utils.XmippLabelstatic
MSG_RENDER_IMGxmipp.utils.XmippLabelstatic
MSG_SHOW_LABELxmipp.utils.XmippLabelstatic
OPERATION_ANISOTROPIC_DIFFUSIONxmipp.utils.XmippLabelstatic
OPERATION_AUTOCORRELATIONxmipp.utils.XmippLabelstatic
OPERATION_BCxmipp.utils.XmippLabelstatic
OPERATION_CLAHExmipp.utils.XmippLabelstatic
OPERATION_CLOSExmipp.utils.XmippLabelstatic
OPERATION_CONCENTRIC_CIRCLESxmipp.utils.XmippLabelstatic
OPERATION_CONTOUR_PLOTTERxmipp.utils.XmippLabelstatic
OPERATION_CONVOLVExmipp.utils.XmippLabelstatic
OPERATION_CROPxmipp.utils.XmippLabelstatic
OPERATION_DILATExmipp.utils.XmippLabelstatic
OPERATION_DISTANCE_MAPxmipp.utils.XmippLabelstatic
OPERATION_DOTTED_AND_DASHED_LINESxmipp.utils.XmippLabelstatic
OPERATION_DUPLICATExmipp.utils.XmippLabelstatic
OPERATION_ENHANCE_CONTRASTxmipp.utils.XmippLabelstatic
OPERATION_ERODExmipp.utils.XmippLabelstatic
OPERATION_FEATUREJxmipp.utils.XmippLabelstatic
OPERATION_FFTxmipp.utils.XmippLabelstatic
OPERATION_FFT_BAND_PASS_FILTERxmipp.utils.XmippLabelstatic
OPERATION_FILL_HOLESxmipp.utils.XmippLabelstatic
OPERATION_FLIP_HORIZONTALxmipp.utils.XmippLabelstatic
OPERATION_FLIP_VERTICALxmipp.utils.XmippLabelstatic
OPERATION_FLOAT_MORPHOLOGYxmipp.utils.XmippLabelstatic
OPERATION_GAUSSIAN_BLURxmipp.utils.XmippLabelstatic
OPERATION_GO_TO_SLICExmipp.utils.XmippLabelstatic
OPERATION_HISTOGRAMxmipp.utils.XmippLabelstatic
OPERATION_LINE_ANALYZERxmipp.utils.XmippLabelstatic
OPERATION_MASKS_TOOLBARxmipp.utils.XmippLabelstatic
OPERATION_MAXIMUM_ENTROPY_THRESHOLDINGxmipp.utils.XmippLabelstatic
OPERATION_MEANxmipp.utils.XmippLabelstatic
OPERATION_MEAN_SHIFT_FILTERxmipp.utils.XmippLabelstatic
OPERATION_MEASUREMENTSxmipp.utils.XmippLabelstatic
OPERATION_MEDIANxmipp.utils.XmippLabelstatic
OPERATION_MENU_BINARYxmipp.utils.XmippLabelstatic
OPERATION_MENU_DENOISINGxmipp.utils.XmippLabelstatic
OPERATION_MENU_DRAWxmipp.utils.XmippLabelstatic
OPERATION_MENU_FLIPxmipp.utils.XmippLabelstatic
OPERATION_MENU_GO_TOxmipp.utils.XmippLabelstatic
OPERATION_MENU_INFOxmipp.utils.XmippLabelstatic
OPERATION_MENU_MASKSxmipp.utils.XmippLabelstatic
OPERATION_MENU_OPEN_WITHxmipp.utils.XmippLabelstatic
OPERATION_MENU_PROCESSxmipp.utils.XmippLabelstatic
OPERATION_MENU_ROTATExmipp.utils.XmippLabelstatic
OPERATION_MENU_THRESHOLDxmipp.utils.XmippLabelstatic
OPERATION_MENU_THRESHOLDINGxmipp.utils.XmippLabelstatic
OPERATION_MENU_TRANSFORMxmipp.utils.XmippLabelstatic
OPERATION_MIXTURE_MODELING_THRESHOLDINGxmipp.utils.XmippLabelstatic
OPERATION_MULTI_OTSU_THRESHOLDINGxmipp.utils.XmippLabelstatic
OPERATION_MULTI_THRESHOLDERxmipp.utils.XmippLabelstatic
OPERATION_OPENxmipp.utils.XmippLabelstatic
OPERATION_OPEN_AS_3Dxmipp.utils.XmippLabelstatic
OPERATION_OPEN_AS_3D_VOLUMExmipp.utils.XmippLabelstatic
OPERATION_OPEN_AS_METADATAxmipp.utils.XmippLabelstatic
OPERATION_OPEN_AS_STACKxmipp.utils.XmippLabelstatic
OPERATION_OPTIONSxmipp.utils.XmippLabelstatic
OPERATION_OTSU_THRESHOLDINGxmipp.utils.XmippLabelstatic
OPERATION_OUTLINExmipp.utils.XmippLabelstatic
OPERATION_OVAL_PROFILER_PLOTxmipp.utils.XmippLabelstatic
OPERATION_PCAxmipp.utils.XmippLabelstatic
OPERATION_PLOT_PROFILExmipp.utils.XmippLabelstatic
OPERATION_POLAR_TRANSFORMERxmipp.utils.XmippLabelstatic
OPERATION_POLLxmipp.utils.XmippLabelstatic
OPERATION_RADIAL_GRIDxmipp.utils.XmippLabelstatic
OPERATION_RADIAL_PROFILE_PLOT_ANGLExmipp.utils.XmippLabelstatic
OPERATION_RADIAL_PROFILE_PLOT_HEIGHTxmipp.utils.XmippLabelstatic
OPERATION_RADIAL_RESLICExmipp.utils.XmippLabelstatic
OPERATION_RATSxmipp.utils.XmippLabelstatic
OPERATION_RESLICE_RIGHTxmipp.utils.XmippLabelstatic
OPERATION_RESLICE_TOPxmipp.utils.XmippLabelstatic
OPERATION_ROTATE_LEFTxmipp.utils.XmippLabelstatic
OPERATION_ROTATE_RIGHTxmipp.utils.XmippLabelstatic
OPERATION_SIOXxmipp.utils.XmippLabelstatic
OPERATION_SKELETONIZExmipp.utils.XmippLabelstatic
OPERATION_STACK_SLICERxmipp.utils.XmippLabelstatic
OPERATION_STRAIGHTEN_CURVED_OBJECTSxmipp.utils.XmippLabelstatic
OPERATION_SUBSTACK_MAKERxmipp.utils.XmippLabelstatic
OPERATION_SUBTRACTBGxmipp.utils.XmippLabelstatic
OPERATION_SURFACEJxmipp.utils.XmippLabelstatic
OPERATION_SYNC_MEASURE_3Dxmipp.utils.XmippLabelstatic
OPERATION_SYNC_WINDOWSxmipp.utils.XmippLabelstatic
OPERATION_TEMPLATE_MATCHINGxmipp.utils.XmippLabelstatic
OPERATION_THRESHOLDxmipp.utils.XmippLabelstatic
OPERATION_TJABOUTxmipp.utils.XmippLabelstatic
OPERATION_TJAFFINExmipp.utils.XmippLabelstatic
OPERATION_TJCROPxmipp.utils.XmippLabelstatic
OPERATION_TJEMBEDxmipp.utils.XmippLabelstatic
OPERATION_TJMIRRORxmipp.utils.XmippLabelstatic
OPERATION_TJOPTIONSxmipp.utils.XmippLabelstatic
OPERATION_TJPANELxmipp.utils.XmippLabelstatic
OPERATION_TJROTATExmipp.utils.XmippLabelstatic
OPERATION_TJSCALExmipp.utils.XmippLabelstatic
OPERATION_TJSHIFTxmipp.utils.XmippLabelstatic
OPERATION_TJTURNxmipp.utils.XmippLabelstatic
OPERATION_TJWEBSITExmipp.utils.XmippLabelstatic
OPERATION_TO_GALLERYxmipp.utils.XmippLabelstatic
OPERATION_TRANSFORMJxmipp.utils.XmippLabelstatic
OPERATION_ULTIMATE_POINTSxmipp.utils.XmippLabelstatic
OPERATION_UNTILT_STACKxmipp.utils.XmippLabelstatic
OPERATION_VOLUME_VIEWER_3D_SLICERxmipp.utils.XmippLabelstatic
OPERATION_VOLUMEJxmipp.utils.XmippLabelstatic
OPERATION_VORONOIxmipp.utils.XmippLabelstatic
OPERATION_VOXEL_COUNTERxmipp.utils.XmippLabelstatic
OPERATION_WATERSHEDxmipp.utils.XmippLabelstatic
TITLE_ABOUTxmipp.utils.XmippLabelstatic
TITLE_ERRORxmipp.utils.XmippLabelstatic
TITLE_FSCxmipp.utils.XmippLabelstatic
TITLE_GO_TO_SLICExmipp.utils.XmippLabelstatic
TITLE_PREVIEWxmipp.utils.XmippLabelstatic
TITLE_SEND2WINDOWxmipp.utils.XmippLabelstatic
TITLE_UNTITLEDxmipp.utils.XmippLabelstatic
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- - diff --git a/html/classxmipp_1_1utils_1_1XmippLabel.html b/html/classxmipp_1_1utils_1_1XmippLabel.html deleted file mode 100644 index 32831e6d..00000000 --- a/html/classxmipp_1_1utils_1_1XmippLabel.html +++ /dev/null @@ -1,5297 +0,0 @@ - - - - - - - -Xmipp: xmipp.utils.XmippLabel Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Static Public Attributes | -List of all members
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xmipp.utils.XmippLabel Class Reference
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-Static Public Attributes

static final String APP_NAME = "XmippJ"
 
static final String MESAGE_ABOUT = "About " + APP_NAME
 
static final String TITLE_ABOUT = "About " + APP_NAME
 
static final String TITLE_ERROR = "Memory error"
 
static final String TITLE_GO_TO_SLICE = "Go to slice"
 
static final String TITLE_PREVIEW = "Preview:"
 
static final String TITLE_SEND2WINDOW = "Send image to window"
 
static final String TITLE_FSC = "FSC: "
 
static final String TITLE_UNTITLED = "Untitled"
 
static final String BUTTON_IMAGE_STATS = "Mean & Std"
 
static final String BUTTON_CANCEL = "Cancel"
 
static final String BUTTON_INVERT_SELECTION = "Invert Selection"
 
static final String BUTTON_NORMALIZE = "Normalize"
 
static final String OPERATION_OPEN_AS_3D_VOLUME = "3D Volume"
 
static final String OPERATION_OPEN_AS_METADATA = "Metadata"
 
static final String OPERATION_OPEN_AS_STACK = "Stack"
 
static final String BUTTON_OK = "Ok"
 
static final String BUTTON_CLOSE = "Close"
 
static final String BUTTON_RELOAD_GALLERY = "Reload"
 
static final String BUTTON_REFRESH = "Refresh"
 
static final String BUTTON_SAVE = "Save"
 
static final String BUTTON_SELECT_ALL = "Select All"
 
static final String BUTTON_STD_DEVIATION = "Std. Deviation"
 
static final String BUTTON_PCA = "PCA"
 
static final String BUTTON_FSC = "FSC"
 
static final String BUTTON_TO_STACK = "To Stack"
 
static final String BUTTON_EXPORT_PROFILE = "Export Profiles"
 
static final String BUTTON_EXPORT_RADIAL_AVERAGE = "Export Radial AVG."
 
static final String CB_PLOT_PROFILE = "Profile"
 
static final String CB_PLOT_BGNOISE = "Log(BGNoise)"
 
static final String CB_PLOT_ENVELOPE = "Log(Envelope)"
 
static final String CB_PLOT_PSD = "PSD"
 
static final String CB_PLOT_CTF = "CTF"
 
static final String CB_PLOT_DIFFERENCE = "Difference"
 
static final String OPERATION_MENU_TRANSFORM = "Transform"
 
static final String OPERATION_TO_GALLERY = "To Gallery"
 
static final String OPERATION_MENU_FLIP = "Flip"
 
static final String OPERATION_MENU_ROTATE = "Rotate"
 
static final String OPERATION_CROP = "Crop"
 
static final String OPERATION_MENU_DENOISING = "Denoising"
 
static final String OPERATION_MENU_OPEN_WITH = "Open with..."
 
static final String OPERATION_MENU_THRESHOLDING = "Thresholding"
 
static final String OPERATION_MENU_BINARY = "Binary"
 
static final String OPERATION_MENU_INFO = "Info"
 
static final String OPERATION_MENU_PROCESS = "Process"
 
static final String OPERATION_MENU_GO_TO = "Go to"
 
static final String OPERATION_MENU_THRESHOLD = "Threshold"
 
static final String OPERATION_MENU_DRAW = "Draw"
 
static final String OPERATION_FLIP_VERTICAL = "Flip Vertical"
 
static final String OPERATION_FLIP_HORIZONTAL = "Flip Horizontal"
 
static final String OPERATION_ROTATE_LEFT = "Rotate Left"
 
static final String OPERATION_ROTATE_RIGHT = "Rotate Right"
 
static final String OPERATION_HISTOGRAM = "Histogram"
 
static final String OPERATION_PLOT_PROFILE = "Plot Profile"
 
static final String OPERATION_MEASUREMENTS = "Measurements"
 
static final String OPERATION_BC = "Bright&Contrast"
 
static final String OPERATION_ENHANCE_CONTRAST = "Enhance Contrast"
 
static final String OPERATION_THRESHOLD = "Threshold"
 
static final String OPERATION_SUBTRACTBG = "Subtract Background"
 
static final String OPERATION_GAUSSIAN_BLUR = "Gaussian Blur"
 
static final String OPERATION_CONVOLVE = "Convolve"
 
static final String OPERATION_MEDIAN = "Median"
 
static final String OPERATION_MEAN = "Mean"
 
static final String OPERATION_FFT = "FFT"
 
static final String OPERATION_FFT_BAND_PASS_FILTER = "FFT Band Pass Filter"
 
static final String OPERATION_RESLICE_TOP = "Reslice Top"
 
static final String OPERATION_RESLICE_RIGHT = "Reslice Right"
 
static final String OPERATION_STACK_SLICER = "StackSlicer (dynamic orthogonal views)"
 
static final String OPERATION_RADIAL_RESLICE = "Radial Reslice (orthogonal reconstructions)"
 
static final String OPERATION_STRAIGHTEN_CURVED_OBJECTS = "Straighten Curved Objects"
 
static final String OPERATION_UNTILT_STACK = "Untilt Stack (removes tilt from a stack of images)"
 
static final String OPERATION_TRANSFORMJ = "TransformJ"
 
static final String OPERATION_TJABOUT = "TJ About"
 
static final String OPERATION_TJAFFINE = "TJ Affine"
 
static final String OPERATION_TJCROP = "TJ Crop"
 
static final String OPERATION_TJEMBED = "TJ Embed"
 
static final String OPERATION_TJMIRROR = "TJ Mirror"
 
static final String OPERATION_TJOPTIONS = "TJ Options"
 
static final String OPERATION_TJPANEL = "TJ Panel"
 
static final String OPERATION_TJROTATE = "TJ Rotate"
 
static final String OPERATION_TJSCALE = "TJ Scale"
 
static final String OPERATION_TJSHIFT = "TJ Shift"
 
static final String OPERATION_TJTURN = "TJ Turn"
 
static final String OPERATION_TJWEBSITE = "TJ Website"
 
static final String OPERATION_SURFACEJ = "SurfaceJ"
 
static final String OPERATION_OPEN_AS_3D = "3D Viewer"
 
static final String OPERATION_POLL = "Poll"
 
static final String OPERATION_DUPLICATE = "Duplicate"
 
static final String OPERATION_GO_TO_SLICE = "Go to slice"
 
static final String OPERATION_SUBSTACK_MAKER = "Substack Maker"
 
static final String OPERATION_ANISOTROPIC_DIFFUSION = "Anisotropic Diffusion"
 
static final String OPERATION_MEAN_SHIFT_FILTER = "Mean Shift Filter"
 
static final String OPERATION_VOLUME_VIEWER_3D_SLICER = "Volume Viewer/3D-Slicer"
 
static final String OPERATION_VOLUMEJ = "VolumeJ"
 
static final String OPERATION_AUTOCORRELATION = "Autocorrelation"
 
static final String OPERATION_CONCENTRIC_CIRCLES = "Concentric Circles"
 
static final String OPERATION_LINE_ANALYZER = "Line Analyzer"
 
static final String OPERATION_OVAL_PROFILER_PLOT = "Oval Profile Plot"
 
static final String OPERATION_RADIAL_PROFILE_PLOT_ANGLE = "Radial Profile Plot Angle"
 
static final String OPERATION_RADIAL_PROFILE_PLOT_HEIGHT = "Radial Profile Plot Height"
 
static final String OPERATION_CONTOUR_PLOTTER = "Contour Plotter"
 
static final String OPERATION_FEATUREJ = "FeatureJ"
 
static final String OPERATION_SYNC_WINDOWS = "Sync Windows"
 
static final String OPERATION_SYNC_MEASURE_3D = "Sync Measure 3D"
 
static final String OPERATION_OTSU_THRESHOLDING = "Otsu Thresholding"
 
static final String OPERATION_MULTI_OTSU_THRESHOLDING = "Multi Otsu Threshold"
 
static final String OPERATION_MIXTURE_MODELING_THRESHOLDING = "Mixture Modeling Thresholding"
 
static final String OPERATION_MAXIMUM_ENTROPY_THRESHOLDING = "Maximum Entropy Thresholding"
 
static final String OPERATION_MULTI_THRESHOLDER = "MultiThresholder"
 
static final String OPERATION_SIOX = "SIOX Simple Interactive Object Extraction"
 
static final String OPERATION_RATS = "RATS Robust Automatic Threshold Selection"
 
static final String OPERATION_VOXEL_COUNTER = "Voxel Counter"
 
static final String OPERATION_ERODE = "Erode"
 
static final String OPERATION_DILATE = "Dilate"
 
static final String OPERATION_OPEN = "Open"
 
static final String OPERATION_CLOSE = "Close"
 
static final String OPERATION_FLOAT_MORPHOLOGY = "Float Morphology"
 
static final String OPERATION_OUTLINE = "Outline"
 
static final String OPERATION_FILL_HOLES = "Fill holes"
 
static final String OPERATION_SKELETONIZE = "Skeletonize"
 
static final String OPERATION_DISTANCE_MAP = "Distance map"
 
static final String OPERATION_ULTIMATE_POINTS = "Ultimate points"
 
static final String OPERATION_WATERSHED = "Watershed"
 
static final String OPERATION_VORONOI = "Voronoi"
 
static final String OPERATION_OPTIONS = "Options"
 
static final String OPERATION_CLAHE = "CLAHE Contrast Limited Adaptive Histogram Equalization"
 
static final String OPERATION_PCA = "PCA Principal Component Analysis"
 
static final String OPERATION_POLAR_TRANSFORMER = "Polar Transformer convert to polar coordinates"
 
static final String OPERATION_DOTTED_AND_DASHED_LINES = "Dotted and Dashed Lines"
 
static final String OPERATION_RADIAL_GRID = "Radial Grid"
 
static final String OPERATION_TEMPLATE_MATCHING = "Template Matching"
 
static final String OPERATION_MENU_MASKS = "Masks"
 
static final String OPERATION_MASKS_TOOLBAR = "Masks Tool Bar"
 
static final String LABEL_SHOW_CTF_INFO = "Show CTF info"
 
static final String LABEL_EXTRACT_COLUMN_ENABLED = "Extract Column (enabled)"
 
static final String LABEL_EXTRACT_COLUMN_ALL = "Extract Column (all)"
 
static final String LABEL_RECALCULATE_CTF = "Recalculate CTF"
 
static final String LABEL_VIEW_CTF_PROFILE = "View CTF Profile"
 
static final String LABEL_DIGITAL_FREQUENCY = "Digital frequency"
 
static final String LABEL_AUTO_AJUST_COLS = "Auto adjust columns"
 
static final String LABEL_SHOW_LABELS = "Show label: "
 
static final String LABEL_ROTSPECTRA_SHOW_NIMAGES = "Show #images"
 
static final String LABEL_SORT_BY_LABEL = "Sort by label"
 
static final String LABEL_USE_GEOMETRY = "Use geometry"
 
static final String LABEL_WIDTH = "Width: "
 
static final String LABEL_HEIGHT = "Height: "
 
static final String LABEL_DEPTH = "Depth: "
 
static final String LABEL_NIMAGES = "#Images: "
 
static final String LABEL_LOAD_PREVIEW = "Load preview"
 
static final String LABEL_GALLERY_DISABLE = "Disable"
 
static final String LABEL_GALLERY_ENABLE = "Enable"
 
static final String LABEL_GALLERY_ENABLE_ALL = "Enable All"
 
static final String LABEL_GALLERY_ENABLE_FROM = "Enable from here"
 
static final String LABEL_GALLERY_ENABLE_TO = "Enable to here"
 
static final String LABEL_GALLERY_HIDE_DISABLED = "Hide disabled"
 
static final String LABEL_GALLERY_DISABLE_ALL = "Disable All"
 
static final String LABEL_GALLERY_DISABLE_FROM = "Disable from here"
 
static final String LABEL_GALLERY_DISABLE_TO = "Disable to here"
 
static final String LABEL_GALLERY_FILE = "File"
 
static final String LABEL_GALLERY_SAVE = "Save"
 
static final String LABEL_GALLERY_SAVEAS = "Save as"
 
static final String LABEL_GALLERY_EXIT = "Exit"
 
static final String LABEL_VIEW_MD = "Go to TABLE view"
 
static final String LABEL_VIEW_GALLERY = "Go to GALLERY view"
 
static final String LABEL_GALLERY_SAVE_AS_METADATA = "Save as metadata"
 
static final String LABEL_GALLERY_SAVE_SELECTION_AS_METADATA = "Save selection as metadata"
 
static final String LABEL_GALLERY_SAVE_AS_IMAGE = "Save as image"
 
static final String LABEL_GALLERY_SAVE_SELECTION_AS_IMAGE = "Save selection as image"
 
static final String LABEL_RESLICE = "Reslice"
 
static final String LABEL_RESLICE_TOP = "Reslice Top (Y)"
 
static final String LABEL_RESLICE_RIGHT = "Reslice Right (X)"
 
static final String LABEL_CTF = "CTF"
 
static final String LABEL_PSD = "Log(PSD)"
 
static final String LABEL_SAMPLING = "1/A"
 
static final String LABEL_PROFILES = "Profiles"
 
static final String LABEL_RADIAL_AVERAGE = "Radial Average"
 
static final String LABEL_RADIAL_AVG = "Radial Average"
 
static final String LABEL_TAB_PROFILE = "Profiles"
 
static final String LABEL_TAB_RADIAL_AVERAGE = "Radial Average"
 
static final String LABEL_ZOOM = "Zoom (%): "
 
static final String LABEL_ROWS = " Rows"
 
static final String LABEL_COLUMNS = " Cols"
 
static final String LABEL_BLOCK = " Block"
 
static final String LABEL_VOLUME = " Volume"
 
static final String LABEL_GOTO_ITEM = "Go to item"
 
static final String LABEL_UNKNOWN = "Unknown label"
 
static final String MENU_STATS = "Statistics"
 
static final String MENU_OPEN_WITH = "Open with..."
 
static final String MENU_OPEN_WITH_CHIMERA = "UCSF Chimera"
 
static final String MENU_OPEN_WITH_IJ = "ImageJ"
 
static final String MSG_NO_ITEMS_SELECTED = "No items selected (or not enabled)"
 
static final String MESSAGE_OVERWRITE_FILE = "Overwrite existing file?"
 
static final String MESSAGE_OVERWRITE_FILE_TITLE = "Confirm Overwrite"
 
static final String MESSAGE_FILE_SAVED = "File saved: "
 
static final String MESSAGE_FILE_SAVED_TITLE = "Saved!"
 
static final String MSG_NORMALIZE = "Global normalization"
 
static final String MSG_APPLY_GEO = "Apply geometry"
 
static final String MSG_SHOW_LABEL = "Show labels"
 
static final String MSG_RENDER_IMG = "Render images"
 
static final String MSG_ADJUST_COLS = "Adjust columns when resizing"
 
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Detailed Description

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Definition at line 11 of file XmippLabel.java.

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Member Data Documentation

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◆ APP_NAME

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Definition at line 13 of file XmippLabel.java.

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◆ BUTTON_CANCEL

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final String xmipp.utils.XmippLabel.BUTTON_CANCEL = "Cancel"
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Definition at line 38 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.BUTTON_CLOSE = "Close"
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Definition at line 48 of file XmippLabel.java.

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◆ BUTTON_EXPORT_PROFILE

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final String xmipp.utils.XmippLabel.BUTTON_EXPORT_PROFILE = "Export Profiles"
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Definition at line 59 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.BUTTON_EXPORT_RADIAL_AVERAGE = "Export Radial AVG."
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Definition at line 60 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.BUTTON_FSC = "FSC"
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Definition at line 57 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.BUTTON_IMAGE_STATS = "Mean & Std"
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Definition at line 37 of file XmippLabel.java.

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◆ BUTTON_INVERT_SELECTION

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- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_INVERT_SELECTION = "Invert Selection"
- 		-static
-
- -

Definition at line 40 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_NORMALIZE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_NORMALIZE = "Normalize"
- 		-static
-
- -

Definition at line 41 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_OK

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_OK = "Ok"
- 		-static
-
- -

Definition at line 47 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_PCA

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_PCA = "PCA"
- 		-static
-
- -

Definition at line 56 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_REFRESH

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_REFRESH = "Refresh"
- 		-static
-
- -

Definition at line 51 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_RELOAD_GALLERY

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_RELOAD_GALLERY = "Reload"
- 		-static
-
- -

Definition at line 50 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_SAVE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_SAVE = "Save"
- 		-static
-
- -

Definition at line 53 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_SELECT_ALL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_SELECT_ALL = "Select All"
- 		-static
-
- -

Definition at line 54 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_STD_DEVIATION

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_STD_DEVIATION = "Std. Deviation"
- 		-static
-
- -

Definition at line 55 of file XmippLabel.java.

- -
-
- -

◆ BUTTON_TO_STACK

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.BUTTON_TO_STACK = "To Stack"
- 		-static
-
- -

Definition at line 58 of file XmippLabel.java.

- -
-
- -

◆ CB_PLOT_BGNOISE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.CB_PLOT_BGNOISE = "Log(BGNoise)"
- 		-static
-
- -

Definition at line 62 of file XmippLabel.java.

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-
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◆ CB_PLOT_CTF

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.CB_PLOT_CTF = "CTF"
- 		-static
-
- -

Definition at line 65 of file XmippLabel.java.

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-
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◆ CB_PLOT_DIFFERENCE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.CB_PLOT_DIFFERENCE = "Difference"
- 		-static
-
- -

Definition at line 66 of file XmippLabel.java.

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-
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◆ CB_PLOT_ENVELOPE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.CB_PLOT_ENVELOPE = "Log(Envelope)"
- 		-static
-
- -

Definition at line 63 of file XmippLabel.java.

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◆ CB_PLOT_PROFILE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.CB_PLOT_PROFILE = "Profile"
- 		-static
-
- -

Definition at line 61 of file XmippLabel.java.

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-
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◆ CB_PLOT_PSD

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.CB_PLOT_PSD = "PSD"
- 		-static
-
- -

Definition at line 64 of file XmippLabel.java.

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-
- -

◆ LABEL_AUTO_AJUST_COLS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_AUTO_AJUST_COLS = "Auto adjust columns"
- 		-static
-
- -

Definition at line 184 of file XmippLabel.java.

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-
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◆ LABEL_BLOCK

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_BLOCK = " Block"
- 		-static
-
- -

Definition at line 231 of file XmippLabel.java.

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-
- -

◆ LABEL_COLUMNS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_COLUMNS = " Cols"
- 		-static
-
- -

Definition at line 230 of file XmippLabel.java.

- -
-
- -

◆ LABEL_CTF

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_CTF = "CTF"
- 		-static
-
- -

Definition at line 218 of file XmippLabel.java.

- -
-
- -

◆ LABEL_DEPTH

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_DEPTH = "Depth: "
- 		-static
-
- -

Definition at line 192 of file XmippLabel.java.

- -
-
- -

◆ LABEL_DIGITAL_FREQUENCY

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_DIGITAL_FREQUENCY = "Digital frequency"
- 		-static
-
-

Labels

- -

Definition at line 183 of file XmippLabel.java.

- -
-
- -

◆ LABEL_EXTRACT_COLUMN_ALL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_EXTRACT_COLUMN_ALL = "Extract Column (all)"
- 		-static
-
- -

Definition at line 177 of file XmippLabel.java.

- -
-
- -

◆ LABEL_EXTRACT_COLUMN_ENABLED

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_EXTRACT_COLUMN_ENABLED = "Extract Column (enabled)"
- 		-static
-
- -

Definition at line 176 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_DISABLE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_DISABLE = "Disable"
- 		-static
-
- -

Definition at line 195 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_DISABLE_ALL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_DISABLE_ALL = "Disable All"
- 		-static
-
- -

Definition at line 201 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_DISABLE_FROM

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_DISABLE_FROM = "Disable from here"
- 		-static
-
- -

Definition at line 202 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_DISABLE_TO

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_DISABLE_TO = "Disable to here"
- 		-static
-
- -

Definition at line 203 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_ENABLE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_ENABLE = "Enable"
- 		-static
-
- -

Definition at line 196 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_ENABLE_ALL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_ENABLE_ALL = "Enable All"
- 		-static
-
- -

Definition at line 197 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_ENABLE_FROM

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_ENABLE_FROM = "Enable from here"
- 		-static
-
- -

Definition at line 198 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_ENABLE_TO

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_ENABLE_TO = "Enable to here"
- 		-static
-
- -

Definition at line 199 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_EXIT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_EXIT = "Exit"
- 		-static
-
- -

Definition at line 207 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_FILE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_FILE = "File"
- 		-static
-
- -

Definition at line 204 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_HIDE_DISABLED

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_HIDE_DISABLED = "Hide disabled"
- 		-static
-
- -

Definition at line 200 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_SAVE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE = "Save"
- 		-static
-
- -

Definition at line 205 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_SAVE_AS_IMAGE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE_AS_IMAGE = "Save as image"
- 		-static
-
- -

Definition at line 213 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_SAVE_AS_METADATA

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE_AS_METADATA = "Save as metadata"
- 		-static
-
- -

Definition at line 211 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_SAVE_SELECTION_AS_IMAGE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE_SELECTION_AS_IMAGE = "Save selection as image"
- 		-static
-
- -

Definition at line 214 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_SAVE_SELECTION_AS_METADATA

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_SAVE_SELECTION_AS_METADATA = "Save selection as metadata"
- 		-static
-
- -

Definition at line 212 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GALLERY_SAVEAS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GALLERY_SAVEAS = "Save as"
- 		-static
-
- -

Definition at line 206 of file XmippLabel.java.

- -
-
- -

◆ LABEL_GOTO_ITEM

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_GOTO_ITEM = "Go to item"
- 		-static
-
- -

Definition at line 233 of file XmippLabel.java.

- -
-
- -

◆ LABEL_HEIGHT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_HEIGHT = "Height: "
- 		-static
-
- -

Definition at line 191 of file XmippLabel.java.

- -
-
- -

◆ LABEL_LOAD_PREVIEW

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_LOAD_PREVIEW = "Load preview"
- 		-static
-
- -

Definition at line 194 of file XmippLabel.java.

- -
-
- -

◆ LABEL_NIMAGES

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_NIMAGES = "#Images: "
- 		-static
-
- -

Definition at line 193 of file XmippLabel.java.

- -
-
- -

◆ LABEL_PROFILES

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_PROFILES = "Profiles"
- 		-static
-
- -

Definition at line 221 of file XmippLabel.java.

- -
-
- -

◆ LABEL_PSD

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_PSD = "Log(PSD)"
- 		-static
-
- -

Definition at line 219 of file XmippLabel.java.

- -
-
- -

◆ LABEL_RADIAL_AVERAGE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_RADIAL_AVERAGE = "Radial Average"
- 		-static
-
- -

Definition at line 222 of file XmippLabel.java.

- -
-
- -

◆ LABEL_RADIAL_AVG

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_RADIAL_AVG = "Radial Average"
- 		-static
-
- -

Definition at line 225 of file XmippLabel.java.

- -
-
- -

◆ LABEL_RECALCULATE_CTF

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_RECALCULATE_CTF = "Recalculate CTF"
- 		-static
-
- -

Definition at line 178 of file XmippLabel.java.

- -
-
- -

◆ LABEL_RESLICE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_RESLICE = "Reslice"
- 		-static
-
- -

Definition at line 215 of file XmippLabel.java.

- -
-
- -

◆ LABEL_RESLICE_RIGHT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_RESLICE_RIGHT = "Reslice Right (X)"
- 		-static
-
- -

Definition at line 217 of file XmippLabel.java.

- -
-
- -

◆ LABEL_RESLICE_TOP

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_RESLICE_TOP = "Reslice Top (Y)"
- 		-static
-
- -

Definition at line 216 of file XmippLabel.java.

- -
-
- -

◆ LABEL_ROTSPECTRA_SHOW_NIMAGES

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_ROTSPECTRA_SHOW_NIMAGES = "Show #images"
- 		-static
-
- -

Definition at line 186 of file XmippLabel.java.

- -
-
- -

◆ LABEL_ROWS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_ROWS = " Rows"
- 		-static
-
- -

Definition at line 229 of file XmippLabel.java.

- -
-
- -

◆ LABEL_SAMPLING

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_SAMPLING = "1/A"
- 		-static
-
- -

Definition at line 220 of file XmippLabel.java.

- -
-
- -

◆ LABEL_SHOW_CTF_INFO

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_SHOW_CTF_INFO = "Show CTF info"
- 		-static
-
- -

Definition at line 175 of file XmippLabel.java.

- -
-
- -

◆ LABEL_SHOW_LABELS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_SHOW_LABELS = "Show label: "
- 		-static
-
- -

Definition at line 185 of file XmippLabel.java.

- -
-
- -

◆ LABEL_SORT_BY_LABEL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_SORT_BY_LABEL = "Sort by label"
- 		-static
-
- -

Definition at line 187 of file XmippLabel.java.

- -
-
- -

◆ LABEL_TAB_PROFILE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_TAB_PROFILE = "Profiles"
- 		-static
-
- -

Definition at line 226 of file XmippLabel.java.

- -
-
- -

◆ LABEL_TAB_RADIAL_AVERAGE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_TAB_RADIAL_AVERAGE = "Radial Average"
- 		-static
-
- -

Definition at line 227 of file XmippLabel.java.

- -
-
- -

◆ LABEL_UNKNOWN

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_UNKNOWN = "Unknown label"
- 		-static
-
- -

Definition at line 240 of file XmippLabel.java.

- -
-
- -

◆ LABEL_USE_GEOMETRY

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_USE_GEOMETRY = "Use geometry"
- 		-static
-
- -

Definition at line 188 of file XmippLabel.java.

- -
-
- -

◆ LABEL_VIEW_CTF_PROFILE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_VIEW_CTF_PROFILE = "View CTF Profile"
- 		-static
-
- -

Definition at line 179 of file XmippLabel.java.

- -
-
- -

◆ LABEL_VIEW_GALLERY

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_VIEW_GALLERY = "Go to GALLERY view"
- 		-static
-
- -

Definition at line 209 of file XmippLabel.java.

- -
-
- -

◆ LABEL_VIEW_MD

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_VIEW_MD = "Go to TABLE view"
- 		-static
-
- -

Definition at line 208 of file XmippLabel.java.

- -
-
- -

◆ LABEL_VOLUME

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_VOLUME = " Volume"
- 		-static
-
- -

Definition at line 232 of file XmippLabel.java.

- -
-
- -

◆ LABEL_WIDTH

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_WIDTH = "Width: "
- 		-static
-
- -

Definition at line 190 of file XmippLabel.java.

- -
-
- -

◆ LABEL_ZOOM

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.LABEL_ZOOM = "Zoom (%): "
- 		-static
-
- -

Definition at line 228 of file XmippLabel.java.

- -
-
- -

◆ MENU_OPEN_WITH

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MENU_OPEN_WITH = "Open with..."
- 		-static
-
- -

Definition at line 248 of file XmippLabel.java.

- -
-
- -

◆ MENU_OPEN_WITH_CHIMERA

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MENU_OPEN_WITH_CHIMERA = "UCSF Chimera"
- 		-static
-
- -

Definition at line 249 of file XmippLabel.java.

- -
-
- -

◆ MENU_OPEN_WITH_IJ

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MENU_OPEN_WITH_IJ = "ImageJ"
- 		-static
-
- -

Definition at line 250 of file XmippLabel.java.

- -
-
- -

◆ MENU_STATS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MENU_STATS = "Statistics"
- 		-static
-
- -

Definition at line 247 of file XmippLabel.java.

- -
-
- -

◆ MESAGE_ABOUT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MESAGE_ABOUT = "About " + APP_NAME
- 		-static
-
- -

Definition at line 14 of file XmippLabel.java.

- -
-
- -

◆ MESSAGE_FILE_SAVED

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MESSAGE_FILE_SAVED = "File saved: "
- 		-static
-
- -

Definition at line 263 of file XmippLabel.java.

- -
-
- -

◆ MESSAGE_FILE_SAVED_TITLE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MESSAGE_FILE_SAVED_TITLE = "Saved!"
- 		-static
-
- -

Definition at line 264 of file XmippLabel.java.

- -
-
- -

◆ MESSAGE_OVERWRITE_FILE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MESSAGE_OVERWRITE_FILE = "Overwrite existing file?"
- 		-static
-
- -

Definition at line 261 of file XmippLabel.java.

- -
-
- -

◆ MESSAGE_OVERWRITE_FILE_TITLE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MESSAGE_OVERWRITE_FILE_TITLE = "Confirm Overwrite"
- 		-static
-
- -

Definition at line 262 of file XmippLabel.java.

- -
-
- -

◆ MSG_ADJUST_COLS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MSG_ADJUST_COLS = "Adjust columns when resizing"
- 		-static
-
- -

Definition at line 269 of file XmippLabel.java.

- -
-
- -

◆ MSG_APPLY_GEO

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MSG_APPLY_GEO = "Apply geometry"
- 		-static
-
- -

Definition at line 266 of file XmippLabel.java.

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-
- -

◆ MSG_NO_ITEMS_SELECTED

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MSG_NO_ITEMS_SELECTED = "No items selected (or not enabled)"
- 		-static
-
- -

Definition at line 259 of file XmippLabel.java.

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-
- -

◆ MSG_NORMALIZE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MSG_NORMALIZE = "Global normalization"
- 		-static
-
- -

Definition at line 265 of file XmippLabel.java.

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-
- -

◆ MSG_RENDER_IMG

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MSG_RENDER_IMG = "Render images"
- 		-static
-
- -

Definition at line 268 of file XmippLabel.java.

- -
-
- -

◆ MSG_SHOW_LABEL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.MSG_SHOW_LABEL = "Show labels"
- 		-static
-
- -

Definition at line 267 of file XmippLabel.java.

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-
- -

◆ OPERATION_ANISOTROPIC_DIFFUSION

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_ANISOTROPIC_DIFFUSION = "Anisotropic Diffusion"
- 		-static
-
- -

Definition at line 129 of file XmippLabel.java.

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-
- -

◆ OPERATION_AUTOCORRELATION

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_AUTOCORRELATION = "Autocorrelation"
- 		-static
-
- -

Definition at line 133 of file XmippLabel.java.

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-
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◆ OPERATION_BC

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_BC = "Bright&Contrast"
- 		-static
-
- -

Definition at line 94 of file XmippLabel.java.

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-
- -

◆ OPERATION_CLAHE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_CLAHE = "CLAHE Contrast Limited Adaptive Histogram Equalization"
- 		-static
-
- -

Definition at line 164 of file XmippLabel.java.

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-
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◆ OPERATION_CLOSE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_CLOSE = "Close"
- 		-static
-
- -

Definition at line 154 of file XmippLabel.java.

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-
- -

◆ OPERATION_CONCENTRIC_CIRCLES

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_CONCENTRIC_CIRCLES = "Concentric Circles"
- 		-static
-
- -

Definition at line 134 of file XmippLabel.java.

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-
- -

◆ OPERATION_CONTOUR_PLOTTER

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_CONTOUR_PLOTTER = "Contour Plotter"
- 		-static
-
- -

Definition at line 139 of file XmippLabel.java.

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◆ OPERATION_CONVOLVE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_CONVOLVE = "Convolve"
- 		-static
-
- -

Definition at line 99 of file XmippLabel.java.

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◆ OPERATION_CROP

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-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_CROP = "Crop"
- 		-static
-
- -

Definition at line 76 of file XmippLabel.java.

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-
- -

◆ OPERATION_DILATE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_DILATE = "Dilate"
- 		-static
-
- -

Definition at line 152 of file XmippLabel.java.

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-
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◆ OPERATION_DISTANCE_MAP

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_DISTANCE_MAP = "Distance map"
- 		-static
-
- -

Definition at line 159 of file XmippLabel.java.

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-
- -

◆ OPERATION_DOTTED_AND_DASHED_LINES

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_DOTTED_AND_DASHED_LINES = "Dotted and Dashed Lines"
- 		-static
-
- -

Definition at line 167 of file XmippLabel.java.

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-
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◆ OPERATION_DUPLICATE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_DUPLICATE = "Duplicate"
- 		-static
-
- -

Definition at line 126 of file XmippLabel.java.

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-
- -

◆ OPERATION_ENHANCE_CONTRAST

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_ENHANCE_CONTRAST = "Enhance Contrast"
- 		-static
-
- -

Definition at line 95 of file XmippLabel.java.

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-
- -

◆ OPERATION_ERODE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_ERODE = "Erode"
- 		-static
-
- -

Definition at line 151 of file XmippLabel.java.

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-
- -

◆ OPERATION_FEATUREJ

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_FEATUREJ = "FeatureJ"
- 		-static
-
- -

Definition at line 140 of file XmippLabel.java.

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-
- -

◆ OPERATION_FFT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_FFT = "FFT"
- 		-static
-
- -

Definition at line 102 of file XmippLabel.java.

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-
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◆ OPERATION_FFT_BAND_PASS_FILTER

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_FFT_BAND_PASS_FILTER = "FFT Band Pass Filter"
- 		-static
-
- -

Definition at line 103 of file XmippLabel.java.

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-
- -

◆ OPERATION_FILL_HOLES

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_FILL_HOLES = "Fill holes"
- 		-static
-
- -

Definition at line 157 of file XmippLabel.java.

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-
- -

◆ OPERATION_FLIP_HORIZONTAL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_FLIP_HORIZONTAL = "Flip Horizontal"
- 		-static
-
- -

Definition at line 88 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_FLIP_VERTICAL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_FLIP_VERTICAL = "Flip Vertical"
- 		-static
-
- -

Definition at line 87 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_FLOAT_MORPHOLOGY

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_FLOAT_MORPHOLOGY = "Float Morphology"
- 		-static
-
- -

Definition at line 155 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_GAUSSIAN_BLUR

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_GAUSSIAN_BLUR = "Gaussian Blur"
- 		-static
-
- -

Definition at line 98 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_GO_TO_SLICE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_GO_TO_SLICE = "Go to slice"
- 		-static
-
- -

Definition at line 127 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_HISTOGRAM

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_HISTOGRAM = "Histogram"
- 		-static
-
- -

Definition at line 91 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_LINE_ANALYZER

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_LINE_ANALYZER = "Line Analyzer"
- 		-static
-
- -

Definition at line 135 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MASKS_TOOLBAR

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MASKS_TOOLBAR = "Masks Tool Bar"
- 		-static
-
- -

Definition at line 171 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MAXIMUM_ENTROPY_THRESHOLDING

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MAXIMUM_ENTROPY_THRESHOLDING = "Maximum Entropy Thresholding"
- 		-static
-
- -

Definition at line 146 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MEAN

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MEAN = "Mean"
- 		-static
-
- -

Definition at line 101 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MEAN_SHIFT_FILTER

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MEAN_SHIFT_FILTER = "Mean Shift Filter"
- 		-static
-
- -

Definition at line 130 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MEASUREMENTS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MEASUREMENTS = "Measurements"
- 		-static
-
- -

Definition at line 93 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MEDIAN

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MEDIAN = "Median"
- 		-static
-
- -

Definition at line 100 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_BINARY

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_BINARY = "Binary"
- 		-static
-
- -

Definition at line 80 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_DENOISING

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_DENOISING = "Denoising"
- 		-static
-
- -

Definition at line 77 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_DRAW

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_DRAW = "Draw"
- 		-static
-
- -

Definition at line 86 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_FLIP

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_FLIP = "Flip"
- 		-static
-
- -

Definition at line 74 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_GO_TO

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_GO_TO = "Go to"
- 		-static
-
- -

Definition at line 84 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_INFO

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_INFO = "Info"
- 		-static
-
- -

Definition at line 81 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_MASKS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_MASKS = "Masks"
- 		-static
-
- -

Definition at line 170 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_OPEN_WITH

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_OPEN_WITH = "Open with..."
- 		-static
-
- -

Definition at line 78 of file XmippLabel.java.

- -
-
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◆ OPERATION_MENU_PROCESS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_PROCESS = "Process"
- 		-static
-
- -

Definition at line 82 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_ROTATE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_ROTATE = "Rotate"
- 		-static
-
- -

Definition at line 75 of file XmippLabel.java.

- -
-
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◆ OPERATION_MENU_THRESHOLD

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_THRESHOLD = "Threshold"
- 		-static
-
- -

Definition at line 85 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_THRESHOLDING

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_THRESHOLDING = "Thresholding"
- 		-static
-
- -

Definition at line 79 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MENU_TRANSFORM

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MENU_TRANSFORM = "Transform"
- 		-static
-
-

Operations

- -

Definition at line 72 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MIXTURE_MODELING_THRESHOLDING

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MIXTURE_MODELING_THRESHOLDING = "Mixture Modeling Thresholding"
- 		-static
-
- -

Definition at line 145 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MULTI_OTSU_THRESHOLDING

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MULTI_OTSU_THRESHOLDING = "Multi Otsu Threshold"
- 		-static
-
- -

Definition at line 144 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_MULTI_THRESHOLDER

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_MULTI_THRESHOLDER = "MultiThresholder"
- 		-static
-
- -

Definition at line 147 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_OPEN

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OPEN = "Open"
- 		-static
-
- -

Definition at line 153 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_OPEN_AS_3D

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OPEN_AS_3D = "3D Viewer"
- 		-static
-
- -

Definition at line 124 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_OPEN_AS_3D_VOLUME

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OPEN_AS_3D_VOLUME = "3D Volume"
- 		-static
-
- -

Definition at line 44 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_OPEN_AS_METADATA

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OPEN_AS_METADATA = "Metadata"
- 		-static
-
- -

Definition at line 45 of file XmippLabel.java.

- -
-
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◆ OPERATION_OPEN_AS_STACK

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OPEN_AS_STACK = "Stack"
- 		-static
-
- -

Definition at line 46 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_OPTIONS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OPTIONS = "Options"
- 		-static
-
- -

Definition at line 163 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_OTSU_THRESHOLDING

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OTSU_THRESHOLDING = "Otsu Thresholding"
- 		-static
-
- -

Definition at line 143 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_OUTLINE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OUTLINE = "Outline"
- 		-static
-
- -

Definition at line 156 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_OVAL_PROFILER_PLOT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_OVAL_PROFILER_PLOT = "Oval Profile Plot"
- 		-static
-
- -

Definition at line 136 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_PCA

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_PCA = "PCA Principal Component Analysis"
- 		-static
-
- -

Definition at line 165 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_PLOT_PROFILE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_PLOT_PROFILE = "Plot Profile"
- 		-static
-
- -

Definition at line 92 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_POLAR_TRANSFORMER

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_POLAR_TRANSFORMER = "Polar Transformer convert to polar coordinates"
- 		-static
-
- -

Definition at line 166 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_POLL

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_POLL = "Poll"
- 		-static
-
- -

Definition at line 125 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_RADIAL_GRID

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_RADIAL_GRID = "Radial Grid"
- 		-static
-
- -

Definition at line 168 of file XmippLabel.java.

- -
-
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◆ OPERATION_RADIAL_PROFILE_PLOT_ANGLE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_RADIAL_PROFILE_PLOT_ANGLE = "Radial Profile Plot Angle"
- 		-static
-
- -

Definition at line 137 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_RADIAL_PROFILE_PLOT_HEIGHT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_RADIAL_PROFILE_PLOT_HEIGHT = "Radial Profile Plot Height"
- 		-static
-
- -

Definition at line 138 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_RADIAL_RESLICE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_RADIAL_RESLICE = "Radial Reslice (orthogonal reconstructions)"
- 		-static
-
- -

Definition at line 107 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_RATS

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_RATS = "RATS Robust Automatic Threshold Selection"
- 		-static
-
- -

Definition at line 149 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_RESLICE_RIGHT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_RESLICE_RIGHT = "Reslice Right"
- 		-static
-
- -

Definition at line 105 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_RESLICE_TOP

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_RESLICE_TOP = "Reslice Top"
- 		-static
-
- -

Definition at line 104 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_ROTATE_LEFT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_ROTATE_LEFT = "Rotate Left"
- 		-static
-
- -

Definition at line 89 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_ROTATE_RIGHT

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_ROTATE_RIGHT = "Rotate Right"
- 		-static
-
- -

Definition at line 90 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_SIOX

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_SIOX = "SIOX Simple Interactive Object Extraction"
- 		-static
-
- -

Definition at line 148 of file XmippLabel.java.

- -
-
- -

◆ OPERATION_SKELETONIZE

- -
-
- - - - - -
- - - - -
final String xmipp.utils.XmippLabel.OPERATION_SKELETONIZE = "Skeletonize"
- 		-static
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Definition at line 158 of file XmippLabel.java.

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◆ OPERATION_STACK_SLICER

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final String xmipp.utils.XmippLabel.OPERATION_STACK_SLICER = "StackSlicer (dynamic orthogonal views)"
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Definition at line 106 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_STRAIGHTEN_CURVED_OBJECTS = "Straighten Curved Objects"
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Definition at line 108 of file XmippLabel.java.

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◆ OPERATION_SUBSTACK_MAKER

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final String xmipp.utils.XmippLabel.OPERATION_SUBSTACK_MAKER = "Substack Maker"
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Definition at line 128 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_SUBTRACTBG = "Subtract Background"
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Definition at line 97 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_SURFACEJ = "SurfaceJ"
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Definition at line 123 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_SYNC_MEASURE_3D = "Sync Measure 3D"
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Definition at line 142 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_SYNC_WINDOWS = "Sync Windows"
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Definition at line 141 of file XmippLabel.java.

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Definition at line 169 of file XmippLabel.java.

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Definition at line 96 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_TJABOUT = "TJ About"
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Definition at line 111 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_TJAFFINE = "TJ Affine"
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Definition at line 112 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_TJCROP = "TJ Crop"
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Definition at line 113 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_TJEMBED = "TJ Embed"
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Definition at line 114 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_TJMIRROR = "TJ Mirror"
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Definition at line 115 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_TJOPTIONS = "TJ Options"
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Definition at line 116 of file XmippLabel.java.

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Definition at line 117 of file XmippLabel.java.

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Definition at line 118 of file XmippLabel.java.

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Definition at line 120 of file XmippLabel.java.

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Definition at line 121 of file XmippLabel.java.

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Definition at line 122 of file XmippLabel.java.

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Definition at line 73 of file XmippLabel.java.

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Definition at line 110 of file XmippLabel.java.

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Definition at line 160 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_UNTILT_STACK = "Untilt Stack (removes tilt from a stack of images)"
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Definition at line 109 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_VOLUME_VIEWER_3D_SLICER = "Volume Viewer/3D-Slicer"
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Definition at line 131 of file XmippLabel.java.

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Definition at line 132 of file XmippLabel.java.

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Definition at line 162 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.OPERATION_VOXEL_COUNTER = "Voxel Counter"
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Definition at line 150 of file XmippLabel.java.

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Definition at line 161 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.TITLE_ABOUT = "About " + APP_NAME
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Definition at line 15 of file XmippLabel.java.

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Definition at line 26 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.TITLE_FSC = "FSC: "
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Definition at line 31 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.TITLE_GO_TO_SLICE = "Go to slice"
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Definition at line 27 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.TITLE_PREVIEW = "Preview:"
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Definition at line 28 of file XmippLabel.java.

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final String xmipp.utils.XmippLabel.TITLE_SEND2WINDOW = "Send image to window"
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Definition at line 30 of file XmippLabel.java.

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Definition at line 32 of file XmippLabel.java.

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This is the complete list of members for xmipp.utils.XmippMenuBarCreator, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippMenuCreatorinline
addItem(String key, String text, String... values)xmipp.utils.XmippMenuCreatorinline
addSeparator(String key)xmipp.utils.XmippMenuBarCreatorinline
createItems()xmipp.utils.XmippMenuCreatorprotected
CTF_PROFILExmipp.utils.XmippMenuCreatorstatic
CTF_RECALCULATExmipp.utils.XmippMenuCreatorstatic
DISABLEDxmipp.utils.XmippMenuCreatorstatic
DISPLAYxmipp.utils.XmippMenuCreator
DISPLAY_APPLYGEOxmipp.utils.XmippMenuCreator
DISPLAY_COLUMNSxmipp.utils.XmippMenuCreator
DISPLAY_INVERTYxmipp.utils.XmippMenuCreator
DISPLAY_NORMALIZExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGESxmipp.utils.XmippMenuCreator
DISPLAY_RESLICExmipp.utils.XmippMenuCreator
DISPLAY_RESLICE_VIEWSxmipp.utils.XmippMenuCreator
DISPLAY_SHOWLABELSxmipp.utils.XmippMenuCreator
DISPLAY_WRAPxmipp.utils.XmippMenuCreator
ENABLEDxmipp.utils.XmippMenuCreatorstatic
FILExmipp.utils.XmippMenuCreator
FILE_EXITxmipp.utils.XmippMenuCreator
FILE_EXPORTIMAGESxmipp.utils.XmippMenuCreator
FILE_INFOxmipp.utils.XmippMenuCreator
FILE_LINK_CHIMERAxmipp.utils.XmippMenuCreator
FILE_LOAD_SELxmipp.utils.XmippMenuCreator
FILE_OPENxmipp.utils.XmippMenuCreator
FILE_OPENMICROGRAPHSxmipp.utils.XmippMenuCreator
FILE_OPENWITH_CHIMERAxmipp.utils.XmippMenuCreator
FILE_OPENWITH_IJxmipp.utils.XmippMenuCreator
FILE_REFRESHxmipp.utils.XmippMenuCreator
FILE_SAVExmipp.utils.XmippMenuCreator
FILE_SAVE_SELxmipp.utils.XmippMenuCreator
FILE_SAVEASxmipp.utils.XmippMenuCreator
getItem(String key)xmipp.utils.XmippMenuCreatorinline
getItemEnabled(String key)xmipp.utils.XmippMenuCreatorinline
getItemSelected(String key)xmipp.utils.XmippMenuCreatorinline
getMenuBar()xmipp.utils.XmippMenuBarCreatorinline
groupsxmipp.utils.XmippMenuCreatorprotected
handleActionPerformed(ActionEvent evt)xmipp.utils.XmippMenuCreatorprotected
HELPxmipp.utils.XmippMenuCreator
HELP_ONLINExmipp.utils.XmippMenuCreator
initItems()xmipp.utils.XmippMenuCreatorinline
INVERT_SELECTxmipp.utils.XmippMenuCreatorstatic
itemsxmipp.utils.XmippMenuCreatorprotected
KEY_ASSISTxmipp.utils.XmippMenuCreator
MD_ADD_OBJECTxmipp.utils.XmippMenuCreator
MD_CLASSESxmipp.utils.XmippMenuCreator
MD_EDIT_COLSxmipp.utils.XmippMenuCreator
MD_FIND_REPLACExmipp.utils.XmippMenuCreator
MD_REMOVE_DISABLEDxmipp.utils.XmippMenuCreator
MD_REMOVE_SELECTIONxmipp.utils.XmippMenuCreator
MD_SAVE_SELECTIONxmipp.utils.XmippMenuCreator
menuxmipp.utils.XmippMenuCreatorprotected
METADATAxmipp.utils.XmippMenuCreator
OPENxmipp.utils.XmippMenuCreatorstatic
OPEN_ASTEXTxmipp.utils.XmippMenuCreatorstatic
OPEN_IMAGESxmipp.utils.XmippMenuCreatorstatic
REFRESHxmipp.utils.XmippMenuCreatorstatic
SAVE_IMAGESxmipp.utils.XmippMenuCreatorstatic
SELECTxmipp.utils.XmippMenuCreatorstatic
SELECT_ALLxmipp.utils.XmippMenuCreatorstatic
SELECT_FROMHERExmipp.utils.XmippMenuCreatorstatic
SELECT_TOHERExmipp.utils.XmippMenuCreatorstatic
SET_CLASSxmipp.utils.XmippMenuCreatorstatic
setItemEnabled(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemSelected(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemVisible(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
TOOLSxmipp.utils.XmippMenuCreator
TOOLS_AVGSTDxmipp.utils.XmippMenuCreator
TOOLS_FSCxmipp.utils.XmippMenuCreator
TOOLS_PCAxmipp.utils.XmippMenuCreator
TOOLS_PLOTxmipp.utils.XmippMenuCreator
XmippMenuBarCreator()xmipp.utils.XmippMenuBarCreatorinline
XmippMenuCreator(JComponent menu)xmipp.utils.XmippMenuCreatorinline
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- - diff --git a/html/classxmipp_1_1utils_1_1XmippMenuBarCreator.html b/html/classxmipp_1_1utils_1_1XmippMenuBarCreator.html deleted file mode 100644 index b46608a3..00000000 --- a/html/classxmipp_1_1utils_1_1XmippMenuBarCreator.html +++ /dev/null @@ -1,349 +0,0 @@ - - - - - - - -Xmipp: xmipp.utils.XmippMenuBarCreator Class Reference - - - - - - - - - -
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xmipp.utils.XmippMenuBarCreator Class Referenceabstract
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-Public Member Functions

 XmippMenuBarCreator ()
 
JMenuBar getMenuBar ()
 
void addSeparator (String key)
 
- Public Member Functions inherited from xmipp.utils.XmippMenuCreator
 XmippMenuCreator (JComponent menu)
 
JMenuItem addItem (String key, String text, String... values)
 
JMenuItem getItem (String key)
 
boolean getItemEnabled (String key)
 
void setItemEnabled (String key, boolean value)
 
boolean getItemSelected (String key)
 
void setItemSelected (String key, boolean value)
 
void setItemVisible (String key, boolean value)
 
void actionPerformed (ActionEvent evt)
 
void initItems ()
 
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-Additional Inherited Members

- Public Attributes inherited from xmipp.utils.XmippMenuCreator
final String FILE = "File"
 
final String FILE_OPEN = "File.Open_mi"
 
final String FILE_OPENWITH_IJ = "File.OpenWithIJ_mi"
 
final String FILE_OPENMICROGRAPHS = "File.OpenMicrographs_mi"
 
final String FILE_OPENWITH_CHIMERA = "File.OpenWithChimera_mi"
 
final String FILE_INFO = "File.FileInfo_mi"
 
final String FILE_SAVE = "File.Save_mi"
 
final String FILE_SAVEAS = "File.SaveAs_mi"
 
final String FILE_LOAD_SEL = "File.LoadSel_mi"
 
final String FILE_SAVE_SEL = "File.SaveSel_mi"
 
final String FILE_EXPORTIMAGES = "File.ExportImages_mi"
 
final String FILE_REFRESH = "File.Refresh_mi"
 
final String FILE_EXIT = "File.Exit_mi"
 
final String FILE_LINK_CHIMERA = "File.LinkWithChimera_mi"
 
final String DISPLAY = "Display"
 
final String DISPLAY_SHOWLABELS = "Display.ShowLabel"
 
final String DISPLAY_RENDERIMAGES = "Display.RenderImages_cb"
 
final String DISPLAY_RENDERIMAGE = "Display.RenderImage"
 
final String DISPLAY_INVERTY = "Display.InvertY_cb"
 
final String DISPLAY_APPLYGEO = "Display.ApplyGeo_cb"
 
final String DISPLAY_WRAP = "Display.Wrap_cb"
 
final String DISPLAY_NORMALIZE = "Display.Normalize_cb"
 
final String DISPLAY_COLUMNS = "Display.Columns_mi"
 
final String DISPLAY_RESLICE = "Display.Reslice"
 
final String DISPLAY_RESLICE_VIEWS []
 
final String METADATA = "Metadata"
 
final String MD_CLASSES = "Metadata.Classes_mi"
 
final String MD_EDIT_COLS = "Metadata.EditCols_mi"
 
final String MD_ADD_OBJECT = "Metadata.AddObject_mi"
 
final String MD_REMOVE_SELECTION = "Metadata.RemoveSelection_mi"
 
final String MD_SAVE_SELECTION = "Metadata.SaveSelection_mi"
 
final String MD_REMOVE_DISABLED = "Metadata.RemoveDisabled_mi"
 
final String TOOLS = "Tools"
 
final String TOOLS_AVGSTD = "Tools.AvgStd_mi"
 
final String TOOLS_PCA = "Tools.Pca_mi"
 
final String TOOLS_FSC = "Tools.Fsc_mi"
 
final String TOOLS_PLOT = "Tools.Plot_mi"
 
final String MD_FIND_REPLACE = "Tools.FindReplace_mi"
 
final String HELP = "Help"
 
final String HELP_ONLINE = "Help.Online_mi"
 
final String KEY_ASSIST = "Help.Key_mi"
 
- Static Public Attributes inherited from xmipp.utils.XmippMenuCreator
static final String ENABLED = "Enabled_mi"
 
static final String DISABLED = "Disabled_mi"
 
static final String REFRESH = "Refresh_mi"
 
static final String OPEN = "Open_mi"
 
static final String OPEN_ASTEXT = "OpenAsText_mi"
 
static final String CTF_PROFILE = "CTFProfile_mi"
 
static final String CTF_RECALCULATE = "CTFRecalculate_cb"
 
static final String SELECT = "Select"
 
static final String SELECT_ALL = "Select.All_mi"
 
static final String SELECT_TOHERE = "Select.ToHere_mi"
 
static final String SELECT_FROMHERE = "Select.FromHere_mi"
 
static final String INVERT_SELECT = "Select.InvertSelection_mi"
 
static final String SET_CLASS = "SetClass_mi"
 
static final String OPEN_IMAGES = "OpenImages_mi"
 
static final String SAVE_IMAGES = "SaveImages_mi"
 
- Protected Member Functions inherited from xmipp.utils.XmippMenuCreator
abstract void handleActionPerformed (ActionEvent evt)
 
abstract void createItems () throws Exception
 
- Protected Attributes inherited from xmipp.utils.XmippMenuCreator
Map< String, JMenuItem > items
 
Map< String, ButtonGroup > groups
 
JComponent menu
 
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Detailed Description

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Definition at line 31 of file XmippMenuBarCreator.java.

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Constructor & Destructor Documentation

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◆ XmippMenuBarCreator()

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xmipp.utils.XmippMenuBarCreator.XmippMenuBarCreator ()
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Definition at line 33 of file XmippMenuBarCreator.java.

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◆ addSeparator()

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void xmipp.utils.XmippMenuBarCreator.addSeparator (String key)
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Definition at line 41 of file XmippMenuBarCreator.java.

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41  {
42  JMenu menu = (JMenu) items.get(key);
43  menu.addSeparator();
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Definition: XmippMenuCreator.java:24
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◆ getMenuBar()

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JMenuBar xmipp.utils.XmippMenuBarCreator.getMenuBar ()
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Definition at line 37 of file XmippMenuBarCreator.java.

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37  {
38  return (JMenuBar)menu;
39  }
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xmipp.utils.XmippMenuCreator Member List
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This is the complete list of members for xmipp.utils.XmippMenuCreator, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippMenuCreatorinline
addItem(String key, String text, String... values)xmipp.utils.XmippMenuCreatorinline
createItems()xmipp.utils.XmippMenuCreatorprotected
CTF_PROFILExmipp.utils.XmippMenuCreatorstatic
CTF_RECALCULATExmipp.utils.XmippMenuCreatorstatic
DISABLEDxmipp.utils.XmippMenuCreatorstatic
DISPLAYxmipp.utils.XmippMenuCreator
DISPLAY_APPLYGEOxmipp.utils.XmippMenuCreator
DISPLAY_COLUMNSxmipp.utils.XmippMenuCreator
DISPLAY_INVERTYxmipp.utils.XmippMenuCreator
DISPLAY_NORMALIZExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGESxmipp.utils.XmippMenuCreator
DISPLAY_RESLICExmipp.utils.XmippMenuCreator
DISPLAY_RESLICE_VIEWSxmipp.utils.XmippMenuCreator
DISPLAY_SHOWLABELSxmipp.utils.XmippMenuCreator
DISPLAY_WRAPxmipp.utils.XmippMenuCreator
ENABLEDxmipp.utils.XmippMenuCreatorstatic
FILExmipp.utils.XmippMenuCreator
FILE_EXITxmipp.utils.XmippMenuCreator
FILE_EXPORTIMAGESxmipp.utils.XmippMenuCreator
FILE_INFOxmipp.utils.XmippMenuCreator
FILE_LINK_CHIMERAxmipp.utils.XmippMenuCreator
FILE_LOAD_SELxmipp.utils.XmippMenuCreator
FILE_OPENxmipp.utils.XmippMenuCreator
FILE_OPENMICROGRAPHSxmipp.utils.XmippMenuCreator
FILE_OPENWITH_CHIMERAxmipp.utils.XmippMenuCreator
FILE_OPENWITH_IJxmipp.utils.XmippMenuCreator
FILE_REFRESHxmipp.utils.XmippMenuCreator
FILE_SAVExmipp.utils.XmippMenuCreator
FILE_SAVE_SELxmipp.utils.XmippMenuCreator
FILE_SAVEASxmipp.utils.XmippMenuCreator
getItem(String key)xmipp.utils.XmippMenuCreatorinline
getItemEnabled(String key)xmipp.utils.XmippMenuCreatorinline
getItemSelected(String key)xmipp.utils.XmippMenuCreatorinline
groupsxmipp.utils.XmippMenuCreatorprotected
handleActionPerformed(ActionEvent evt)xmipp.utils.XmippMenuCreatorprotected
HELPxmipp.utils.XmippMenuCreator
HELP_ONLINExmipp.utils.XmippMenuCreator
initItems()xmipp.utils.XmippMenuCreatorinline
INVERT_SELECTxmipp.utils.XmippMenuCreatorstatic
itemsxmipp.utils.XmippMenuCreatorprotected
KEY_ASSISTxmipp.utils.XmippMenuCreator
MD_ADD_OBJECTxmipp.utils.XmippMenuCreator
MD_CLASSESxmipp.utils.XmippMenuCreator
MD_EDIT_COLSxmipp.utils.XmippMenuCreator
MD_FIND_REPLACExmipp.utils.XmippMenuCreator
MD_REMOVE_DISABLEDxmipp.utils.XmippMenuCreator
MD_REMOVE_SELECTIONxmipp.utils.XmippMenuCreator
MD_SAVE_SELECTIONxmipp.utils.XmippMenuCreator
menuxmipp.utils.XmippMenuCreatorprotected
METADATAxmipp.utils.XmippMenuCreator
OPENxmipp.utils.XmippMenuCreatorstatic
OPEN_ASTEXTxmipp.utils.XmippMenuCreatorstatic
OPEN_IMAGESxmipp.utils.XmippMenuCreatorstatic
REFRESHxmipp.utils.XmippMenuCreatorstatic
SAVE_IMAGESxmipp.utils.XmippMenuCreatorstatic
SELECTxmipp.utils.XmippMenuCreatorstatic
SELECT_ALLxmipp.utils.XmippMenuCreatorstatic
SELECT_FROMHERExmipp.utils.XmippMenuCreatorstatic
SELECT_TOHERExmipp.utils.XmippMenuCreatorstatic
SET_CLASSxmipp.utils.XmippMenuCreatorstatic
setItemEnabled(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemSelected(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemVisible(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
TOOLSxmipp.utils.XmippMenuCreator
TOOLS_AVGSTDxmipp.utils.XmippMenuCreator
TOOLS_FSCxmipp.utils.XmippMenuCreator
TOOLS_PCAxmipp.utils.XmippMenuCreator
TOOLS_PLOTxmipp.utils.XmippMenuCreator
XmippMenuCreator(JComponent menu)xmipp.utils.XmippMenuCreatorinline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1utils_1_1XmippMenuCreator.html b/html/classxmipp_1_1utils_1_1XmippMenuCreator.html deleted file mode 100644 index b25d15df..00000000 --- a/html/classxmipp_1_1utils_1_1XmippMenuCreator.html +++ /dev/null @@ -1,1761 +0,0 @@ - - - - - - - -Xmipp: xmipp.utils.XmippMenuCreator Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Public Attributes | -Static Public Attributes | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.utils.XmippMenuCreator Class Referenceabstract
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-Public Member Functions

 XmippMenuCreator (JComponent menu)
 
JMenuItem addItem (String key, String text, String... values)
 
JMenuItem getItem (String key)
 
boolean getItemEnabled (String key)
 
void setItemEnabled (String key, boolean value)
 
boolean getItemSelected (String key)
 
void setItemSelected (String key, boolean value)
 
void setItemVisible (String key, boolean value)
 
void actionPerformed (ActionEvent evt)
 
void initItems ()
 
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-Public Attributes

final String FILE = "File"
 
final String FILE_OPEN = "File.Open_mi"
 
final String FILE_OPENWITH_IJ = "File.OpenWithIJ_mi"
 
final String FILE_OPENMICROGRAPHS = "File.OpenMicrographs_mi"
 
final String FILE_OPENWITH_CHIMERA = "File.OpenWithChimera_mi"
 
final String FILE_INFO = "File.FileInfo_mi"
 
final String FILE_SAVE = "File.Save_mi"
 
final String FILE_SAVEAS = "File.SaveAs_mi"
 
final String FILE_LOAD_SEL = "File.LoadSel_mi"
 
final String FILE_SAVE_SEL = "File.SaveSel_mi"
 
final String FILE_EXPORTIMAGES = "File.ExportImages_mi"
 
final String FILE_REFRESH = "File.Refresh_mi"
 
final String FILE_EXIT = "File.Exit_mi"
 
final String FILE_LINK_CHIMERA = "File.LinkWithChimera_mi"
 
final String DISPLAY = "Display"
 
final String DISPLAY_SHOWLABELS = "Display.ShowLabel"
 
final String DISPLAY_RENDERIMAGES = "Display.RenderImages_cb"
 
final String DISPLAY_RENDERIMAGE = "Display.RenderImage"
 
final String DISPLAY_INVERTY = "Display.InvertY_cb"
 
final String DISPLAY_APPLYGEO = "Display.ApplyGeo_cb"
 
final String DISPLAY_WRAP = "Display.Wrap_cb"
 
final String DISPLAY_NORMALIZE = "Display.Normalize_cb"
 
final String DISPLAY_COLUMNS = "Display.Columns_mi"
 
final String DISPLAY_RESLICE = "Display.Reslice"
 
final String DISPLAY_RESLICE_VIEWS []
 
final String METADATA = "Metadata"
 
final String MD_CLASSES = "Metadata.Classes_mi"
 
final String MD_EDIT_COLS = "Metadata.EditCols_mi"
 
final String MD_ADD_OBJECT = "Metadata.AddObject_mi"
 
final String MD_REMOVE_SELECTION = "Metadata.RemoveSelection_mi"
 
final String MD_SAVE_SELECTION = "Metadata.SaveSelection_mi"
 
final String MD_REMOVE_DISABLED = "Metadata.RemoveDisabled_mi"
 
final String TOOLS = "Tools"
 
final String TOOLS_AVGSTD = "Tools.AvgStd_mi"
 
final String TOOLS_PCA = "Tools.Pca_mi"
 
final String TOOLS_FSC = "Tools.Fsc_mi"
 
final String TOOLS_PLOT = "Tools.Plot_mi"
 
final String MD_FIND_REPLACE = "Tools.FindReplace_mi"
 
final String HELP = "Help"
 
final String HELP_ONLINE = "Help.Online_mi"
 
final String KEY_ASSIST = "Help.Key_mi"
 
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-Static Public Attributes

static final String ENABLED = "Enabled_mi"
 
static final String DISABLED = "Disabled_mi"
 
static final String REFRESH = "Refresh_mi"
 
static final String OPEN = "Open_mi"
 
static final String OPEN_ASTEXT = "OpenAsText_mi"
 
static final String CTF_PROFILE = "CTFProfile_mi"
 
static final String CTF_RECALCULATE = "CTFRecalculate_cb"
 
static final String SELECT = "Select"
 
static final String SELECT_ALL = "Select.All_mi"
 
static final String SELECT_TOHERE = "Select.ToHere_mi"
 
static final String SELECT_FROMHERE = "Select.FromHere_mi"
 
static final String INVERT_SELECT = "Select.InvertSelection_mi"
 
static final String SET_CLASS = "SetClass_mi"
 
static final String OPEN_IMAGES = "OpenImages_mi"
 
static final String SAVE_IMAGES = "SaveImages_mi"
 
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-Protected Member Functions

abstract void handleActionPerformed (ActionEvent evt)
 
abstract void createItems () throws Exception
 
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-Protected Attributes

Map< String, JMenuItem > items
 
Map< String, ButtonGroup > groups
 
JComponent menu
 
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Detailed Description

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This a menu creator to provide some useful functions to define menu structures It will allow creation of JMenuBar and JPopupMenu

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Definition at line 22 of file XmippMenuCreator.java.

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Constructor & Destructor Documentation

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◆ XmippMenuCreator()

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xmipp.utils.XmippMenuCreator.XmippMenuCreator (JComponent menu)
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Definition at line 33 of file XmippMenuCreator.java.

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33  {
34  try {
35  this.menu = menu;
36  items = new Hashtable<String, JMenuItem>();
37  groups = new HashMap<String, ButtonGroup>();
38  createItems();
39  } catch (Exception e){
40  e.printStackTrace();
41  }
42  }
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xmipp.utils.XmippMenuCreator.groups
Map< String, ButtonGroup > groups
Definition: XmippMenuCreator.java:29
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Map< String, JMenuItem > items
Definition: XmippMenuCreator.java:24
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◆ actionPerformed()

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void xmipp.utils.XmippMenuCreator.actionPerformed (ActionEvent evt)
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Definition at line 165 of file XmippMenuCreator.java.

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165  {
166  handleActionPerformed(evt);
167  }
xmipp.utils.XmippMenuCreator.handleActionPerformed
abstract void handleActionPerformed(ActionEvent evt)
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JMenuItem xmipp.utils.XmippMenuCreator.addItem (String key,
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The idea behind this method is simplify the creation of menu options. The name of the menu item should be Parent.Item to refer to parent, and also the prefix cb_ and rb_ shoulb be used to create JCheckBoxMenuItem and JRadioButtonMenuItem respectively Example: addItem("File", "File"); addItem("File.SaveAs", "Save as...", "save_as.gif")

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Definition at line 56 of file XmippMenuCreator.java.

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56  {
57 
58  String name = key;
59  String parentname = null;
60  JMenuItem item = null;
61  JMenu parent = null;
62  boolean isMenu = false;
63 
64  try {
65  if (key.contains(".")) {
66  int pos = key.lastIndexOf(".");
67  name = key.substring(pos + 1);
68  parentname = key.substring(0, pos);
69  parent = (JMenu)getItem(parentname);
70  }
71 
72  // Create the right type of menu item
73  if (name.endsWith("cb"))
74  item = new JCheckBoxMenuItem();
75  else if (name.endsWith("rb")){
76  ButtonGroup group = groups.get(parentname);
77  if (group == null)
78  {
79  group = new ButtonGroup();
80  groups.put(parentname, group);
81  }
82  item = new JRadioButtonMenuItem();
83  group.add(item);
84 
85  }
86  else if (name.endsWith("mi"))
87  {
88  item = new JMenuItem();
89 
90  }
91  else {
92  item = new JMenu();
93  isMenu = true;
94  }
95  // Setup the item
96  item.setText(text);
97  item.setActionCommand(key);
98  item.addActionListener(this);
99  // Store item and add to menu
100  items.put(key, item);
101 
102  if (!isMenu) {
103  int n = values.length;
104  switch (n) {
105  case 2:
106  // The second argument could be the keystroke, be careful
107  item.setAccelerator(KeyStroke.getKeyStroke(values[1]));
108  case 1:
109  if (values[0] != null)
110  item.setIcon(XmippResource.getIcon(values[0]));
111  break;
112  case 0:
113  break; // ignore if no arguments
114  default:
115  throw new Exception(
116  "No more than 2 arguments to create menu item!!!");
117  }
118  }
119 
120  if (parent == null)
121  menu.add(item);
122  else
123  parent.add(item);
124  } catch (Exception e){
125  e.printStackTrace();
126  }
127  return item;
128  }
xmipp.utils.XmippMenuCreator.getItem
JMenuItem getItem(String key)
Definition: XmippMenuCreator.java:130
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Map< String, ButtonGroup > groups
Definition: XmippMenuCreator.java:29
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Map< String, JMenuItem > items
Definition: XmippMenuCreator.java:24
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abstract void xmipp.utils.XmippMenuCreator.createItems () throws Exception
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This abstract method will be called from constructor to create the items

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Definition at line 130 of file XmippMenuCreator.java.

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130  {
131  return items.get(key);
132  }
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Map< String, JMenuItem > items
Definition: XmippMenuCreator.java:24
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Definition at line 134 of file XmippMenuCreator.java.

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134  {
135  return getItem(key).isEnabled();
136  }
xmipp.utils.XmippMenuCreator.getItem
JMenuItem getItem(String key)
Definition: XmippMenuCreator.java:130
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Definition at line 142 of file XmippMenuCreator.java.

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142  {
143  // Create the right type of menu item
144  if (key.endsWith("rb"))
145  return ((JRadioButtonMenuItem)getItem(key)).isSelected();
146  if (key.endsWith("cb"))
147  return ((JCheckBoxMenuItem)getItem(key)).isSelected();
148  return false;
149  }
xmipp.utils.XmippMenuCreator.getItem
JMenuItem getItem(String key)
Definition: XmippMenuCreator.java:130
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Method to initialize items state

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Definition at line 178 of file XmippMenuCreator.java.

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Definition at line 138 of file XmippMenuCreator.java.

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138  {
139  getItem(key).setEnabled(value);
140  }
xmipp.utils.XmippMenuCreator.getItem
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Definition: XmippMenuCreator.java:130
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Definition at line 151 of file XmippMenuCreator.java.

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151  {
152  //DEBUG.printMessage("setItemSelected -> key:" + key);
153  // Create the right type of menu item
154  if (key.endsWith("rb"))
155  ((JRadioButtonMenuItem)getItem(key)).setSelected(value);
156  else if (key.endsWith("cb"))
157  ((JCheckBoxMenuItem)getItem(key)).setSelected(value);
158  }
xmipp.utils.XmippMenuCreator.getItem
JMenuItem getItem(String key)
Definition: XmippMenuCreator.java:130
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void xmipp.utils.XmippMenuCreator.setItemVisible (String key,
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Definition at line 160 of file XmippMenuCreator.java.

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160  {
161  getItem(key).setVisible(value);
162  }
xmipp.utils.XmippMenuCreator.getItem
JMenuItem getItem(String key)
Definition: XmippMenuCreator.java:130
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Member Data Documentation

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◆ CTF_PROFILE

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final String xmipp.utils.XmippMenuCreator.CTF_PROFILE = "CTFProfile_mi"
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Definition at line 243 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.CTF_RECALCULATE = "CTFRecalculate_cb"
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Definition at line 244 of file XmippMenuCreator.java.

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◆ DISABLED

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final String xmipp.utils.XmippMenuCreator.DISABLED = "Disabled_mi"
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Definition at line 239 of file XmippMenuCreator.java.

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◆ DISPLAY

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final String xmipp.utils.XmippMenuCreator.DISPLAY = "Display"
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Definition at line 196 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.DISPLAY_APPLYGEO = "Display.ApplyGeo_cb"
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Definition at line 205 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.DISPLAY_COLUMNS = "Display.Columns_mi"
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Definition at line 208 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.DISPLAY_INVERTY = "Display.InvertY_cb"
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Definition at line 204 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.DISPLAY_NORMALIZE = "Display.Normalize_cb"
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Definition at line 207 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.DISPLAY_RENDERIMAGE = "Display.RenderImage"
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Definition at line 202 of file XmippMenuCreator.java.

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◆ DISPLAY_RENDERIMAGES

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final String xmipp.utils.XmippMenuCreator.DISPLAY_RENDERIMAGES = "Display.RenderImages_cb"
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Definition at line 200 of file XmippMenuCreator.java.

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◆ DISPLAY_RESLICE

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final String xmipp.utils.XmippMenuCreator.DISPLAY_RESLICE = "Display.Reslice"
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Definition at line 209 of file XmippMenuCreator.java.

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◆ DISPLAY_RESLICE_VIEWS

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final String xmipp.utils.XmippMenuCreator.DISPLAY_RESLICE_VIEWS[]
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-Initial value:
= {
"Display.Reslice.ZNeg_rb",
"Display.Reslice.YNeg_rb",
"Display.Reslice.XNeg_rb",
"Display.Reslice.YPos_rb",
"Display.Reslice.XPos_rb"}
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Definition at line 210 of file XmippMenuCreator.java.

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◆ DISPLAY_SHOWLABELS

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final String xmipp.utils.XmippMenuCreator.DISPLAY_SHOWLABELS = "Display.ShowLabel"
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Definition at line 199 of file XmippMenuCreator.java.

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◆ DISPLAY_WRAP

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final String xmipp.utils.XmippMenuCreator.DISPLAY_WRAP = "Display.Wrap_cb"
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Definition at line 206 of file XmippMenuCreator.java.

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◆ ENABLED

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final String xmipp.utils.XmippMenuCreator.ENABLED = "Enabled_mi"
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Definition at line 238 of file XmippMenuCreator.java.

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◆ FILE

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final String xmipp.utils.XmippMenuCreator.FILE = "File"
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Definition at line 182 of file XmippMenuCreator.java.

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◆ FILE_EXIT

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final String xmipp.utils.XmippMenuCreator.FILE_EXIT = "File.Exit_mi"
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Definition at line 194 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_EXPORTIMAGES = "File.ExportImages_mi"
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Definition at line 192 of file XmippMenuCreator.java.

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◆ FILE_INFO

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final String xmipp.utils.XmippMenuCreator.FILE_INFO = "File.FileInfo_mi"
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Definition at line 187 of file XmippMenuCreator.java.

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◆ FILE_LINK_CHIMERA

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final String xmipp.utils.XmippMenuCreator.FILE_LINK_CHIMERA = "File.LinkWithChimera_mi"
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Definition at line 195 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_LOAD_SEL = "File.LoadSel_mi"
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Definition at line 190 of file XmippMenuCreator.java.

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◆ FILE_OPEN

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final String xmipp.utils.XmippMenuCreator.FILE_OPEN = "File.Open_mi"
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Definition at line 183 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_OPENMICROGRAPHS = "File.OpenMicrographs_mi"
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Definition at line 185 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_OPENWITH_CHIMERA = "File.OpenWithChimera_mi"
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Definition at line 186 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_OPENWITH_IJ = "File.OpenWithIJ_mi"
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Definition at line 184 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_REFRESH = "File.Refresh_mi"
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Definition at line 193 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_SAVE = "File.Save_mi"
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Definition at line 188 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_SAVE_SEL = "File.SaveSel_mi"
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Definition at line 191 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.FILE_SAVEAS = "File.SaveAs_mi"
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Definition at line 189 of file XmippMenuCreator.java.

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This will be used to group Radiobuttons under a Menu A new menu defines a new group and also a separator in the same menu defines a new group;

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Definition at line 29 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.HELP = "Help"
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Definition at line 232 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.HELP_ONLINE = "Help.Online_mi"
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Definition at line 233 of file XmippMenuCreator.java.

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Definition at line 249 of file XmippMenuCreator.java.

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Definition at line 24 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.KEY_ASSIST = "Help.Key_mi"
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Definition at line 234 of file XmippMenuCreator.java.

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Definition at line 221 of file XmippMenuCreator.java.

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Definition at line 219 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.MD_EDIT_COLS = "Metadata.EditCols_mi"
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Definition at line 220 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.MD_FIND_REPLACE = "Tools.FindReplace_mi"
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Definition at line 230 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.MD_REMOVE_DISABLED = "Metadata.RemoveDisabled_mi"
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Definition at line 224 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.MD_REMOVE_SELECTION = "Metadata.RemoveSelection_mi"
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Definition at line 222 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.MD_SAVE_SELECTION = "Metadata.SaveSelection_mi"
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Definition at line 223 of file XmippMenuCreator.java.

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Definition at line 30 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.METADATA = "Metadata"
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Definition at line 217 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.OPEN = "Open_mi"
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Definition at line 241 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.OPEN_ASTEXT = "OpenAsText_mi"
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Definition at line 242 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.OPEN_IMAGES = "OpenImages_mi"
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Definition at line 251 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.REFRESH = "Refresh_mi"
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Definition at line 240 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.SAVE_IMAGES = "SaveImages_mi"
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Definition at line 252 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.SELECT = "Select"
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Definition at line 245 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.SELECT_ALL = "Select.All_mi"
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Definition at line 246 of file XmippMenuCreator.java.

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◆ SELECT_FROMHERE

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final String xmipp.utils.XmippMenuCreator.SELECT_FROMHERE = "Select.FromHere_mi"
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Definition at line 248 of file XmippMenuCreator.java.

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◆ SELECT_TOHERE

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final String xmipp.utils.XmippMenuCreator.SELECT_TOHERE = "Select.ToHere_mi"
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Definition at line 247 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.SET_CLASS = "SetClass_mi"
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Definition at line 250 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.TOOLS = "Tools"
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Definition at line 225 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.TOOLS_AVGSTD = "Tools.AvgStd_mi"
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Definition at line 226 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.TOOLS_FSC = "Tools.Fsc_mi"
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Definition at line 228 of file XmippMenuCreator.java.

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final String xmipp.utils.XmippMenuCreator.TOOLS_PCA = "Tools.Pca_mi"
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Definition at line 227 of file XmippMenuCreator.java.

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◆ TOOLS_PLOT

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final String xmipp.utils.XmippMenuCreator.TOOLS_PLOT = "Tools.Plot_mi"
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Definition at line 229 of file XmippMenuCreator.java.

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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1utils_1_1XmippMenuCreator__coll__graph.dot b/html/classxmipp_1_1utils_1_1XmippMenuCreator__coll__graph.dot deleted file mode 100644 index 6a2dfbb9..00000000 --- a/html/classxmipp_1_1utils_1_1XmippMenuCreator__coll__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.utils.XmippMenuCreator" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node7 [label="xmipp.utils.XmippMenuCreator",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node8 -> Node7 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node8 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node7 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" groups" ,fontname="Helvetica"]; - Node9 [label="Map\< String, ButtonGroup \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node7 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" menu" ,fontname="Helvetica"]; - Node10 [label="JComponent",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node11 -> Node7 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" items" ,fontname="Helvetica"]; - Node11 [label="Map\< String, JMenuItem \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1XmippMenuCreator__coll__graph.md5 b/html/classxmipp_1_1utils_1_1XmippMenuCreator__coll__graph.md5 deleted file mode 100644 index c170925d..00000000 --- a/html/classxmipp_1_1utils_1_1XmippMenuCreator__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -b61399745e6f349cd0b58cebcd304515 \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1XmippMenuCreator__inherit__graph.dot b/html/classxmipp_1_1utils_1_1XmippMenuCreator__inherit__graph.dot deleted file mode 100644 index 7e7b8db8..00000000 --- a/html/classxmipp_1_1utils_1_1XmippMenuCreator__inherit__graph.dot +++ /dev/null @@ -1,19 +0,0 @@ -digraph "xmipp.utils.XmippMenuCreator" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node0 [label="xmipp.utils.XmippMenuCreator",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node0 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.utils.XmippMenuBar\lCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuBarCreator.html"]; - Node2 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.windows.Gallery\lJFrame.GalleryMenu",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu.html"]; - Node3 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="xmipp.viewer.scipion.Scipion\lGalleryJFrame.ScipionGalleryMenu",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu.html"]; - Node0 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="xmipp.utils.XmippPopupMenu\lCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippPopupMenuCreator.html"]; - Node5 -> Node6 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="xmipp.viewer.windows.Gallery\lJFrame.GalleryPopupMenu",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1XmippMenuCreator__inherit__graph.md5 b/html/classxmipp_1_1utils_1_1XmippMenuCreator__inherit__graph.md5 deleted file mode 100644 index 013ab94c..00000000 --- a/html/classxmipp_1_1utils_1_1XmippMenuCreator__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -21b2b31b3c3dcec65f7e027855248fff \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1XmippMessage-members.html b/html/classxmipp_1_1utils_1_1XmippMessage-members.html deleted file mode 100644 index 62f0c8bb..00000000 --- a/html/classxmipp_1_1utils_1_1XmippMessage-members.html +++ /dev/null @@ -1,96 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.utils.XmippMessage Member List
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This is the complete list of members for xmipp.utils.XmippMessage, including all inherited members.

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getAlreadyExistsGroupNameMsg(String name)xmipp.utils.XmippMessageinlinestatic
getAssociatedDataMsg(String field)xmipp.utils.XmippMessageinlinestatic
getEmptyFieldMsg(String field)xmipp.utils.XmippMessageinlinestatic
getFileTypeNotSupportedMsg(String path)xmipp.utils.XmippMessageinlinestatic
getIllegalDeleteMsg(String item)xmipp.utils.XmippMessageinlinestatic
getIllegalStateForOperationMsg(String field, String value)xmipp.utils.XmippMessageinlinestatic
getIllegalValueMsg(String field, Object value)xmipp.utils.XmippMessageinlinestatic
getIllegalValueMsgWithInfo(String field, Object value, String message)xmipp.utils.XmippMessageinlinestatic
getInvalidDirectoryMsg(String outputdir)xmipp.utils.XmippMessageinlinestatic
getNoSuchFieldValueMsg(String field, Object value)xmipp.utils.XmippMessageinlinestatic
getNotImplementedYetMsg()xmipp.utils.XmippMessageinlinestatic
getOutOfBoundsMsg(Object o)xmipp.utils.XmippMessageinlinestatic
getPathNotExistsMsg(String path)xmipp.utils.XmippMessageinlinestatic
getUnexpectedErrorMsg()xmipp.utils.XmippMessageinlinestatic
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Xmipp -  v20.07 -
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xmipp.utils.XmippMessage Class Reference
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-Static Public Member Functions

static String getIllegalDeleteMsg (String item)
 
static String getAlreadyExistsGroupNameMsg (String name)
 
static String getEmptyFieldMsg (String field)
 
static String getAssociatedDataMsg (String field)
 
static String getNoSuchFieldValueMsg (String field, Object value)
 
static String getOutOfBoundsMsg (Object o)
 
static String getNotImplementedYetMsg ()
 
static String getIllegalValueMsg (String field, Object value)
 
static String getPathNotExistsMsg (String path)
 
static String getIllegalStateForOperationMsg (String field, String value)
 
static String getIllegalValueMsgWithInfo (String field, Object value, String message)
 
static String getUnexpectedErrorMsg ()
 
static String getInvalidDirectoryMsg (String outputdir)
 
static String getFileTypeNotSupportedMsg (String path)
 
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Detailed Description

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This class will contains methods to return formatted text messages

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Definition at line 30 of file XmippMessage.java.

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Member Function Documentation

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◆ getAlreadyExistsGroupNameMsg()

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static String xmipp.utils.XmippMessage.getAlreadyExistsGroupNameMsg (String name)
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Definition at line 39 of file XmippMessage.java.

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40  {
41  return String.format("Group %s already exists", name);
42  }
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◆ getAssociatedDataMsg()

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static String xmipp.utils.XmippMessage.getAssociatedDataMsg (String field)
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Definition at line 48 of file XmippMessage.java.

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48  {
49  return String.format("%s has associated data. Can not be removed");
50  }
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◆ getEmptyFieldMsg()

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Definition at line 44 of file XmippMessage.java.

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44  {
45  return String.format("Must specify %s", field);
46  }
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◆ getFileTypeNotSupportedMsg()

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static String xmipp.utils.XmippMessage.getFileTypeNotSupportedMsg (String path)
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Definition at line 93 of file XmippMessage.java.

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93  {
94  return String.format("Extension not supported: %s", path); //To change body of generated methods, choose Tools | Templates.
95  }
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◆ getIllegalDeleteMsg()

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static String xmipp.utils.XmippMessage.getIllegalDeleteMsg (String item)
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Particle Picker messages

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Definition at line 34 of file XmippMessage.java.

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35  {
36  return String.format("There it must be at least one %s defined", item);
37  }
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static String xmipp.utils.XmippMessage.getIllegalStateForOperationMsg (String field,
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Definition at line 75 of file XmippMessage.java.

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75  {
76  return String.format("Invalid operation for %s on state %s", field, value);
77  }
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static String xmipp.utils.XmippMessage.getIllegalValueMsg (String field,
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Definition at line 66 of file XmippMessage.java.

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67  {
68  return String.format("Illegal value for %s: %s", field, value);
69  }
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Definition at line 79 of file XmippMessage.java.

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80  {
81  return String.format("%s=%s\n%s", field, value, message);
82  }
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Definition at line 89 of file XmippMessage.java.

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89  {
90  return String.format("Directory %s doesn't exists.", outputdir);
91  }
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Definition at line 52 of file XmippMessage.java.

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52  {
53  return String.format("No such %s %s exists", field, value);
54  }
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Definition at line 61 of file XmippMessage.java.

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62  {
63  return "Not implemented yet";
64  }
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Definition at line 56 of file XmippMessage.java.

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57  {
58  return String.format("%s out of bounds", o);
59  }
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Definition at line 71 of file XmippMessage.java.

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71  {
72  return String.format("Path '%s' doesn't exists.", path);
73  }
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Definition at line 84 of file XmippMessage.java.

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85  {
86  return "Unexpected error";
87  }
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This is the complete list of members for xmipp.utils.XmippMessageDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippMessageDialoginlineprotected
createContent(JPanel panel)xmipp.utils.XmippMessageDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
handleActionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
init(String message, String iconPath)xmipp.utils.XmippMessageDialoginlineprotected
initComponents()xmipp.utils.XmippDialoginlineprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippMessageDialog(JFrame parent, String title)xmipp.utils.XmippMessageDialoginline
XmippMessageDialog(Dialog parent, String title)xmipp.utils.XmippMessageDialoginline
XmippMessageDialog(JFrame parent, String title, String message, String iconPath)xmipp.utils.XmippMessageDialoginline
XmippMessageDialog(Dialog parent, String title, String message, String iconPath)xmipp.utils.XmippMessageDialoginline
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-Public Member Functions

 XmippMessageDialog (JFrame parent, String title)
 
 XmippMessageDialog (Dialog parent, String title)
 
 XmippMessageDialog (JFrame parent, String title, String message, String iconPath)
 
 XmippMessageDialog (Dialog parent, String title, String message, String iconPath)
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
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-Protected Member Functions

void init (String message, String iconPath)
 
void createContent (JPanel panel)
 
void createButtons ()
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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Detailed Description

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Special case of XmippDialog to display message (info, error, warning)

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Definition at line 40 of file XmippMessageDialog.java.

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Constructor & Destructor Documentation

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◆ XmippMessageDialog() [1/4]

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Definition at line 45 of file XmippMessageDialog.java.

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45  {
46  super(parent, title, true);
47  }
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Definition at line 49 of file XmippMessageDialog.java.

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49  {
50  super(parent, title, true);
51  }
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Definition at line 53 of file XmippMessageDialog.java.

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54  {
55  super(parent, title, true);
56  init(removeColors(message), iconPath);
57  }
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static String removeColors(String message)
Definition: XmippDialog.java:280
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Definition at line 59 of file XmippMessageDialog.java.

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60  {
61  super(parent, title, true);
62  init(message, iconPath);
63  }
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Definition: XmippMessageDialog.java:66
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◆ createButtons()

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void xmipp.utils.XmippMessageDialog.createButtons ()
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Definition at line 93 of file XmippMessageDialog.java.

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93  {
94  super.createButtons();
95  panelBtn.setLayout(new FlowLayout());
96  }
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Definition at line 73 of file XmippMessageDialog.java.

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73  {
74  panel.setLayout(new BorderLayout());
75  JPanel iconPanel = new JPanel();
76  iconPanel.add(XmippWindowUtil.getIconLabel(iconPath));
77  iconPanel.setBackground(Color.white);
78  panel.add(iconPanel, BorderLayout.LINE_START);
79  JTextArea text = new JTextArea(message, 5, 40);
80  text.setEditable(false);
81  text.setBackground(Color.white);
82  text.setBorder(BorderFactory.createEmptyBorder());
83  text.setLineWrap(true);
84  text.setWrapStyleWord(true);
85  // text
86  JScrollPane scrollPane = new JScrollPane(text);
87  scrollPane.setBorder(BorderFactory.createEmptyBorder());
88  scrollPane.setBackground(Color.white);
89  panel.add(scrollPane, BorderLayout.CENTER);
90  }
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void xmipp.utils.XmippMessageDialog.init (String message,
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Definition at line 66 of file XmippMessageDialog.java.

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66  {
67  this.message = message;
68  this.iconPath = iconPath;
69  initComponents();
70  }
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xmipp.utils.XmippPopupMenuCreator Member List
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This is the complete list of members for xmipp.utils.XmippPopupMenuCreator, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippMenuCreatorinline
addItem(String key, String text, String... values)xmipp.utils.XmippMenuCreatorinline
addSeparator()xmipp.utils.XmippPopupMenuCreatorinline
createItems()xmipp.utils.XmippMenuCreatorprotected
CTF_PROFILExmipp.utils.XmippMenuCreatorstatic
CTF_RECALCULATExmipp.utils.XmippMenuCreatorstatic
DISABLEDxmipp.utils.XmippMenuCreatorstatic
DISPLAYxmipp.utils.XmippMenuCreator
DISPLAY_APPLYGEOxmipp.utils.XmippMenuCreator
DISPLAY_COLUMNSxmipp.utils.XmippMenuCreator
DISPLAY_INVERTYxmipp.utils.XmippMenuCreator
DISPLAY_NORMALIZExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGESxmipp.utils.XmippMenuCreator
DISPLAY_RESLICExmipp.utils.XmippMenuCreator
DISPLAY_RESLICE_VIEWSxmipp.utils.XmippMenuCreator
DISPLAY_SHOWLABELSxmipp.utils.XmippMenuCreator
DISPLAY_WRAPxmipp.utils.XmippMenuCreator
ENABLEDxmipp.utils.XmippMenuCreatorstatic
FILExmipp.utils.XmippMenuCreator
FILE_EXITxmipp.utils.XmippMenuCreator
FILE_EXPORTIMAGESxmipp.utils.XmippMenuCreator
FILE_INFOxmipp.utils.XmippMenuCreator
FILE_LINK_CHIMERAxmipp.utils.XmippMenuCreator
FILE_LOAD_SELxmipp.utils.XmippMenuCreator
FILE_OPENxmipp.utils.XmippMenuCreator
FILE_OPENMICROGRAPHSxmipp.utils.XmippMenuCreator
FILE_OPENWITH_CHIMERAxmipp.utils.XmippMenuCreator
FILE_OPENWITH_IJxmipp.utils.XmippMenuCreator
FILE_REFRESHxmipp.utils.XmippMenuCreator
FILE_SAVExmipp.utils.XmippMenuCreator
FILE_SAVE_SELxmipp.utils.XmippMenuCreator
FILE_SAVEASxmipp.utils.XmippMenuCreator
getItem(String key)xmipp.utils.XmippMenuCreatorinline
getItemEnabled(String key)xmipp.utils.XmippMenuCreatorinline
getItemSelected(String key)xmipp.utils.XmippMenuCreatorinline
getPopupMenu()xmipp.utils.XmippPopupMenuCreatorinline
groupsxmipp.utils.XmippMenuCreatorprotected
handleActionPerformed(ActionEvent evt)xmipp.utils.XmippMenuCreatorprotected
HELPxmipp.utils.XmippMenuCreator
HELP_ONLINExmipp.utils.XmippMenuCreator
initItems()xmipp.utils.XmippMenuCreatorinline
INVERT_SELECTxmipp.utils.XmippMenuCreatorstatic
itemsxmipp.utils.XmippMenuCreatorprotected
KEY_ASSISTxmipp.utils.XmippMenuCreator
MD_ADD_OBJECTxmipp.utils.XmippMenuCreator
MD_CLASSESxmipp.utils.XmippMenuCreator
MD_EDIT_COLSxmipp.utils.XmippMenuCreator
MD_FIND_REPLACExmipp.utils.XmippMenuCreator
MD_REMOVE_DISABLEDxmipp.utils.XmippMenuCreator
MD_REMOVE_SELECTIONxmipp.utils.XmippMenuCreator
MD_SAVE_SELECTIONxmipp.utils.XmippMenuCreator
menuxmipp.utils.XmippMenuCreatorprotected
METADATAxmipp.utils.XmippMenuCreator
OPENxmipp.utils.XmippMenuCreatorstatic
OPEN_ASTEXTxmipp.utils.XmippMenuCreatorstatic
OPEN_IMAGESxmipp.utils.XmippMenuCreatorstatic
REFRESHxmipp.utils.XmippMenuCreatorstatic
SAVE_IMAGESxmipp.utils.XmippMenuCreatorstatic
SELECTxmipp.utils.XmippMenuCreatorstatic
SELECT_ALLxmipp.utils.XmippMenuCreatorstatic
SELECT_FROMHERExmipp.utils.XmippMenuCreatorstatic
SELECT_TOHERExmipp.utils.XmippMenuCreatorstatic
SET_CLASSxmipp.utils.XmippMenuCreatorstatic
setItemEnabled(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemSelected(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemVisible(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
TOOLSxmipp.utils.XmippMenuCreator
TOOLS_AVGSTDxmipp.utils.XmippMenuCreator
TOOLS_FSCxmipp.utils.XmippMenuCreator
TOOLS_PCAxmipp.utils.XmippMenuCreator
TOOLS_PLOTxmipp.utils.XmippMenuCreator
XmippMenuCreator(JComponent menu)xmipp.utils.XmippMenuCreatorinline
XmippPopupMenuCreator()xmipp.utils.XmippPopupMenuCreatorinline
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xmipp.utils.XmippPopupMenuCreator Class Referenceabstract
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-Public Member Functions

 XmippPopupMenuCreator ()
 
JPopupMenu getPopupMenu ()
 
void addSeparator ()
 
- Public Member Functions inherited from xmipp.utils.XmippMenuCreator
 XmippMenuCreator (JComponent menu)
 
JMenuItem addItem (String key, String text, String... values)
 
JMenuItem getItem (String key)
 
boolean getItemEnabled (String key)
 
void setItemEnabled (String key, boolean value)
 
boolean getItemSelected (String key)
 
void setItemSelected (String key, boolean value)
 
void setItemVisible (String key, boolean value)
 
void actionPerformed (ActionEvent evt)
 
void initItems ()
 
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-Additional Inherited Members

- Public Attributes inherited from xmipp.utils.XmippMenuCreator
final String FILE = "File"
 
final String FILE_OPEN = "File.Open_mi"
 
final String FILE_OPENWITH_IJ = "File.OpenWithIJ_mi"
 
final String FILE_OPENMICROGRAPHS = "File.OpenMicrographs_mi"
 
final String FILE_OPENWITH_CHIMERA = "File.OpenWithChimera_mi"
 
final String FILE_INFO = "File.FileInfo_mi"
 
final String FILE_SAVE = "File.Save_mi"
 
final String FILE_SAVEAS = "File.SaveAs_mi"
 
final String FILE_LOAD_SEL = "File.LoadSel_mi"
 
final String FILE_SAVE_SEL = "File.SaveSel_mi"
 
final String FILE_EXPORTIMAGES = "File.ExportImages_mi"
 
final String FILE_REFRESH = "File.Refresh_mi"
 
final String FILE_EXIT = "File.Exit_mi"
 
final String FILE_LINK_CHIMERA = "File.LinkWithChimera_mi"
 
final String DISPLAY = "Display"
 
final String DISPLAY_SHOWLABELS = "Display.ShowLabel"
 
final String DISPLAY_RENDERIMAGES = "Display.RenderImages_cb"
 
final String DISPLAY_RENDERIMAGE = "Display.RenderImage"
 
final String DISPLAY_INVERTY = "Display.InvertY_cb"
 
final String DISPLAY_APPLYGEO = "Display.ApplyGeo_cb"
 
final String DISPLAY_WRAP = "Display.Wrap_cb"
 
final String DISPLAY_NORMALIZE = "Display.Normalize_cb"
 
final String DISPLAY_COLUMNS = "Display.Columns_mi"
 
final String DISPLAY_RESLICE = "Display.Reslice"
 
final String DISPLAY_RESLICE_VIEWS []
 
final String METADATA = "Metadata"
 
final String MD_CLASSES = "Metadata.Classes_mi"
 
final String MD_EDIT_COLS = "Metadata.EditCols_mi"
 
final String MD_ADD_OBJECT = "Metadata.AddObject_mi"
 
final String MD_REMOVE_SELECTION = "Metadata.RemoveSelection_mi"
 
final String MD_SAVE_SELECTION = "Metadata.SaveSelection_mi"
 
final String MD_REMOVE_DISABLED = "Metadata.RemoveDisabled_mi"
 
final String TOOLS = "Tools"
 
final String TOOLS_AVGSTD = "Tools.AvgStd_mi"
 
final String TOOLS_PCA = "Tools.Pca_mi"
 
final String TOOLS_FSC = "Tools.Fsc_mi"
 
final String TOOLS_PLOT = "Tools.Plot_mi"
 
final String MD_FIND_REPLACE = "Tools.FindReplace_mi"
 
final String HELP = "Help"
 
final String HELP_ONLINE = "Help.Online_mi"
 
final String KEY_ASSIST = "Help.Key_mi"
 
- Static Public Attributes inherited from xmipp.utils.XmippMenuCreator
static final String ENABLED = "Enabled_mi"
 
static final String DISABLED = "Disabled_mi"
 
static final String REFRESH = "Refresh_mi"
 
static final String OPEN = "Open_mi"
 
static final String OPEN_ASTEXT = "OpenAsText_mi"
 
static final String CTF_PROFILE = "CTFProfile_mi"
 
static final String CTF_RECALCULATE = "CTFRecalculate_cb"
 
static final String SELECT = "Select"
 
static final String SELECT_ALL = "Select.All_mi"
 
static final String SELECT_TOHERE = "Select.ToHere_mi"
 
static final String SELECT_FROMHERE = "Select.FromHere_mi"
 
static final String INVERT_SELECT = "Select.InvertSelection_mi"
 
static final String SET_CLASS = "SetClass_mi"
 
static final String OPEN_IMAGES = "OpenImages_mi"
 
static final String SAVE_IMAGES = "SaveImages_mi"
 
- Protected Member Functions inherited from xmipp.utils.XmippMenuCreator
abstract void handleActionPerformed (ActionEvent evt)
 
abstract void createItems () throws Exception
 
- Protected Attributes inherited from xmipp.utils.XmippMenuCreator
Map< String, JMenuItem > items
 
Map< String, ButtonGroup > groups
 
JComponent menu
 
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Detailed Description

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Definition at line 30 of file XmippPopupMenuCreator.java.

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Constructor & Destructor Documentation

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◆ XmippPopupMenuCreator()

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Definition at line 32 of file XmippPopupMenuCreator.java.

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32  {
33  super(new JPopupMenu());
34  }
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◆ addSeparator()

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void xmipp.utils.XmippPopupMenuCreator.addSeparator ()
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Definition at line 40 of file XmippPopupMenuCreator.java.

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40  {
41  getPopupMenu().addSeparator();
42  }
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◆ getPopupMenu()

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Definition at line 36 of file XmippPopupMenuCreator.java.

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36  {
37  return (JPopupMenu)menu;
38  }
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- - diff --git a/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__coll__graph.dot b/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__coll__graph.dot deleted file mode 100644 index 8aa99448..00000000 --- a/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__coll__graph.dot +++ /dev/null @@ -1,16 +0,0 @@ -digraph "xmipp.utils.XmippPopupMenuCreator" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node4 [label="xmipp.utils.XmippPopupMenu\lCreator",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node5 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="xmipp.utils.XmippMenuCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuCreator.html"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" groups" ,fontname="Helvetica"]; - Node7 [label="Map\< String, ButtonGroup \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" menu" ,fontname="Helvetica"]; - Node8 [label="JComponent",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" items" ,fontname="Helvetica"]; - Node9 [label="Map\< String, JMenuItem \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__coll__graph.md5 b/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__coll__graph.md5 deleted file mode 100644 index 7426bb6f..00000000 --- a/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -f46254473ae8cfba16cc85bd4b8856d7 \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__inherit__graph.dot b/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__inherit__graph.dot deleted file mode 100644 index e47e7b11..00000000 --- a/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__inherit__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.utils.XmippPopupMenuCreator" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.utils.XmippPopupMenu\lCreator",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.utils.XmippMenuCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuCreator.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node0 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.windows.Gallery\lJFrame.GalleryPopupMenu",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__inherit__graph.md5 b/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__inherit__graph.md5 deleted file mode 100644 index dcfb4602..00000000 --- a/html/classxmipp_1_1utils_1_1XmippPopupMenuCreator__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -fb59722c5e6a19735539505d16371642 \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1XmippQuestionDialog-members.html b/html/classxmipp_1_1utils_1_1XmippQuestionDialog-members.html deleted file mode 100644 index 7b6e0fc6..00000000 --- a/html/classxmipp_1_1utils_1_1XmippQuestionDialog-members.html +++ /dev/null @@ -1,141 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.utils.XmippQuestionDialog Member List
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This is the complete list of members for xmipp.utils.XmippQuestionDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
btnQuestionCancelxmipp.utils.XmippQuestionDialogprotected
btnQuestionCancelDisplayxmipp.utils.XmippQuestionDialogprotected
btnQuestionCancelTextxmipp.utils.XmippQuestionDialogprotected
CANCEL_OPTIONxmipp.utils.XmippQuestionDialogstatic
canceledxmipp.utils.XmippQuestionDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippQuestionDialoginlineprotected
createContent(JPanel panel)xmipp.utils.XmippMessageDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
getOption()xmipp.utils.XmippQuestionDialoginline
handleActionPerformed(ActionEvent evt)xmipp.utils.XmippQuestionDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
init(String message, String iconPath)xmipp.utils.XmippMessageDialoginlineprotected
initComponents()xmipp.utils.XmippDialoginlineprotected
isCanceled()xmipp.utils.XmippQuestionDialoginline
NO_OPTIONxmipp.utils.XmippQuestionDialogstatic
optionxmipp.utils.XmippQuestionDialogprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippMessageDialog(JFrame parent, String title)xmipp.utils.XmippMessageDialoginline
XmippMessageDialog(Dialog parent, String title)xmipp.utils.XmippMessageDialoginline
XmippMessageDialog(JFrame parent, String title, String message, String iconPath)xmipp.utils.XmippMessageDialoginline
XmippMessageDialog(Dialog parent, String title, String message, String iconPath)xmipp.utils.XmippMessageDialoginline
XmippQuestionDialog(JFrame parent, String message)xmipp.utils.XmippQuestionDialoginline
XmippQuestionDialog(Dialog parent, String message)xmipp.utils.XmippQuestionDialoginline
XmippQuestionDialog(JFrame parent, String message, boolean showCancel)xmipp.utils.XmippQuestionDialoginline
XmippQuestionDialog(Dialog parent, String message, boolean showCancel)xmipp.utils.XmippQuestionDialoginline
YES_OPTIONxmipp.utils.XmippQuestionDialogstatic
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-Public Member Functions

 XmippQuestionDialog (JFrame parent, String message)
 
 XmippQuestionDialog (Dialog parent, String message)
 
 XmippQuestionDialog (JFrame parent, String message, boolean showCancel)
 
 XmippQuestionDialog (Dialog parent, String message, boolean showCancel)
 
void handleActionPerformed (ActionEvent evt)
 
boolean isCanceled ()
 
int getOption ()
 
- Public Member Functions inherited from xmipp.utils.XmippMessageDialog
 XmippMessageDialog (JFrame parent, String title)
 
 XmippMessageDialog (Dialog parent, String title)
 
 XmippMessageDialog (JFrame parent, String title, String message, String iconPath)
 
 XmippMessageDialog (Dialog parent, String title, String message, String iconPath)
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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static int YES_OPTION = 0
 
static int NO_OPTION = 1
 
static int CANCEL_OPTION = 2
 
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-Protected Member Functions

void createButtons ()
 
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void init (String message, String iconPath)
 
void createContent (JPanel panel)
 
void createButtons ()
 
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void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Protected Attributes

JButton btnQuestionCancel
 
String btnQuestionCancelText = "Cancel"
 
boolean btnQuestionCancelDisplay = true
 
boolean canceled = false
 
int option
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
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Special type of message with Yes, No, Cancel options

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Definition at line 34 of file XmippQuestionDialog.java.

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Definition at line 49 of file XmippQuestionDialog.java.

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49  {
50  super(parent, TITLE);
51  init(message, ICON);
52  }
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Definition at line 54 of file XmippQuestionDialog.java.

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54  {
55  super(parent, TITLE);
56  init(message, ICON);
57  }
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Definition at line 59 of file XmippQuestionDialog.java.

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59  {
60  super(parent, TITLE);
61  btnQuestionCancelDisplay = showCancel;
62  init(message, ICON);
63  }
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Definition at line 65 of file XmippQuestionDialog.java.

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65  {
66  super(parent, TITLE);
67  btnQuestionCancelDisplay = showCancel;
68  init(message, ICON);
69  }
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Definition at line 82 of file XmippQuestionDialog.java.

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82  {
83  btnOkText = "Yes";
84  btnCancelText = "No";
85  super.createButtons();
86  if (btnQuestionCancelDisplay) {
87  btnQuestionCancel = XmippWindowUtil.getTextButton(btnQuestionCancelText, this);
88  panelBtn.add(btnQuestionCancel);
89  btnQuestionCancel.addActionListener(this);
90  }
91 
92  // Cancel close!
93  setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
94  }
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Definition at line 100 of file XmippQuestionDialog.java.

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100  {
101  if (result)
102  return YES_OPTION;
103  if (isCanceled())
104  return CANCEL_OPTION;
105  return NO_OPTION;
106  }
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Definition at line 72 of file XmippQuestionDialog.java.

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72  {
73  JButton button = (JButton)evt.getSource();
74  if (btnQuestionCancel == button){
75  canceled = true;
76  close(false);
77  }
78 
79  }
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97  return canceled;
98  }
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Definition at line 37 of file XmippQuestionDialog.java.

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Definition at line 39 of file XmippQuestionDialog.java.

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Definition at line 38 of file XmippQuestionDialog.java.

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Definition at line 46 of file XmippQuestionDialog.java.

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Definition at line 47 of file XmippQuestionDialog.java.

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- - diff --git a/html/classxmipp_1_1utils_1_1XmippQuestionDialog__coll__graph.dot b/html/classxmipp_1_1utils_1_1XmippQuestionDialog__coll__graph.dot deleted file mode 100644 index 9cdb128d..00000000 --- a/html/classxmipp_1_1utils_1_1XmippQuestionDialog__coll__graph.dot +++ /dev/null @@ -1,21 +0,0 @@ -digraph "xmipp.utils.XmippQuestionDialog" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node5 [label="xmipp.utils.XmippQuestion\lDialog",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="xmipp.utils.XmippMessage\lDialog",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMessageDialog.html"]; - Node7 -> Node6 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; 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ADJUST_COLSxmipp.utils.XmippResourcestatic
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DEFAULT_PREVIEW_HEIGHTxmipp.utils.XmippResourcestatic
DEFAULT_PREVIEW_WIDTHxmipp.utils.XmippResourcestatic
DELETE_ICONxmipp.utils.XmippResourcestatic
getIcon(String name)xmipp.utils.XmippResourceinlinestatic
getImage(String name)xmipp.utils.XmippResourceinlinestatic
getPath(String resource)xmipp.utils.XmippResourceinlinestatic
GOTOxmipp.utils.XmippResourcestatic
LOCK_ICONxmipp.utils.XmippResourcestatic
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VIEW_GALLERY_ICONxmipp.utils.XmippResourcestatic
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VIEW_MD_ICONxmipp.utils.XmippResourcestatic
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WAIT_ICONxmipp.utils.XmippResourcestatic
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-Static Public Member Functions

static ImageIcon getIcon (String name)
 
static String getPath (String resource)
 
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-Static Public Attributes

static int DEFAULT_PREVIEW_WIDTH = 80
 
static int DEFAULT_PREVIEW_HEIGHT = 80
 
static String PATH_ICONS
 
static final String MISSING = "missing.png"
 
static final String MISSING2 = "missing2.png"
 
static final String WAIT = "wait.gif"
 
static final String WAIT_MENU = "wait_menu.gif"
 
static final String NORMALIZE = "histogram.png"
 
static final String APPLY_GEO = "rotate.png"
 
static final String ADJUST_COLS = "resize.png"
 
static final String GOTO = "goto.gif"
 
static final String ZOOM = "zoom.png"
 
static final String VIEW_MD = "md_view.gif"
 
static final String VIEW_GALLERY = "table_view.gif"
 
static ImageIcon WAIT_ICON
 
static ImageIcon LOCK_ICON
 
static ImageIcon DELETE_ICON
 
static ImageIcon WAIT_MENU_ICON
 
static ImagePlus MISSING_ITEM
 
static ImageIcon VIEW_MD_ICON
 
static ImageIcon VIEW_GALLERY_ICON
 
static ImageIcon MISSING_ICON
 
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Author
Juanjo Vega
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Definition at line 23 of file XmippResource.java.

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Definition at line 78 of file XmippResource.java.

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78  {
79  ImageIcon ii;
80  if (iconsPool.containsKey(name))
81  ii = iconsPool.get(name);
82  else {
83  String path = String.format("%s%sresources%s%s", PATH_ICONS, File.separator, File.separator, name);
84  ii = new ImageIcon(path);
85  iconsPool.put(name, ii);
86  }
87  return ii;
88  }
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Definition at line 104 of file XmippResource.java.

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105  {
106  try
107  {
108  return ImageIO.read(new File(getPath(name)));
109  }
110  catch (IOException e)
111  {
112  // TODO Auto-generated catch block
113  e.printStackTrace();
114  throw new IllegalArgumentException(e);
115  }
116  }
xmipp.utils.XmippResource.getPath
static String getPath(String resource)
Definition: XmippResource.java:90
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Definition at line 90 of file XmippResource.java.

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91  {
92  try
93  {
94  return String.format("%s%sresources%s%s", Filename.getXmippPath(), File.separator, File.separator, resource);
95  }
96  catch (Exception e)
97  {
98  // TODO Auto-generated catch block
99  e.printStackTrace();
100  throw new IllegalArgumentException(e);
101  }
102  }
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final String xmipp.utils.XmippResource.ADJUST_COLS = "resize.png"
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Definition at line 37 of file XmippResource.java.

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Definition at line 36 of file XmippResource.java.

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Definition at line 45 of file XmippResource.java.

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Definition at line 38 of file XmippResource.java.

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Definition at line 50 of file XmippResource.java.

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Definition at line 35 of file XmippResource.java.

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Definition at line 41 of file XmippResource.java.

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final String xmipp.utils.XmippResource.ZOOM = "zoom.png"
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Definition at line 39 of file XmippResource.java.

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- - diff --git a/html/classxmipp_1_1utils_1_1XmippResource__coll__graph.dot b/html/classxmipp_1_1utils_1_1XmippResource__coll__graph.dot deleted file mode 100644 index c88745d9..00000000 --- a/html/classxmipp_1_1utils_1_1XmippResource__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.utils.XmippResource" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node1 [label="xmipp.utils.XmippResource",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node2 -> Node1 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" MISSING_ITEM" ,fontname="Helvetica"]; - Node2 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node1 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" WAIT_MENU_ICON\nMISSING_ICON\nWAIT_ICON\nLOCK_ICON\nVIEW_MD_ICON\nVIEW_GALLERY_ICON\nDELETE_ICON" ,fontname="Helvetica"]; - Node3 [label="ImageIcon",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1XmippResource__coll__graph.md5 b/html/classxmipp_1_1utils_1_1XmippResource__coll__graph.md5 deleted file mode 100644 index 09f0c939..00000000 --- a/html/classxmipp_1_1utils_1_1XmippResource__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -4d3130e8471a09459ed7c71bd6827c62 \ No newline at end of file diff --git a/html/classxmipp_1_1utils_1_1XmippStringUtils-members.html b/html/classxmipp_1_1utils_1_1XmippStringUtils-members.html deleted file mode 100644 index 5b840b0c..00000000 --- a/html/classxmipp_1_1utils_1_1XmippStringUtils-members.html +++ /dev/null @@ -1,85 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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commonPathPrefix(String [] strings)xmipp.utils.XmippStringUtilsinlinestatic
commonPrefix(String[] strings)xmipp.utils.XmippStringUtilsinlinestatic
getFileExtension(String filename)xmipp.utils.XmippStringUtilsinlinestatic
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-Static Public Member Functions

static String commonPrefix (String[] strings)
 
static String commonPathPrefix (String [] strings)
 
static String getFileExtension (String filename)
 
-

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Implement some string utilities

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Definition at line 29 of file XmippStringUtils.java.

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◆ commonPathPrefix()

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static String xmipp.utils.XmippStringUtils.commonPathPrefix (String [] strings)
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Common prefix until the last "/" This will only work for unix path separator "/"

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Definition at line 56 of file XmippStringUtils.java.

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56  {
57  String prefix = commonPrefix(strings);
58 
59  int pos = prefix.lastIndexOf('/');
60  if (pos > 0) {
61  ++pos; //If found /, also include in prefix
62  prefix = prefix.substring(0, pos);
63  }
64  else
65  prefix = "";
66 
67  return prefix;
68  }
xmipp.utils.XmippStringUtils.commonPrefix
static String commonPrefix(String[] strings)
Definition: XmippStringUtils.java:32
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static String xmipp.utils.XmippStringUtils.commonPrefix (String [] strings)
- 		-inlinestatic
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Find the greatest common prefix of a group of strings

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Definition at line 32 of file XmippStringUtils.java.

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32  {
33  String prefix = "";
34 
35  int n = strings.length;
36  boolean common = true;
37 
38  int minLenght = Integer.MAX_VALUE;
39 
40  for (int i = 0; i < n; ++i)
41  minLenght = Math.min(minLenght, strings[i].length());
42 
43  for (int j = 0; j < minLenght && common; ++j){
44  char c = strings[0].charAt(j);
45  for (int i = 1; i < strings.length && common; ++i)
46  if (c != strings[i].charAt(j))
47  common = false;
48  prefix += c;
49  }
50 
51  return prefix;
52  }//function commonPrefix
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◆ getFileExtension()

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static String xmipp.utils.XmippStringUtils.getFileExtension (String filename)
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Definition at line 70 of file XmippStringUtils.java.

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70  {
71 
72  try {
73  return filename.substring(filename.lastIndexOf("."));
74 
75  } catch (Exception e) {
76  return "";
77  }
78 
79 }
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blockGUI(JFrame window, String status)xmipp.utils.XmippWindowUtilinlinestatic
blockGUI(JFrame window, String status, boolean hideContent)xmipp.utils.XmippWindowUtilinlinestatic
centerWindows(Window w)xmipp.utils.XmippWindowUtilinlinestatic
centerWindows(Container w, Container parent)xmipp.utils.XmippWindowUtilinlinestatic
env2Map()xmipp.utils.XmippWindowUtilinlinestatic
executeCommand(String[] command, boolean wait)xmipp.utils.XmippWindowUtilinlinestatic
executeCommand(String command, boolean wait, String dir)xmipp.utils.XmippWindowUtilinlinestatic
executeCommand(String command, boolean wait)xmipp.utils.XmippWindowUtilinlinestatic
executeCommand(String command, boolean wait, HashMap< String, String > envVars)xmipp.utils.XmippWindowUtilinlinestatic
executeGUICommand(final String[] command, final JFrame frame, String msg)xmipp.utils.XmippWindowUtilinlinestatic
firebrickxmipp.utils.XmippWindowUtilstatic
getConstraints(GridBagConstraints constraints, int x, int y)xmipp.utils.XmippWindowUtilinlinestatic
getConstraints(GridBagConstraints constraints, int x, int y, int columns)xmipp.utils.XmippWindowUtilinlinestatic
getConstraints(GridBagConstraints constraints, int x, int y, int columns, int rows, int fill)xmipp.utils.XmippWindowUtilinlinestatic
getConstraints(GridBagConstraints constraints, int x, int y, int columns, int rows)xmipp.utils.XmippWindowUtilinlinestatic
getIconButton(String icon, ActionListener listener)xmipp.utils.XmippWindowUtilinlinestatic
getIconLabel(String icon)xmipp.utils.XmippWindowUtilinlinestatic
getScipionIconButton(String text)xmipp.utils.XmippWindowUtilinlinestatic
getScreenRectangle()xmipp.utils.XmippWindowUtilinlinestatic
getTextButton(String text, ActionListener listener)xmipp.utils.XmippWindowUtilinlinestatic
getTextIconButton(String text, String icon, ActionListener listener)xmipp.utils.XmippWindowUtilinlinestatic
LIGHT_BLUExmipp.utils.XmippWindowUtilstatic
lightgreyxmipp.utils.XmippWindowUtilstatic
openURI(String uri)xmipp.utils.XmippWindowUtilinlinestatic
readProcessOutput(Process p)xmipp.utils.XmippWindowUtilinlinestatic
releaseGUI(JRootPane panel)xmipp.utils.XmippWindowUtilinlinestatic
runCommand(String command, Integer port)xmipp.utils.XmippWindowUtilinlinestatic
setLocation(double positionx, double positiony, Window w)xmipp.utils.XmippWindowUtilinlinestatic
setLocation(float positionx, float positiony, Container w, Container parent)xmipp.utils.XmippWindowUtilinlinestatic
setScipionImageIcon(Window w)xmipp.utils.XmippWindowUtilinlinestatic
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static void setLocation (double positionx, double positiony, Window w)
 
static Rectangle getScreenRectangle ()
 
static void setLocation (float positionx, float positiony, Container w, Container parent)
 
static void centerWindows (Window w)
 
static void centerWindows (Container w, Container parent)
 
static GridBagConstraints getConstraints (GridBagConstraints constraints, int x, int y)
 
static GridBagConstraints getConstraints (GridBagConstraints constraints, int x, int y, int columns)
 
static GridBagConstraints getConstraints (GridBagConstraints constraints, int x, int y, int columns, int rows, int fill)
 
static JButton getIconButton (String icon, ActionListener listener)
 
static JButton getTextIconButton (String text, String icon, ActionListener listener)
 
static JButton getTextButton (String text, ActionListener listener)
 
static JLabel getIconLabel (String icon)
 
static JButton getScipionIconButton (String text)
 
static GridBagConstraints getConstraints (GridBagConstraints constraints, int x, int y, int columns, int rows)
 
static void openURI (String uri)
 
static void blockGUI (JFrame window, String status)
 
static void blockGUI (JFrame window, String status, boolean hideContent)
 
static void releaseGUI (JRootPane panel)
 
static void executeGUICommand (final String[] command, final JFrame frame, String msg)
 
static String executeCommand (String[] command, boolean wait) throws Exception
 
static String executeCommand (String command, boolean wait, String dir) throws Exception
 
static String executeCommand (String command, boolean wait) throws Exception
 
static Map< String, String > env2Map ()
 
static String executeCommand (String command, boolean wait, HashMap< String, String > envVars) throws Exception
 
static void runCommand (String command, Integer port)
 
static String readProcessOutput (Process p) throws IOException
 
static void setScipionImageIcon (Window w)
 
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-Static Public Attributes

static final Color firebrick = Color.decode("#B22222")
 
static final Color lightgrey = Color.decode("#EAEBEC")
 
static final Color LIGHT_BLUE = new Color(173, 216, 230)
 
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Definition at line 55 of file XmippWindowUtil.java.

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◆ blockGUI() [1/2]

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static void xmipp.utils.XmippWindowUtil.blockGUI (JFrame window,
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Block the gui and show the InfiniteProgressPanel without hiding the content

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Definition at line 219 of file XmippWindowUtil.java.

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219  {
220 
221  blockGUI(window, status, false);
222  }
xmipp.utils.XmippWindowUtil.blockGUI
static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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Block the gui and show the InfiniteProgressPanel The hide content parameter is needed for the galleryData export process. If the content is hidden, there will not be any refresh and therefore there will not be a concurrency access to the metadata object in different threads (painting the window and exporting).

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Definition at line 231 of file XmippWindowUtil.java.

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232  {
233  final InfiniteProgressPanel progressPanel = new InfiniteProgressPanel(window, status);
234  window.setGlassPane(progressPanel);
235  if (hideContent) {
236  window.getLayeredPane().setVisible(false);
237  }
238  progressPanel.start();
239  }
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Center the component in the screen

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95  {
96  setLocation(0.5f, 0.5f, w);
97  }
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Center the component relative to parent component

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Definition at line 100 of file XmippWindowUtil.java.

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101  {
102  setLocation(0.5f, 0.5f, w, parent.getBounds());
103  }
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Definition at line 309 of file XmippWindowUtil.java.

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309  {
310 
311  Map<String, String> editableEnv = new HashMap<>();
312 
313  for (Map.Entry<String,String> var: System.getenv().entrySet()){
314  editableEnv.put(var.getKey(), var.getValue());
315  };
316  return editableEnv;
317  }
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Definition at line 276 of file XmippWindowUtil.java.

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276  {
277  //System.out.println(Arrays.toString(command));
278  Process p = Runtime.getRuntime().exec(command);
279  if(wait)
280  {
281  p.waitFor();
282  return readProcessOutput(p);
283  }
284  return null;
285  }
xmipp.utils.XmippWindowUtil.readProcessOutput
static String readProcessOutput(Process p)
Definition: XmippWindowUtil.java:369
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String dir 
) throws Exception
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Definition at line 287 of file XmippWindowUtil.java.

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287  {
288  //System.out.println(command);
289  Process p = Runtime.getRuntime().exec(command, null, new File(dir));
290  if(wait)
291  {
292  p.waitFor();
293  return readProcessOutput(p);
294  }
295  return null;
296 }
xmipp.utils.XmippWindowUtil.readProcessOutput
static String readProcessOutput(Process p)
Definition: XmippWindowUtil.java:369
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Definition at line 298 of file XmippWindowUtil.java.

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298  {
299  DEBUG.printMessage(command);
300  Process p = Runtime.getRuntime().exec(new String[] { "bash", "-c", command });
301  if(wait)
302  {
303  p.waitFor();
304  return readProcessOutput(p);
305  }
306  return null;
307  }
xmipp.utils.XmippWindowUtil.readProcessOutput
static String readProcessOutput(Process p)
Definition: XmippWindowUtil.java:369
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boolean wait,
HashMap< String, String > envVars 
) throws Exception
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Definition at line 318 of file XmippWindowUtil.java.

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318  {
319 
320  Map<String,String> curentEnv = env2Map();
321 
322  for (Map.Entry<String,String> newVar: envVars.entrySet()){
323  curentEnv.put(newVar.getKey(), newVar.getValue());
324  };
325 
326  List<String> env2Exec = new ArrayList<String>();
327  for (Map.Entry<String,String> var: curentEnv.entrySet()){
328  env2Exec.add(var.getKey() + "=" + var.getValue());
329  };
330 
331  DEBUG.printMessage(command);
332  Process p = Runtime.getRuntime().exec(command, env2Exec.toArray(new String[0]));
333  if(wait)
334  {
335  p.waitFor();
336  return readProcessOutput(p);
337  }
338  return null;
339 
340  }
xmipp.utils.XmippWindowUtil.readProcessOutput
static String readProcessOutput(Process p)
Definition: XmippWindowUtil.java:369
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Definition: XmippWindowUtil.java:309
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String msg 
)
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Definition at line 250 of file XmippWindowUtil.java.

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251  {
252 
253 
254  XmippWindowUtil.blockGUI(frame, msg);
255  new Thread(new Runnable() {
256 
257  @Override
258  public void run() {
259 
260  try {
261 
262  String output = executeCommand(command, true);
263  XmippWindowUtil.releaseGUI(frame.getRootPane());
264 
265  if(output != null && !output.isEmpty())
266  System.out.println(output);
267 
268  } catch (Exception ex) {
269  throw new IllegalArgumentException(ex.getMessage());
270  }
271 
272  }
273  }).start();
274  }
xmipp.utils.XmippWindowUtil.executeCommand
static String executeCommand(String[] command, boolean wait)
Definition: XmippWindowUtil.java:276
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int x,
int y 
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Definition at line 105 of file XmippWindowUtil.java.

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106  {
107  return getConstraints(constraints, x, y, 1, 1);
108  }
xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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int x,
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Definition at line 110 of file XmippWindowUtil.java.

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111  {
112  return getConstraints(constraints, x, y, columns, 1);
113  }
xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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int x,
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int fill 
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Definition at line 116 of file XmippWindowUtil.java.

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117  {
118  constraints = getConstraints(constraints, x, y, columns, rows);
119  constraints.fill = fill;
120  return constraints;
121  }
xmipp.utils.XmippWindowUtil.getConstraints
static GridBagConstraints getConstraints(GridBagConstraints constraints, int x, int y)
Definition: XmippWindowUtil.java:105
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int rows 
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Definition at line 165 of file XmippWindowUtil.java.

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166  {
167  constraints.gridx = x;
168  constraints.gridy = y;
169  constraints.gridwidth = columns;
170  constraints.gridheight = rows;
171  if (columns > 1 && rows > 1)
172  {
173  constraints.fill = GridBagConstraints.BOTH;
174  }
175  else if (columns > 1)
176  {
177  constraints.fill = GridBagConstraints.HORIZONTAL;
178  }
179  else if (rows > 1)
180  {
181  constraints.fill = GridBagConstraints.VERTICAL;
182  }
183  else
184  {
185  constraints.fill = GridBagConstraints.NONE;
186  }
187  return constraints;
188  }
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Definition at line 124 of file XmippWindowUtil.java.

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124  {
125  JButton btn = new JButton();
126  btn.setIcon(XmippResource.getIcon(icon));
127  Dimension dim = btn.getPreferredSize();
128  dim.width = dim.height;
129  btn.setPreferredSize(dim);
130  btn.addActionListener(listener);
131  return btn;
132  }
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Definition at line 149 of file XmippWindowUtil.java.

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150  {
151  JLabel label = new JLabel();
152  label.setIcon(XmippResource.getIcon(icon));
153  return label;
154  }
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Definition at line 156 of file XmippWindowUtil.java.

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156  {
157  Icon icon = XmippResource.getIcon("fa-plus-circle.png");
158  JButton button = new JButton(text.replace("Create ", ""), icon);
159  button.setToolTipText(text);
160  button.setBackground(firebrick);
161  button.setForeground(Color.WHITE);
162  return button;
163  }
xmipp.utils.XmippWindowUtil.firebrick
static final Color firebrick
Definition: XmippWindowUtil.java:57
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Definition at line 82 of file XmippWindowUtil.java.

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83  {
84  GraphicsDevice gd = GraphicsEnvironment.getLocalGraphicsEnvironment().getDefaultScreenDevice();
85  return gd.getDefaultConfiguration().getBounds();
86  }
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Definition at line 140 of file XmippWindowUtil.java.

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141  {
142  JButton btn = new JButton(text);
143  //if(!isScipion)
144  // btn.setBackground(LIGHT_BLUE);
145  btn.addActionListener(listener);
146  return btn;
147  }
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Definition at line 134 of file XmippWindowUtil.java.

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134  {
135  JButton btn = new JButton(text, XmippResource.getIcon(icon));
136  btn.addActionListener(listener);
137  return btn;
138  }
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Definition at line 190 of file XmippWindowUtil.java.

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191  {
192 
193  if (!java.awt.Desktop.isDesktopSupported())
194  throw new IllegalArgumentException("Desktop is not supported (fatal)");
195 
196  if (uri == null)
197  throw new IllegalArgumentException("Usage: OpenURI [URI [URI ... ]]");
198 
199  java.awt.Desktop desktop = java.awt.Desktop.getDesktop();
200 
201  if (!desktop.isSupported(java.awt.Desktop.Action.BROWSE))
202  {
203 
204  throw new IllegalArgumentException("Desktop doesn't support the browse action (fatal)");
205  }
206  try
207  {
208 
209  java.net.URI myuri = new java.net.URI(uri);
210  desktop.browse(myuri);
211  }
212  catch (Exception e)
213  {
214  throw new IllegalArgumentException(e);
215  }
216  }
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Definition at line 369 of file XmippWindowUtil.java.

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370  {
371  StringBuffer output = new StringBuffer();
372  BufferedReader reader
373  = new BufferedReader(new InputStreamReader(p.getInputStream()));
374 
375 
376  String line = "";
377  while ((line = reader.readLine()) != null) {
378  output.append(line + "\n");
379  }
380  reader = new BufferedReader(new InputStreamReader(p.getErrorStream()));
381 
382  while ((line = reader.readLine()) != null) {
383  output.append(line + "\n");
384  }
385  return output.toString();
386 
387  }
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Release the gui from a previous block

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Definition at line 242 of file XmippWindowUtil.java.

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243  {
244  InfiniteProgressPanel progressPanel = (InfiniteProgressPanel) panel.getGlassPane();
245  progressPanel.stop();
246  progressPanel.setVisible(false);
247  panel.getLayeredPane().setVisible(true);
248  }
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Definition at line 342 of file XmippWindowUtil.java.

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342  {
343  //System.out.println(command);
344  if(port == null)
345  {
346  XmippDialog.showError(null, XmippMessage.getEmptyFieldMsg("Scipion port"));
347  return;
348  }
349  String hostName = "";
350 
351  try {
352  Socket socket = new Socket(hostName, port);
353  PrintWriter out = new PrintWriter(socket.getOutputStream(), true);
354  BufferedReader in = new BufferedReader(new InputStreamReader(socket.getInputStream()));
355  DEBUG.printMessage("Sending to socket: " + command);
356  out.println(command);
357  in.readLine();
358  socket.close();
359 
360 
361  } catch (UnknownHostException e) {
362  System.err.println("Don't know about host " + hostName);
363  } catch (IOException e) {
364  System.err.println("Couldn't get I/O for the connection to " +
365  hostName);
366  }
367  }
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Window w 
)
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Definition at line 77 of file XmippWindowUtil.java.

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78  {
79  setLocation(positionx, positiony, w, getScreenRectangle());
80  }
xmipp.utils.XmippWindowUtil.getScreenRectangle
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Definition: XmippWindowUtil.java:82
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Definition at line 88 of file XmippWindowUtil.java.

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89  {
90  setLocation(positionx, positiony, w, parent.getBounds());
91  }
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Definition at line 389 of file XmippWindowUtil.java.

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390  {
391  Image img = XmippResource.getIcon("scipion_logo.png").getImage();
392  w.setIconImage(img);
393  }
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◆ firebrick

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final Color xmipp.utils.XmippWindowUtil.firebrick = Color.decode("#B22222")
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Definition at line 57 of file XmippWindowUtil.java.

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◆ LIGHT_BLUE

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final Color xmipp.utils.XmippWindowUtil.LIGHT_BLUE = new Color(173, 216, 230)
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Definition at line 61 of file XmippWindowUtil.java.

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◆ lightgrey

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final Color xmipp.utils.XmippWindowUtil.lightgrey = Color.decode("#EAEBEC")
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Definition at line 58 of file XmippWindowUtil.java.

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- - diff --git a/html/classxmipp_1_1utils_1_1XmippWindowUtil__coll__graph.dot b/html/classxmipp_1_1utils_1_1XmippWindowUtil__coll__graph.dot deleted file mode 100644 index dfac0e81..00000000 --- a/html/classxmipp_1_1utils_1_1XmippWindowUtil__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.utils.XmippWindowUtil" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node1 [label="xmipp.utils.XmippWindowUtil",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node2 -> Node1 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" LIGHT_BLUE\nfirebrick\nlightgrey" ,fontname="Helvetica"]; - Node2 [label="Color",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1utils_1_1XmippWindowUtil__coll__graph.md5 b/html/classxmipp_1_1utils_1_1XmippWindowUtil__coll__graph.md5 deleted file mode 100644 index 7b6094b7..00000000 --- a/html/classxmipp_1_1utils_1_1XmippWindowUtil__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -2a3372125d7eaa3942f8c4326940ff3a \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1FloatRenderer-members.html b/html/classxmipp_1_1viewer_1_1FloatRenderer-members.html deleted file mode 100644 index 574fd127..00000000 --- a/html/classxmipp_1_1viewer_1_1FloatRenderer-members.html +++ /dev/null @@ -1,84 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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This is the complete list of members for xmipp.viewer.FloatRenderer, including all inherited members.

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FloatRenderer()xmipp.viewer.FloatRendererinline
getTableCellRendererComponent(JTable table, Object object, boolean isSelected, boolean hasFocus, int row, int column)xmipp.viewer.FloatRendererinline
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-Public Member Functions

 FloatRenderer ()
 
Component getTableCellRendererComponent (JTable table, Object object, boolean isSelected, boolean hasFocus, int row, int column)
 
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Definition at line 10 of file FloatRenderer.java.

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◆ FloatRenderer()

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Definition at line 13 of file FloatRenderer.java.

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13  {
14  super();
15  setOpaque(true);
16  setHorizontalAlignment(JLabel.RIGHT);
17  setHorizontalTextPosition(JLabel.CENTER);
18  setVerticalTextPosition(JLabel.BOTTOM);
19  }
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◆ getTableCellRendererComponent()

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Definition at line 22 of file FloatRenderer.java.

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22  {
23  Object item = object;
24  // Calls super class so foreground, background, borders and rest of stuff is set.
25  super.getTableCellRendererComponent(table, null,
26  item != null && isSelected,
27  item != null && hasFocus, row, column);
28 
29  if (item != null) {
30  //DEBUG.printMessage("*** 2. Rendering: " + item.getLabel());
31  //AbstractXmippTableModel tableModel = (AbstractXmippTableModel) table.getModel();
32  String v = item.toString();
33  try {
34  // float f = Float.parseFloat(v);
35  v = String.format("%10.4f ", (Double)item);
36  } catch (Exception e) {
37  // TODO: handle exception
38  }
39  setText(v);
40  }
41  return this;
42  }
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xmipp.viewer.ImageDimension Member List
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This is the complete list of members for xmipp.viewer.ImageDimension, including all inherited members.

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getNDim()xmipp.viewer.ImageDimensioninline
getXDim()xmipp.viewer.ImageDimensioninline
getYDim()xmipp.viewer.ImageDimensioninline
getZDim()xmipp.viewer.ImageDimensioninline
ImageDimension()xmipp.viewer.ImageDimensioninline
ImageDimension(int x)xmipp.viewer.ImageDimensioninline
ImageDimension(int x, int y)xmipp.viewer.ImageDimensioninline
ImageDimension(int x, int y, int z)xmipp.viewer.ImageDimensioninline
ImageDimension(int x, int y, int z, long n)xmipp.viewer.ImageDimensioninline
ImageDimension(ImageGeneric image)xmipp.viewer.ImageDimensioninline
setNDim(long n)xmipp.viewer.ImageDimensioninline
setXDim(int x)xmipp.viewer.ImageDimensioninline
setYDim(int y)xmipp.viewer.ImageDimensioninline
setZDim(int z)xmipp.viewer.ImageDimensioninline
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xmipp.viewer.ImageDimension Class Reference
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-Public Member Functions

 ImageDimension ()
 
 ImageDimension (int x)
 
 ImageDimension (int x, int y)
 
 ImageDimension (int x, int y, int z)
 
 ImageDimension (int x, int y, int z, long n)
 
 ImageDimension (ImageGeneric image)
 
int getXDim ()
 
int getYDim ()
 
int getZDim ()
 
long getNDim ()
 
void setXDim (int x)
 
void setYDim (int y)
 
void setZDim (int z)
 
void setNDim (long n)
 
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Detailed Description

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Simple class to store image dimensions

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Definition at line 35 of file ImageDimension.java.

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◆ ImageDimension() [1/6]

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xmipp.viewer.ImageDimension.ImageDimension ()
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Definition at line 40 of file ImageDimension.java.

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40  {
41  }
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Definition at line 43 of file ImageDimension.java.

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43  {
44  this(x, x);
45  }
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Definition at line 47 of file ImageDimension.java.

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47  {
48  this(x, y, 1, 1);
49  }
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Definition at line 51 of file ImageDimension.java.

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51  {
52  this(x, y, z, 1);
53  }
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Definition at line 55 of file ImageDimension.java.

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55  {
56  this.xdim = x;
57  this.ydim = y;
58  this.zdim = z;
59  this.ndim = n;
60  }
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Definition at line 62 of file ImageDimension.java.

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62  {
63  try {
64  xdim = image.getXDim();
65  ydim = image.getYDim();
66  zdim = image.getZDim();
67  ndim = image.getNDim();
68  } catch (Exception ex) {
69  IJ.error("Retrieving image dimensions: "+ image);
70  }
71  }
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◆ getNDim()

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Definition at line 85 of file ImageDimension.java.

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85  {
86  return ndim;
87  }
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Definition at line 73 of file ImageDimension.java.

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73  {
74  return xdim;
75  }
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Definition at line 77 of file ImageDimension.java.

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77  {
78  return ydim;
79  }
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Definition at line 81 of file ImageDimension.java.

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81  {
82  return zdim;
83  }
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Definition at line 101 of file ImageDimension.java.

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101  {
102  this.ndim = n;
103  }
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Definition at line 89 of file ImageDimension.java.

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89  {
90  this.xdim = x;
91  }
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Definition at line 93 of file ImageDimension.java.

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93  {
94  this.ydim = y;
95  }
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Definition at line 97 of file ImageDimension.java.

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97  {
98  this.zdim = z;
99  }
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xmipp.viewer.ImageItemRenderer Member List
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cutString(String string, int columnWidth)xmipp.viewer.ImageItemRendererinlineprotected
getTableCellRendererComponent(JTable table, Object object, boolean isSelected, boolean hasFocus, int row, int column)xmipp.viewer.ImageItemRendererinline
hackBordersxmipp.viewer.ImageItemRenderer
ImageItemRenderer()xmipp.viewer.ImageItemRendererinline
ImageItemRenderer(boolean hackBorders)xmipp.viewer.ImageItemRendererinline
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 ImageItemRenderer ()
 
 ImageItemRenderer (boolean hackBorders)
 
Component getTableCellRendererComponent (JTable table, Object object, boolean isSelected, boolean hasFocus, int row, int column)
 
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boolean hackBorders = true
 
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String cutString (String string, int columnWidth)
 
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Detailed Description

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Author
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Definition at line 26 of file ImageItemRenderer.java.

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Definition at line 33 of file ImageItemRenderer.java.

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33  {
34  super();
35  setOpaque(true);
36  setHorizontalAlignment(JLabel.CENTER);
37  setHorizontalTextPosition(JLabel.CENTER);
38  setVerticalTextPosition(JLabel.BOTTOM);
39  }
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Definition at line 41 of file ImageItemRenderer.java.

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41  {
42  this();
43  this.hackBorders = false;//no use of parameter provided???
44  }
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Definition at line 126 of file ImageItemRenderer.java.

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126  {
127  StringBuilder sb = new StringBuilder(string);
128  String str = sb.toString();
129 
130  Font font = getFont();
131  int w = getFontMetrics(font).stringWidth(str);
132 
133  int i = 0;
134  while (w > columnWidth) {
135  str = "..." + sb.substring(i++);
136  w = getFontMetrics(font).stringWidth(str);
137  }
138 
139  return str;
140  }
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Component xmipp.viewer.ImageItemRenderer.getTableCellRendererComponent (JTable table,
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Definition at line 47 of file ImageItemRenderer.java.

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48  {
49  ImageGalleryTableModel.ImageItem item = (ImageGalleryTableModel.ImageItem) object;
50  // DEBUG.printMessage("*** 1. Rendering: " + item.getLabel());
51  // DEBUG.printFormat("*** 1. Rendering: item: %s, index: %d, row: %d, col: %d",
52  // item.getLabel(), item.getIndex(), row, column);
53 // Calls super class so foreground, background, borders and rest of
54 // stuff is set.
55  super.getTableCellRendererComponent(table, null, item != null
56  && item.isSelected(), item != null && hasFocus, row, column);
57 
58  if (item != null) {
59  // DEBUG.printMessage("*** 2. Rendering: " + item.getLabel());
60  // AbstractXmippTableModel tableModel = (AbstractXmippTableModel)
61  // table.getModel();
62 
63  setPreferredSize(item.getCellDim());
64 
65  // Loads image...
66 
67  Image image = item.getImage();
68  Icon icon;
69 
70  if (image != null)
71  icon = new ImageIcon(image);
72  else
73  icon = XmippResource.MISSING_ICON;
74 
75  if (!item.isEnabled()){
76  icon = new CompoundIcon(CompoundIcon.Axis.Z_AXIS, 0,
77  CompoundIcon.RIGHT, CompoundIcon.BOTTOM, icon,
78  XmippResource.DELETE_ICON);
79  //new ColoredRectangleIcon(Color.red, 16, 16));
80  }
81 
82  if (item.isBusy()) {
83  icon = new CompoundIcon(CompoundIcon.Axis.Z_AXIS, 0,
84  CompoundIcon.RIGHT, CompoundIcon.BOTTOM, icon,
85  XmippResource.LOCK_ICON);
86  }
87  ClassInfo cli = item.getClassInfo();
88  if (cli != null){
89  icon = new CompoundIcon(CompoundIcon.Axis.Z_AXIS, 0,
90  CompoundIcon.RIGHT, CompoundIcon.BOTTOM, icon,
91  cli.getIcon());
92 
93  }
94  setIcon(icon);
95  // Tooltip.
96  setToolTipText(item.getLabel());
97 
98  // (Shows label only when required).
99  if (item.getShowLabel()) {
100  String label = cutString(item.getLabel(), table
101  .getColumnModel().getColumn(column).getWidth());
102  setText(label);
103  } else {
104  setText(null);
105  }
106 
107  if (hackBorders) {
108  // Hacking borders to enhance the default one.
109  if (item.isSelected()) {
110  setBorder(BORDER_SELECTED);
111  }
112 
113  // if (hasFocus) {
114  // setBorder(BORDER_FOCUSED);
115  // }
116  }
117  } else {
118  setIcon(null);
119  setText(null);
120  setToolTipText(null);
121  }
122 
123  return this;
124  }
xmipp.viewer.ImageItemRenderer.cutString
String cutString(String string, int columnWidth)
Definition: ImageItemRenderer.java:126
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◆ hackBorders

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Definition at line 31 of file ImageItemRenderer.java.

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saveConfig(SupervisedParticlePicker picker, String path)xmipp.viewer.JMetaDataIOinlinestatic
saveData(SupervisedPickerMicrograph m, String path)xmipp.viewer.JMetaDataIOinlinestatic
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static void saveData (SupervisedPickerMicrograph m, String path)
 
static void saveConfig (SupervisedParticlePicker picker, String path)
 
-

Detailed Description

-
Author
airen
- -

Definition at line 27 of file JMetaDataIO.java.

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Member Function Documentation

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◆ saveConfig()

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static void xmipp.viewer.JMetaDataIO.saveConfig (SupervisedParticlePicker picker,
String path 
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Definition at line 92 of file JMetaDataIO.java.

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93  {
94  //System.out.println("saving data on JMetaDataIO");
95  long id;
96  try
97  {
98 
99  FileWriter fstream = new FileWriter(path);
100  BufferedWriter out = new BufferedWriter(fstream);
101  out.write("# XMIPP_STAR_1 * \n#\ndata_properties\nloop_\n");
102  String cformat = "_%s\n";
103  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_MICROGRAPH)));
104  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_COLOR)));
105  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_PARTICLE_SIZE)));
106  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_AUTOPICKPERCENT)));
107  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_TEMPLATES)));
108  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_STATE)));
109  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE)));
110  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE)));
111 
112  String vformat = "%20s";
113  out.write(String.format(vformat, picker.getMicrograph().getName()));
114  out.write(String.format(vformat, picker.getColor().getRGB()));
115  out.write(String.format(vformat, picker.getSize()));
116  out.write(String.format(vformat, picker.getAutopickpercent()));
117  out.write(String.format(vformat, picker.getTemplatesNumber()));
118  out.write(String.format(vformat, picker.getMode().toString()));
119  out.write(String.format(vformat, picker.getManualParticlesNumber()));
120  out.write(String.format(vformat, picker.getAutomaticParticlesNumber()));
121  out.newLine();
122  String optionsFormat = "%80s";
123  out.write("data_filters\nloop_\n");
124  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_MACRO_CMD)));
125  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_MACRO_CMD_ARGS)));
126  String options;
127  for (IJCommand f : picker.getFilters()) {
128  out.write(String.format(vformat, f.getMdCommand()));
129  options = f.getMdOptions();
130  out.write(String.format(optionsFormat, options));
131  out.newLine();
132 
133  }
134  out.close();
135  }
136  catch (Exception e)
137  {
138  getLogger().log(Level.SEVERE, e.getMessage(), e);
139  throw new IllegalArgumentException(e.getMessage());
140  }
141 
142  }
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static void xmipp.viewer.JMetaDataIO.saveData (SupervisedPickerMicrograph m,
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Definition at line 30 of file JMetaDataIO.java.

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31  {
32  //System.out.println("saving data on JMetaDataIO");
33  try
34  {
35  if (!m.hasData())
36  new File(path).delete();
37  else
38  {
39  FileWriter fstream = new FileWriter(path);
40  BufferedWriter out = new BufferedWriter(fstream);
41  out.write("# XMIPP_STAR_1 * \n#\ndata_header\nloop_\n");
42  String cformat = "_%s\n";
43  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_MICROGRAPH_STATE)));
44  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_PICKING_AUTOPICKPERCENT)));
45  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_COST)));
46  String vformat = "%20s";
47  out.write(String.format(vformat, m.getState().toString()));
48  out.write(String.format(vformat, m.getAutopickpercent()));
49  out.write(String.format(vformat, m.getThreshold()));
50  out.newLine();
51  out.write("data_particles\nloop_\n");
52  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_XCOOR)));
53  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_YCOOR)));
54 
55  for (ManualParticle p : m.getManualParticles())
56  {
57  out.write(String.format(vformat, p.getX()));
58  out.write(String.format(vformat, p.getY()));
59  out.newLine();
60  }
61  if(m.hasAutomaticParticles())
62  {
63  out.write("data_particles_auto\nloop_\n");
64  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_XCOOR)));
65  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_YCOOR)));
66  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_COST)));
67  out.write(String.format(cformat, MetaData.getLabelName(MDLabel.MDL_ENABLED)));
68  int enabled;
69  for (AutomaticParticle p : m.getAutomaticParticles())
70  {
71  out.write(String.format(vformat, p.getX()));
72  out.write(String.format(vformat, p.getY()));
73  out.write(String.format(vformat, p.getCost()));
74 // enabled = !p.isDeleted()? 1 : -1;
75  enabled = !p.isUnavailable() ? 1 : -1;
76  out.write(String.format(vformat, enabled));
77  out.newLine();
78  }
79  }
80  out.close();
81  }
82  }
83  catch (Exception e)
84  {
85  getLogger().log(Level.SEVERE, e.getMessage(), e);
86  throw new IllegalArgumentException(e.getMessage());
87  }
88 
89  }
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The documentation for this class was generated from the following file: -
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- - diff --git a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer-members.html b/html/classxmipp_1_1viewer_1_1RowHeaderRenderer-members.html deleted file mode 100644 index 36a23572..00000000 --- a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer-members.html +++ /dev/null @@ -1,85 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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This is the complete list of members for xmipp.viewer.RowHeaderRenderer, including all inherited members.

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borderxmipp.viewer.RowHeaderRendererprotected
getListCellRendererComponent(JList list, Object value, int index, boolean selected, boolean hasFocus)xmipp.viewer.RowHeaderRendererinline
RowHeaderRenderer()xmipp.viewer.RowHeaderRendererinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer.html b/html/classxmipp_1_1viewer_1_1RowHeaderRenderer.html deleted file mode 100644 index 889fca89..00000000 --- a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.RowHeaderRenderer Class Reference - - - - - - - - - -
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-Public Member Functions

 RowHeaderRenderer ()
 
Component getListCellRendererComponent (JList list, Object value, int index, boolean selected, boolean hasFocus)
 
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-Protected Attributes

Border border
 
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Detailed Description

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Definition at line 11 of file RowHeaderRenderer.java.

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Constructor & Destructor Documentation

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◆ RowHeaderRenderer()

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xmipp.viewer.RowHeaderRenderer.RowHeaderRenderer ()
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Definition at line 15 of file RowHeaderRenderer.java.

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15  {
16  super();
17 
18  setOpaque(true);
19 
20  border = BorderFactory.createCompoundBorder(
21  UIManager.getBorder("TableHeader.cellBorder"),
22  BorderFactory.createEmptyBorder(0, 0, 0, 2));
23 
24  // Border to show the entire label and with the same look and feel as
25  // columns.
26  setBorder(border);
27  }
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◆ getListCellRendererComponent()

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Component xmipp.viewer.RowHeaderRenderer.getListCellRendererComponent (JList list,
Object value,
int index,
boolean selected,
boolean hasFocus 
)
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Definition at line 29 of file RowHeaderRenderer.java.

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30  {
31 
32  setEnabled(list.isEnabled());
33 
34  setFont(list.getFont());
35  setText(value.toString());
36 
37  return this;
38  }
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◆ border

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Border xmipp.viewer.RowHeaderRenderer.border
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Definition at line 13 of file RowHeaderRenderer.java.

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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__coll__graph.dot b/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__coll__graph.dot deleted file mode 100644 index 809a77ca..00000000 --- a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__coll__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.RowHeaderRenderer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node3 [label="xmipp.viewer.RowHeaderRenderer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="JLabel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="ListCellRenderer",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" border" ,fontname="Helvetica"]; - Node6 [label="Border",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__coll__graph.md5 deleted file mode 100644 index a285c104..00000000 --- a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -c787c65d6ec6adef59ed653e834346af \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__inherit__graph.dot deleted file mode 100644 index c27da901..00000000 --- a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__inherit__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.viewer.RowHeaderRenderer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.RowHeaderRenderer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JLabel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="ListCellRenderer",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__inherit__graph.md5 deleted file mode 100644 index 2483732d..00000000 --- a/html/classxmipp_1_1viewer_1_1RowHeaderRenderer__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -8e6d64d9da69ff442d3c950f7a7572fe \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1StrokeBorder-members.html b/html/classxmipp_1_1viewer_1_1StrokeBorder-members.html deleted file mode 100644 index bf033f63..00000000 --- a/html/classxmipp_1_1viewer_1_1StrokeBorder-members.html +++ /dev/null @@ -1,91 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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getBorderInsets(Component c)xmipp.viewer.StrokeBorderinline
getBorderInsets(Component c, Insets insets)xmipp.viewer.StrokeBorderinline
getLineColor()xmipp.viewer.StrokeBorderinline
getThickness()xmipp.viewer.StrokeBorderinline
isBorderOpaque()xmipp.viewer.StrokeBorderinline
lineColorxmipp.viewer.StrokeBorderprotected
paintBorder(Component c, Graphics g, int x, int y, int width, int height)xmipp.viewer.StrokeBorderinline
StrokeBorder(Color color, int thickness)xmipp.viewer.StrokeBorderinline
thicknessxmipp.viewer.StrokeBorderprotected
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 StrokeBorder (Color color, int thickness)
 
void paintBorder (Component c, Graphics g, int x, int y, int width, int height)
 
Insets getBorderInsets (Component c)
 
Insets getBorderInsets (Component c, Insets insets)
 
Color getLineColor ()
 
int getThickness ()
 
boolean isBorderOpaque ()
 
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int thickness
 
Color lineColor
 
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Definition at line 12 of file StrokeBorder.java.

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Definition at line 17 of file StrokeBorder.java.

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17  {
18  this.lineColor = color;
19  this.thickness = thickness;
20  }
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Definition at line 47 of file StrokeBorder.java.

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47  {
48  return new Insets(thickness, thickness, thickness, thickness);
49  }
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Reinitialize the insets parameter with this Border's current Insets.

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Definition at line 57 of file StrokeBorder.java.

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57  {
58  insets.left = insets.top = insets.right = insets.bottom = thickness;
59  return insets;
60  }
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65  {
66  return lineColor;
67  }
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72  {
73  return thickness;
74  }
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80  {
81  return true;
82  }
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Graphics g,
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Paints the border for the specified component with the specified position and size.

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xthe x position of the painted border
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widththe width of the painted border
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Definition at line 33 of file StrokeBorder.java.

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33  {
34  Graphics2D g2d = (Graphics2D) g;
35  g2d.setColor(lineColor);
36  g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
37  float dash[] = {thickness * 2};
38  g2d.setStroke(new BasicStroke(thickness, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_MITER, 1f, dash, 0));
39  g2d.drawRect(x, y, width, height);
40  }
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Definition at line 15 of file StrokeBorder.java.

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Definition at line 14 of file StrokeBorder.java.

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This is the complete list of members for xmipp.viewer.Viewer, including all inherited members.

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main(String args[])xmipp.viewer.Viewerinlinestatic
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xmipp.viewer.Viewer Class Reference
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static void main (String args[])
 
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Detailed Description

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Definition at line 10 of file Viewer.java.

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Member Function Documentation

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◆ main()

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static void xmipp.viewer.Viewer.main (String args[])
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Definition at line 12 of file Viewer.java.

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13  {
14  StopWatch stopWatch = StopWatch.getInstance();
15  stopWatch.printElapsedTime("starting app");
16  // Schedule a job for the event dispatch thread:
17  // creating and showing this application's GUI.
18  final String[] myargs = args;
19  SwingUtilities.invokeLater(new Runnable()
20  {
21  public void run()
22  {
23  Params parameters = new Params(myargs);
24  try
25  {
26  if (parameters.debug)
27  DEBUG.enableDebug(true);
28 
29  if (parameters.files != null)
30  {
31  // DEBUG.enableDebug(true);
32  openFiles(parameters);
33  }
34  }
35  catch (Exception e)
36  {
37  e.printStackTrace();
38  }
39 
40  }
41  });
42  }
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This is the complete list of members for xmipp.viewer.ViewerTest, including all inherited members.

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actionPerformed(ActionEvent e)xmipp.viewer.ViewerTestinline
addButtons(JToolBar toolBar)xmipp.viewer.ViewerTestinlineprotected
createAndShowGUI()xmipp.viewer.ViewerTestinlinestatic
displayResult(String actionDescription)xmipp.viewer.ViewerTestinlineprotected
main(String[] args)xmipp.viewer.ViewerTestinlinestatic
makeNavigationButton(String imageName, String actionCommand, String toolTipText, String altText)xmipp.viewer.ViewerTestinlineprotected
newlinexmipp.viewer.ViewerTestprotected
textAreaxmipp.viewer.ViewerTestprotected
ViewerTest()xmipp.viewer.ViewerTestinline
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 ViewerTest ()
 
void actionPerformed (ActionEvent e)
 
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static void createAndShowGUI ()
 
static void main (String[] args)
 
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void addButtons (JToolBar toolBar)
 
JButton makeNavigationButton (String imageName, String actionCommand, String toolTipText, String altText)
 
void displayResult (String actionDescription)
 
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JTextArea textArea
 
String newline = "\n"
 
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Definition at line 60 of file ViewerTest.java.

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◆ ViewerTest()

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Definition at line 70 of file ViewerTest.java.

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70  {
71  super(new BorderLayout());
72 
73  //Create the toolbar.
74  JToolBar toolBar = new JToolBar("Still draggable");
75  addButtons(toolBar);
76  toolBar.setFloatable(false);
77  toolBar.setRollover(true);
78 
79  //Create the text area used for output. Request
80  //enough space for 5 rows and 30 columns.
81  textArea = new JTextArea(5, 30);
82  textArea.setEditable(false);
83  JScrollPane scrollPane = new JScrollPane(textArea);
84 
85  //Lay out the main panel.
86  setPreferredSize(new Dimension(450, 130));
87  add(toolBar, BorderLayout.PAGE_START);
88  add(scrollPane, BorderLayout.CENTER);
89  }
xmipp.viewer.ViewerTest.addButtons
void addButtons(JToolBar toolBar)
Definition: ViewerTest.java:91
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Definition at line 163 of file ViewerTest.java.

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163  {
164  String cmd = e.getActionCommand();
165  String description = null;
166 
167  // Handle each button.
168  if (PREVIOUS.equals(cmd)) { //first button clicked
169  description = "taken you to the previous <something>.";
170  } else if (UP.equals(cmd)) { // second button clicked
171  description = "taken you up one level to <something>.";
172  } else if (NEXT.equals(cmd)) { // third button clicked
173  description = "taken you to the next <something>.";
174  } else if (SOMETHING_ELSE.equals(cmd)) { // fourth button clicked
175  description = "done something else.";
176  } else if (TEXT_ENTERED.equals(cmd)) { // text field
177  JTextField tf = (JTextField)e.getSource();
178  String text = tf.getText();
179  tf.setText("");
180  description = "done something with this text: "
181  + newline + " \""
182  + text + "\"";
183  }
184 
185  displayResult("If this were a real app, it would have "
186  + description);
187  }
xmipp.viewer.ViewerTest.displayResult
void displayResult(String actionDescription)
Definition: ViewerTest.java:189
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91  {
92  JButton button = null;
93 
94  //first button
95  button = makeNavigationButton("save", PREVIOUS,
96  "Save something",
97  "Save");
98  toolBar.add(button);
99 
100  //first button
101  button = makeNavigationButton("left", PREVIOUS,
102  "Back to previous something-or-other",
103  "Previous");
104  toolBar.add(button);
105 
106  //second button
107  button = makeNavigationButton("up", UP,
108  "Up to something-or-other",
109  "Up");
110  toolBar.add(button);
111 
112  //third button
113  button = makeNavigationButton("right", NEXT,
114  "Forward to something-or-other",
115  "Next");
116  toolBar.add(button);
117 
118  //separator
119  toolBar.addSeparator();
120 
121  //fourth button
122  button = new JButton("Another button");
123  button.setActionCommand(SOMETHING_ELSE);
124  button.setToolTipText("Something else");
125  button.addActionListener(this);
126  toolBar.add(button);
127 
128  //fifth component is NOT a button!
129  JTextField textField = new JTextField("A text field");
130  textField.setColumns(10);
131  textField.addActionListener(this);
132  textField.setActionCommand(TEXT_ENTERED);
133  toolBar.add(textField);
134  }
xmipp.viewer.ViewerTest.makeNavigationButton
JButton makeNavigationButton(String imageName, String actionCommand, String toolTipText, String altText)
Definition: ViewerTest.java:136
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Definition at line 199 of file ViewerTest.java.

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199  {
200  //Create and set up the window.
201  JFrame frame = new JFrame("ToolBarDemo2");
202  frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
203 
204  //Add content to the window.
205  frame.add(new ViewerTest());
206 
207  //Display the window.
208  frame.pack();
209  frame.setLocationRelativeTo(null);
210  frame.setVisible(true);
211  }
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Definition at line 189 of file ViewerTest.java.

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189  {
190  textArea.append(actionDescription + newline);
191  textArea.setCaretPosition(textArea.getDocument().getLength());
192  }
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Definition at line 213 of file ViewerTest.java.

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213  {
214  //Schedule a job for the event dispatch thread:
215  //creating and showing this application's GUI.
216  SwingUtilities.invokeLater(new Runnable() {
217  public void run() {
218  //Turn off metal's use of bold fonts
219  UIManager.put("swing.boldMetal", Boolean.FALSE);
220  createAndShowGUI();
221  }
222  });
223  }
xmipp.viewer.ViewerTest.createAndShowGUI
static void createAndShowGUI()
Definition: ViewerTest.java:199
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Definition at line 136 of file ViewerTest.java.

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139  {
140  //Look for the image.
141  String imgLocation = "/home/josem/xmipp_current/resources/"
142  + imageName
143  + ".png";
144  //URL imageURL = ViewerTest.class.getResource(imgLocation);
145 
146  //Create and initialize the button.
147  JButton button = new JButton();
148  button.setActionCommand(actionCommand);
149  button.setToolTipText(toolTipText);
150  button.addActionListener(this);
151 
152  //if (imageURL != null) { //image found
153  button.setIcon(new ImageIcon(imgLocation, altText));
154 // } else { //no image found
155 // button.setText(altText);
156 // System.err.println("Resource not found: "
157 // + imgLocation);
158 // }
159 
160  return button;
161  }
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Definition at line 63 of file ViewerTest.java.

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Definition at line 62 of file ViewerTest.java.

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CTFAnalyzerImagePane(ImagePlus imp, CTFAnalyzerJFrame frame)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
getProfileangle()xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
getX0()xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
getX1()xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
getY0()xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
getY1()xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
mouseClicked(MouseEvent e)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
mouseDragged(MouseEvent e)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
mouseEntered(MouseEvent arg0)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
mouseExited(MouseEvent arg0)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
mouseMoved(MouseEvent arg0)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
mousePressed(MouseEvent arg0)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
mouseReleased(MouseEvent e)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
mouseWheelMoved(MouseWheelEvent e)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
paintComponent(Graphics g)xmipp.viewer.ctf.CTFAnalyzerImagePaneinline
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Xmipp -  v20.07 -
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xmipp.viewer.ctf.CTFAnalyzerImagePane Class Reference
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-Public Member Functions

 CTFAnalyzerImagePane (ImagePlus imp, CTFAnalyzerJFrame frame)
 
double getProfileangle ()
 
int getX0 ()
 
int getY0 ()
 
int getX1 ()
 
int getY1 ()
 
void paintComponent (Graphics g)
 
void mouseWheelMoved (MouseWheelEvent e)
 
void mouseClicked (MouseEvent e)
 
void mouseEntered (MouseEvent arg0)
 
void mouseExited (MouseEvent arg0)
 
void mousePressed (MouseEvent arg0)
 
void mouseReleased (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseMoved (MouseEvent arg0)
 
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Detailed Description

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Definition at line 16 of file CTFAnalyzerImagePane.java.

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Constructor & Destructor Documentation

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◆ CTFAnalyzerImagePane()

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xmipp.viewer.ctf.CTFAnalyzerImagePane.CTFAnalyzerImagePane (ImagePlus imp,
CTFAnalyzerJFrame frame 
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Definition at line 29 of file CTFAnalyzerImagePane.java.

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30  {
31  this.imp = imp;
32  this.frame = frame;
33  setPreferredSize(new Dimension(imp.getWidth(), imp.getHeight()));
34 
35  radius = imp.getWidth() / 2;
36  x0 = radius;
37  y0 = radius;
38  profileangle = 0;
39  x1 = x0 + (int) (radius * Math.cos(profileangle));
40  y1 = y0 + (int) (radius * Math.sin(profileangle));
41  setToolTipText("Use mouse to move profile");
42  addMouseListener(this);
43  addMouseWheelListener(this);
44  addMouseMotionListener(this);
45  }
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Member Function Documentation

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◆ getProfileangle()

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double xmipp.viewer.ctf.CTFAnalyzerImagePane.getProfileangle ()
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Definition at line 48 of file CTFAnalyzerImagePane.java.

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49  {
50  return profileangle;
51  }
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◆ getX0()

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Definition at line 54 of file CTFAnalyzerImagePane.java.

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55  {
56  return x0;
57  }
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◆ getX1()

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Definition at line 66 of file CTFAnalyzerImagePane.java.

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67  {
68  return x1;
69  }
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Definition at line 60 of file CTFAnalyzerImagePane.java.

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61  {
62  return y0;
63  }
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Definition at line 72 of file CTFAnalyzerImagePane.java.

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73  {
74  return y1;
75  }
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Definition at line 116 of file CTFAnalyzerImagePane.java.

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117  {
118  updateProfile(e);
119 
120  }
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Definition at line 158 of file CTFAnalyzerImagePane.java.

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159  {
160  updateProfile(e);
161 
162  }
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Definition at line 126 of file CTFAnalyzerImagePane.java.

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127  {
128  // TODO Auto-generated method stub
129 
130  }
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Definition at line 134 of file CTFAnalyzerImagePane.java.

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135  {
136  // TODO Auto-generated method stub
137 
138  }
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Definition at line 166 of file CTFAnalyzerImagePane.java.

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167  {
168  // TODO Auto-generated method stub
169 
170  }
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Definition at line 142 of file CTFAnalyzerImagePane.java.

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143  {
144  // TODO Auto-generated method stub
145 
146  }
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Definition at line 150 of file CTFAnalyzerImagePane.java.

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151  {
152  updateProfile(e);
153 
154  }
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Definition at line 107 of file CTFAnalyzerImagePane.java.

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108  {
109  int rotation = e.getWheelRotation();//1 or -1
110  updateProfile(profileangle + rotation * Math.toRadians(5));
111 
112  }
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Definition at line 78 of file CTFAnalyzerImagePane.java.

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79  {
80  super.paintComponent(g);
81 
82  g.drawImage(imp.getImage(), 0, 0, this);
83  g.setColor(Color.green);
84  g.drawLine(x0, y0, x1, y1);
85 
86  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__coll__graph.dot b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__coll__graph.dot deleted file mode 100644 index d5cb1611..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__coll__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.viewer.ctf.CTFAnalyzerImagePane" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node5 [label="xmipp.viewer.ctf.CTFAnalyzer\lImagePane",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="JPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="MouseListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node8 [label="MouseWheelListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node9 [label="MouseMotionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__coll__graph.md5 deleted file mode 100644 index 8942dd97..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -861dd2642070a54cda323ddade2c4b72 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__inherit__graph.dot deleted file mode 100644 index 42973142..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__inherit__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.viewer.ctf.CTFAnalyzerImagePane" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.ctf.CTFAnalyzer\lImagePane",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="MouseListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="MouseWheelListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node4 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="MouseMotionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__inherit__graph.md5 deleted file mode 100644 index f958c2fc..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerImagePane__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -063bc3c3860130cb73e2164500d65807 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerJFrame-members.html b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerJFrame-members.html deleted file mode 100644 index fd2674d1..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFAnalyzerJFrame-members.html +++ /dev/null @@ -1,91 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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This is the complete list of members for xmipp.viewer.ctf.CTFAnalyzerJFrame, including all inherited members.

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actionPerformed(ActionEvent e)xmipp.viewer.ctf.CTFAnalyzerJFrameinline
CTFAnalyzerJFrame(String psdEnhancedFile, String ctffile, String psdfile)xmipp.viewer.ctf.CTFAnalyzerJFrameinline
CTFAnalyzerJFrame(String psdEnhancedFile, CTFDescription ctfdescription, String psdfile, double samplingRate)xmipp.viewer.ctf.CTFAnalyzerJFrameinline
getBGNoiseLabel()xmipp.viewer.ctf.CTFAnalyzerJFrameinline
getCTFLabel()xmipp.viewer.ctf.CTFAnalyzerJFrameinline
getDifferenceLabel()xmipp.viewer.ctf.CTFAnalyzerJFrameinline
getEnvelopeLabel()xmipp.viewer.ctf.CTFAnalyzerJFrameinline
getPSDProfileLabel()xmipp.viewer.ctf.CTFAnalyzerJFrameinline
isRadialProfile()xmipp.viewer.ctf.CTFAnalyzerJFrameinline
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class  EnableDisplayActionListener
 
class  FillGraphicsActionListener
 
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-Public Member Functions

 CTFAnalyzerJFrame (String psdEnhancedFile, String ctffile, String psdfile)
 
 CTFAnalyzerJFrame (String psdEnhancedFile, CTFDescription ctfdescription, String psdfile, double samplingRate)
 
boolean isRadialProfile ()
 
void actionPerformed (ActionEvent e)
 
String getDifferenceLabel ()
 
String getPSDProfileLabel ()
 
String getEnvelopeLabel ()
 
String getCTFLabel ()
 
String getBGNoiseLabel ()
 
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Detailed Description

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Definition at line 47 of file CTFAnalyzerJFrame.java.

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◆ CTFAnalyzerJFrame() [1/2]

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xmipp.viewer.ctf.CTFAnalyzerJFrame.CTFAnalyzerJFrame (String psdEnhancedFile,
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Definition at line 86 of file CTFAnalyzerJFrame.java.

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87  {
88  try
89  {
90  this.imp = this.getThumbnail(psdEnhancedFile);
91  this.psdfile = psdfile;
92  this.profileimp = this.getThumbnail(psdfile);
93  ctfmodel = new CTFDescription(ctffile);
94  double samplingRate = getSamplingRate(ctffile);
95  samples = this.imp.getWidth() / 2;
96  xvalues = getXValues(samples, samplingRate);
97  initComponents();
98  } catch (Exception e) {
99  e.printStackTrace();
100  }
101  }
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xmipp.viewer.ctf.CTFAnalyzerJFrame.CTFAnalyzerJFrame (String psdEnhancedFile,
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Definition at line 103 of file CTFAnalyzerJFrame.java.

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104  {
105  try
106  {
107  this.imp = this.getThumbnail(psdEnhancedFile);
108  this.psdfile = psdfile;
109  this.profileimp = this.getThumbnail(psdfile);
110  ctfmodel = ctfdescription;
111  samples = this.imp.getWidth() / 2;
112  xvalues = getXValues(samples, samplingRate);
113  initComponents();
114  } catch (Exception e) {
115  e.printStackTrace();
116  }
117  }
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Definition at line 557 of file CTFAnalyzerJFrame.java.

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558  {
559  int result = fc.showSaveDialog(this);
560  boolean export = result == XmippFileChooser.APPROVE_OPTION;
561  if (export)
562  {
563  File file = fc.getSelectedFile();
564  if (file != null)
565  {
566 
567  boolean saved = export(file.getAbsolutePath());
568  if (saved)
569  XmippDialog.showInfo(this, "File saved successfully.");
570  }
571  }
572 
573  }
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Definition at line 657 of file CTFAnalyzerJFrame.java.

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658  {
659  return XmippLabel.CB_PLOT_BGNOISE;
660  }
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Definition at line 651 of file CTFAnalyzerJFrame.java.

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652  {
653  return XmippLabel.LABEL_CTF;
654  }
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Definition at line 630 of file CTFAnalyzerJFrame.java.

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631  {
632  return String.format("%s - %s", XmippLabel.LABEL_PSD, XmippLabel.CB_PLOT_BGNOISE);
633  }
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Definition at line 646 of file CTFAnalyzerJFrame.java.

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647  {
648  return XmippLabel.CB_PLOT_ENVELOPE;
649  }
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Definition at line 641 of file CTFAnalyzerJFrame.java.

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642  {
643  return XmippLabel.LABEL_PSD;
644  }
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Definition at line 240 of file CTFAnalyzerJFrame.java.

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241  {
242  return tabspn.getSelectedIndex() == 0;
243  }
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xmipp.viewer.ctf.CTFCanvas Member List
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This is the complete list of members for xmipp.viewer.ctf.CTFCanvas, including all inherited members.

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CTFCanvas(ImagePlus imp)xmipp.viewer.ctf.CTFCanvasinline
paint(Graphics g)xmipp.viewer.ctf.CTFCanvasinline
paintFreqCircle(Graphics g, double freq)xmipp.viewer.ctf.CTFCanvasinline
setMaster(CTFRecalculateImageWindow master)xmipp.viewer.ctf.CTFCanvasinline
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-Public Member Functions

 CTFCanvas (ImagePlus imp)
 
void setMaster (CTFRecalculateImageWindow master)
 
void paint (Graphics g)
 
void paintFreqCircle (Graphics g, double freq)
 
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Definition at line 17 of file CTFCanvas.java.

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◆ CTFCanvas()

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xmipp.viewer.ctf.CTFCanvas.CTFCanvas (ImagePlus imp)
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Definition at line 22 of file CTFCanvas.java.

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22  {
23  super(imp);
24  }
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◆ paint()

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void xmipp.viewer.ctf.CTFCanvas.paint (Graphics g)
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Definition at line 32 of file CTFCanvas.java.

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33  {
34  super.paint(g);
35  g.setColor(Color.blue);
36  paintFreqCircle(g, master.getLowFreq());
37  paintFreqCircle(g, master.getHighFreq());
38  }
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xmipp.viewer.ctf.CTFCanvas.paintFreqCircle
void paintFreqCircle(Graphics g, double freq)
Definition: CTFCanvas.java:40
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void xmipp.viewer.ctf.CTFCanvas.paintFreqCircle (Graphics g,
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Definition at line 40 of file CTFCanvas.java.

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40  {
41  double size = width * magnification;
42  int outer = (int)(size * freq * 2);
43  int offset = (int)(size - outer) / 2;
44  g.drawOval(offset, offset, outer, outer);
45  }
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void xmipp.viewer.ctf.CTFCanvas.setMaster (CTFRecalculateImageWindow master)
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Definition at line 26 of file CTFCanvas.java.

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26  {
27  this.master = master;
28  ImagePlus imp = master.getImagePlus();
29  width = imp.getWidth();
30  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__coll__graph.dot b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__coll__graph.dot deleted file mode 100644 index 8c4ebf00..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.ctf.CTFCanvas" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.ctf.CTFCanvas",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ImageCanvas",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__coll__graph.md5 deleted file mode 100644 index 48934d4f..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -c5420395f8d16a2053353d2f71fd4d55 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__inherit__graph.dot deleted file mode 100644 index d66cfc98..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.ctf.CTFCanvas" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.ctf.CTFCanvas",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="ImageCanvas",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__inherit__graph.md5 deleted file mode 100644 index 5fd1934a..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFCanvas__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -5a6ee2d8d162bd9ac6bc562890cb308f \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFRecalculateImageWindow-members.html b/html/classxmipp_1_1viewer_1_1ctf_1_1CTFRecalculateImageWindow-members.html deleted file mode 100644 index 2059b1ea..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CTFRecalculateImageWindow-members.html +++ /dev/null @@ -1,92 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.ctf.CTFRecalculateImageWindow Member List
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actionPerformed(ActionEvent e)xmipp.viewer.ctf.CTFRecalculateImageWindowinline
CTFRecalculateImageWindow(GalleryData data, boolean[] selection, ImagePlus imp, String psd, EllipseCTF ellipsectf, TasksEngine tasksEngine, int row, String sortFn)xmipp.viewer.ctf.CTFRecalculateImageWindowinline
ellipseFitterxmipp.viewer.ctf.CTFRecalculateImageWindowprotected
exit()xmipp.viewer.ctf.CTFRecalculateImageWindowinline
fitEllipse()xmipp.viewer.ctf.CTFRecalculateImageWindowinline
getHighFreq()xmipp.viewer.ctf.CTFRecalculateImageWindowinline
getLowFreq()xmipp.viewer.ctf.CTFRecalculateImageWindowinline
stateChanged(ChangeEvent arg0)xmipp.viewer.ctf.CTFRecalculateImageWindowinline
tasksEnginexmipp.viewer.ctf.CTFRecalculateImageWindowprotected
windowClosing(WindowEvent e)xmipp.viewer.ctf.CTFRecalculateImageWindowinline
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-Public Member Functions

 CTFRecalculateImageWindow (GalleryData data, boolean[] selection, ImagePlus imp, String psd, EllipseCTF ellipsectf, TasksEngine tasksEngine, int row, String sortFn)
 
double getLowFreq ()
 
double getHighFreq ()
 
boolean fitEllipse ()
 
void actionPerformed (ActionEvent e)
 
void stateChanged (ChangeEvent arg0)
 
void exit ()
 
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-Protected Attributes

EllipseFitter ellipseFitter = new EllipseFitter()
 
TasksEngine tasksEngine
 
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Definition at line 46 of file CTFRecalculateImageWindow.java.

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◆ CTFRecalculateImageWindow()

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xmipp.viewer.ctf.CTFRecalculateImageWindow.CTFRecalculateImageWindow (GalleryData data,
boolean [] selection,
ImagePlus imp,
String psd,
EllipseCTF ellipsectf,
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Definition at line 60 of file CTFRecalculateImageWindow.java.

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61  {
62  super(imp, new CTFCanvas(imp));
63  XmippApplication.addInstance(true);
64  this.selection = selection;
65  this.data = data;
66  this.PSDFilename = psd;
67  this.sortFn = sortFn;
68  this.row = row;
69  this.tasksEngine = tasksEngine;
70  ellipseCTF = ellipsectf;
71 
72  recalculatebt = XmippWindowUtil.getTextButton("Ok", this);
73  recalculatebt.setEnabled(false);
74  cancelbt = XmippWindowUtil.getTextButton("Cancel", new ActionListener() {
75 
76  @Override
77  public void actionPerformed(ActionEvent ae) {
78  exit();
79  }
80  });
81 
82  canvas = (CTFCanvas)imp.getCanvas();
83  canvas.addMouseListener(new MouseListener() {
84 
85  public void mouseClicked(MouseEvent e) {
86  }
87 
88  public void mousePressed(MouseEvent e) {
89  }
90 
91  public void mouseReleased(MouseEvent e) {
92  // If there is no ellipse ROI, button is disabled.
93  recalculatebt.setEnabled(fitEllipse());
94  }
95 
96  public void mouseEntered(MouseEvent e) {
97  }
98 
99  public void mouseExited(MouseEvent e) {
100  }
101  });
102 
103  canvas.setMaster(this);
104 
105 
106  Panel previousContent = new Panel();
107  previousContent.setLayout(new ImageLayout(ic));
108 
109  Component components[] = getComponents();
110  for (int i = 0; i < components.length; i++) {
111  previousContent.add(components[i]);
112  }
113 
114  removeAll();
115  setLayout(new BorderLayout());
116 
117  add(previousContent, BorderLayout.CENTER);
118 
119  Panel panel = new Panel(new GridBagLayout());
120  GridBagConstraints gbc = new GridBagConstraints();
121  gbc.insets = new Insets(5, 5, 5, 5);
122 
123 
124  panel.add(new JLabel("Draw an ellipse to fit the first zero"),XmippWindowUtil.getConstraints(gbc, 0, 0, 4));
125 
126  panel.add(new JLabel("Low freq"), XmippWindowUtil.getConstraints(gbc, 0, 1));
127  spinnerLowFreq = new JSpinner(new SpinnerNumberModel(0.05, 0.0, 0.5, 0.01));
128  panel.add(spinnerLowFreq, XmippWindowUtil.getConstraints(gbc, 1, 1));
129  panel.add(new JLabel("High freq"), XmippWindowUtil.getConstraints(gbc, 2, 1));
130  spinnerLowFreq.addChangeListener(this);
131 
132  spinnerHighFreq = new JSpinner(new SpinnerNumberModel(0.5, 0.0, 0.5, 0.01));
133  panel.add(spinnerHighFreq, XmippWindowUtil.getConstraints(gbc, 3, 1));
134  JPanel actionspn = new JPanel();
135  actionspn.add(cancelbt);
136  actionspn.add(recalculatebt);
137  panel.add(actionspn, XmippWindowUtil.getConstraints(gbc, 1, 2, 3, 1, GridBagConstraints.HORIZONTAL));
138  spinnerHighFreq.addChangeListener(this);
139 
140  add(panel, BorderLayout.SOUTH);
141 
142  setMaximumSize(getPreferredSize());
143 
144  pack();
145  imp.updateImage();
146  IJ.setTool("ellipse");
147  }
xmipp.viewer.ctf.CTFCanvas.setMaster
void setMaster(CTFRecalculateImageWindow master)
Definition: CTFCanvas.java:26
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Definition at line 207 of file CTFRecalculateImageWindow.java.

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207  {
208  recalculateCTF();
209  }
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Definition at line 217 of file CTFRecalculateImageWindow.java.

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218  {
219  setVisible(false);
220  dispose();
221  XmippApplication.removeInstance(true);
222  }
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Definition at line 157 of file CTFRecalculateImageWindow.java.

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157  {
158  boolean fitted = false;
159  Roi roi = imp.getRoi();
160 
161  if (roi != null && roi.isArea()) {
162  IJ.run(imp, "Fit Ellipse", "");
163  ImageStatistics is = imp.getStatistics();
164 
165  ellipseFitter = new EllipseFitter();
166  ellipseFitter.fit(imp.getProcessor(), is);
167 
168  // Centers ellipse in image.
169  roi = imp.getRoi();
170  if (roi != null) {
171  Rectangle r = roi.getBounds();
172 
173  double xCenter = r.x + r.width / 2;
174  double yCenter = r.y + r.height / 2;
175 
176  double dx = imp.getWidth() / 2 - xCenter;
177  double dy = imp.getHeight() / 2 - yCenter;
178 
179  roi.setLocation((int) (r.x + dx), (int) (r.y + dy));
180  imp.draw();
181 
182  // Store values for later use.
183  fitted = true;
184  ellipseCTF.calculateDefocus(ellipseFitter.minor / 2, ellipseFitter.major / 2);
185  IJ.showStatus(String.format("Defocus(U,V)=%f,%f Angstroms", ellipseCTF.getDefocusU(),ellipseCTF.getDefocusV()));
186  }
187  }
188 
189  return fitted;
190  }
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void calculateDefocus(double minor, double major)
Definition: EllipseCTF.java:90
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Definition at line 153 of file CTFRecalculateImageWindow.java.

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153  {
154  return ((Double)spinnerHighFreq.getValue()).doubleValue();
155  }
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Definition at line 149 of file CTFRecalculateImageWindow.java.

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149  {
150  return ((Double)spinnerLowFreq.getValue()).doubleValue();
151  }
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Definition at line 212 of file CTFRecalculateImageWindow.java.

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212  {
213  getImagePlus().updateAndRepaintWindow();
214  }
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Definition at line 225 of file CTFRecalculateImageWindow.java.

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226  {
227 
228  super.windowClosing(e);
229  XmippApplication.removeInstance(true);
230  }
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Definition at line 49 of file CTFRecalculateImageWindow.java.

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Definition at line 57 of file CTFRecalculateImageWindow.java.

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xmipp.viewer.ctf.CommandTask Member List
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This is the complete list of members for xmipp.viewer.ctf.CommandTask, including all inherited members.

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addCommand(String command)xmipp.viewer.ctf.CommandTaskinline
commandsxmipp.viewer.ctf.CommandTaskprotected
commandsListenerxmipp.viewer.ctf.CommandTaskprotected
CommandTask(String command, int row, iTaskCompletionListener commandsListener)xmipp.viewer.ctf.CommandTaskinline
CommandTask(String command, iTaskCompletionListener commandsListener)xmipp.viewer.ctf.CommandTaskinline
CommandTask(String command)xmipp.viewer.ctf.CommandTaskinline
rowxmipp.viewer.ctf.CommandTaskprotected
run()xmipp.viewer.ctf.CommandTaskinline
start()xmipp.viewer.ctf.CommandTaskinline
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xmipp.viewer.ctf.CommandTask Class Reference
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-Public Member Functions

 CommandTask (String command, int row, iTaskCompletionListener commandsListener)
 
 CommandTask (String command, iTaskCompletionListener commandsListener)
 
 CommandTask (String command)
 
void start ()
 
void run ()
 
void addCommand (String command)
 
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-Protected Attributes

ArrayList< String > commands
 
int row = -1
 
iTaskCompletionListener commandsListener
 
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Detailed Description

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Author
Juanjo Vega 
    This class will run different commands and notify when finished
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Definition at line 19 of file CommandTask.java.

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◆ CommandTask() [1/3]

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xmipp.viewer.ctf.CommandTask.CommandTask (String command,
int row,
iTaskCompletionListener commandsListener 
)
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Definition at line 25 of file CommandTask.java.

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26  {
27  this(command, commandsListener);
28  this.row = row;
29  }
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xmipp.viewer.ctf.CommandTask.commandsListener
iTaskCompletionListener commandsListener
Definition: CommandTask.java:23
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Definition at line 31 of file CommandTask.java.

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31  {
32  this(command);
33  this.commandsListener = commandsListener;
34  }
xmipp.viewer.ctf.CommandTask.commandsListener
iTaskCompletionListener commandsListener
Definition: CommandTask.java:23
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Definition at line 36 of file CommandTask.java.

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36  {
37  //System.out.println(command);
38  commands = new ArrayList<String>();
39  addCommand(command);
40  }
xmipp.viewer.ctf.CommandTask.commands
ArrayList< String > commands
Definition: CommandTask.java:21
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void addCommand(String command)
Definition: CommandTask.java:59
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◆ addCommand()

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void xmipp.viewer.ctf.CommandTask.addCommand (String command)
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Definition at line 59 of file CommandTask.java.

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59  {
60  commands.add(command);
61  }
xmipp.viewer.ctf.CommandTask.commands
ArrayList< String > commands
Definition: CommandTask.java:21
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Definition at line 47 of file CommandTask.java.

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47  {
48  try {
49  runTask();
50  } catch (Exception ex) {
51  IJ.error("Error running command: " + ex.getMessage());
52  } finally {
53  if (commandsListener != null) {
54  commandsListener.done(this);
55  }
56  }
57  }
xmipp.viewer.ctf.CommandTask.commandsListener
iTaskCompletionListener commandsListener
Definition: CommandTask.java:23
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Definition at line 42 of file CommandTask.java.

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42  {
43  Thread t = new Thread(this);
44  t.start();
45  }
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◆ commands

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Definition at line 21 of file CommandTask.java.

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Definition at line 23 of file CommandTask.java.

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◆ row

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int xmipp.viewer.ctf.CommandTask.row = -1
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Definition at line 22 of file CommandTask.java.

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- - diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__coll__graph.dot b/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__coll__graph.dot deleted file mode 100644 index 424d4b33..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__coll__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.ctf.CommandTask" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node4 [label="xmipp.viewer.ctf.CommandTask",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node5 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="Runnable",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node4 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" commandsListener" ,fontname="Helvetica"]; - Node6 [label="xmipp.viewer.ctf.iTaskCompletion\lListener",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$interfacexmipp_1_1viewer_1_1ctf_1_1iTaskCompletionListener.html"]; - Node7 -> Node4 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" commands" ,fontname="Helvetica"]; - Node7 [label="ArrayList\< String \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__coll__graph.md5 deleted file mode 100644 index 5361a61f..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -2d77805c3b4263c2c9ff8c5a0b9b92d4 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__inherit__graph.dot deleted file mode 100644 index d91b37b1..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__inherit__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.ctf.CommandTask" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.ctf.CommandTask",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="Runnable",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node0 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.viewer.ctf.Estimate\lFromCTFTask",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1ctf_1_1EstimateFromCTFTask.html"]; - Node0 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.ctf.SortPSDSTask",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1ctf_1_1SortPSDSTask.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__inherit__graph.md5 deleted file mode 100644 index 01471c10..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1CommandTask__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -577ff71f9404d0be5c2110466880f690 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1ctf_1_1EstimateFromCTFTask-members.html b/html/classxmipp_1_1viewer_1_1ctf_1_1EstimateFromCTFTask-members.html deleted file mode 100644 index 466866d9..00000000 --- a/html/classxmipp_1_1viewer_1_1ctf_1_1EstimateFromCTFTask-members.html +++ /dev/null @@ -1,93 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.ctf.EstimateFromCTFTask Member List
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addCommand(String command)xmipp.viewer.ctf.CommandTaskinline
commandsxmipp.viewer.ctf.CommandTaskprotected
commandsListenerxmipp.viewer.ctf.CommandTaskprotected
CommandTask(String command, int row, iTaskCompletionListener commandsListener)xmipp.viewer.ctf.CommandTaskinline
CommandTask(String command, iTaskCompletionListener commandsListener)xmipp.viewer.ctf.CommandTaskinline
CommandTask(String command)xmipp.viewer.ctf.CommandTaskinline
EstimateFromCTFTask(EllipseCTF ellipseCTF, double angle, String PSDFilename, int modelSize, iTaskCompletionListener commandsListener, int row, String sortFn)xmipp.viewer.ctf.EstimateFromCTFTaskinline
getSortCmd(String filename)xmipp.viewer.ctf.EstimateFromCTFTaskinlinestatic
rowxmipp.viewer.ctf.CommandTaskprotected
run()xmipp.viewer.ctf.CommandTaskinline
start()xmipp.viewer.ctf.CommandTaskinline
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-Public Member Functions

 EstimateFromCTFTask (EllipseCTF ellipseCTF, double angle, String PSDFilename, int modelSize, iTaskCompletionListener commandsListener, int row, String sortFn)
 
- Public Member Functions inherited from xmipp.viewer.ctf.CommandTask
 CommandTask (String command, int row, iTaskCompletionListener commandsListener)
 
 CommandTask (String command, iTaskCompletionListener commandsListener)
 
 CommandTask (String command)
 
void start ()
 
void run ()
 
void addCommand (String command)
 
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static String getSortCmd (String filename)
 
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-Additional Inherited Members

- Protected Attributes inherited from xmipp.viewer.ctf.CommandTask
ArrayList< String > commands
 
int row = -1
 
iTaskCompletionListener commandsListener
 
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Detailed Description

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Author
juanjo
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Definition at line 14 of file EstimateFromCTFTask.java.

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Constructor & Destructor Documentation

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◆ EstimateFromCTFTask()

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xmipp.viewer.ctf.EstimateFromCTFTask.EstimateFromCTFTask (EllipseCTF ellipseCTF,
double angle,
String PSDFilename,
int modelSize,
iTaskCompletionListener commandsListener,
int row,
String sortFn 
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Definition at line 18 of file EstimateFromCTFTask.java.

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19  {
20  super(XMIPP_CTF_ESTIMATE_FROM_PSD
21  + " --sampling_rate " + ellipseCTF.getSamplingRate()
22  + " --downSamplingPerformed " + ellipseCTF.getDownsamplingFactor()
23  + " --kV " + ellipseCTF.getVoltage()
24  + " --Cs " + ellipseCTF.getSphericalAberration()
25  + " --defocusU " + ellipseCTF.getDefocusU()
26  + " --defocusV " + ellipseCTF.getDefocusV()
27  + " --azimuthal_angle " + angle
28  + " --psd " + PSDFilename
29  + " --ctfmodelSize " + modelSize
30  + " --min_freq " + ellipseCTF.getLowFreq()
31  + " --max_freq " + ellipseCTF.getHighFreq()
32  + " --Q0 " + ellipseCTF.getQ0()
33  + " --defocus_range 5000"
34 
35  ,//+ " ; " + getSortCmd(sortFn),
36  row,
37  commandsListener);
38 
39  addCommand(getSortCmd(sortFn));
40  }
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xmipp.viewer.ctf.EstimateFromCTFTask.getSortCmd
static String getSortCmd(String filename)
Definition: EstimateFromCTFTask.java:42
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xmipp.viewer.ctf.CommandTask.commandsListener
iTaskCompletionListener commandsListener
Definition: CommandTask.java:23
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xmipp.viewer.ctf.CommandTask.addCommand
void addCommand(String command)
Definition: CommandTask.java:59
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static String xmipp.viewer.ctf.EstimateFromCTFTask.getSortCmd (String filename)
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Definition at line 42 of file EstimateFromCTFTask.java.

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42  {
43  return String.format("xmipp_ctf_sort_psds -i %s -o %s", filename, filename);
44  }
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xmipp.viewer.ctf.SortPSDSTask Member List
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This is the complete list of members for xmipp.viewer.ctf.SortPSDSTask, including all inherited members.

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addCommand(String command)xmipp.viewer.ctf.CommandTaskinline
commandsxmipp.viewer.ctf.CommandTaskprotected
commandsListenerxmipp.viewer.ctf.CommandTaskprotected
CommandTask(String command, int row, iTaskCompletionListener commandsListener)xmipp.viewer.ctf.CommandTaskinline
CommandTask(String command, iTaskCompletionListener commandsListener)xmipp.viewer.ctf.CommandTaskinline
CommandTask(String command)xmipp.viewer.ctf.CommandTaskinline
getCommand(String filename)xmipp.viewer.ctf.SortPSDSTaskinlinestatic
rowxmipp.viewer.ctf.CommandTaskprotected
run()xmipp.viewer.ctf.CommandTaskinline
SortPSDSTask(String filename)xmipp.viewer.ctf.SortPSDSTaskinline
SortPSDSTask(String filename, iTaskCompletionListener commandsListener)xmipp.viewer.ctf.SortPSDSTaskinline
start()xmipp.viewer.ctf.CommandTaskinline
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xmipp.viewer.ctf.SortPSDSTask Class Reference
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-Public Member Functions

 SortPSDSTask (String filename)
 
 SortPSDSTask (String filename, iTaskCompletionListener commandsListener)
 
- Public Member Functions inherited from xmipp.viewer.ctf.CommandTask
 CommandTask (String command, int row, iTaskCompletionListener commandsListener)
 
 CommandTask (String command, iTaskCompletionListener commandsListener)
 
 CommandTask (String command)
 
void start ()
 
void run ()
 
void addCommand (String command)
 
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-Static Public Member Functions

static String getCommand (String filename)
 
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-Additional Inherited Members

- Protected Attributes inherited from xmipp.viewer.ctf.CommandTask
ArrayList< String > commands
 
int row = -1
 
iTaskCompletionListener commandsListener
 
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Detailed Description

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Juanjo Vega
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Definition at line 11 of file SortPSDSTask.java.

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Constructor & Destructor Documentation

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◆ SortPSDSTask() [1/2]

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xmipp.viewer.ctf.SortPSDSTask.SortPSDSTask (String filename)
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Definition at line 13 of file SortPSDSTask.java.

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13  {
14  super(getCommand(filename));
15  }
xmipp.viewer.ctf.SortPSDSTask.getCommand
static String getCommand(String filename)
Definition: SortPSDSTask.java:21
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Definition at line 17 of file SortPSDSTask.java.

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17  {
18  super(getCommand(filename), commandsListener);
19  }
xmipp.viewer.ctf.CommandTask.commandsListener
iTaskCompletionListener commandsListener
Definition: CommandTask.java:23
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xmipp.viewer.ctf.SortPSDSTask.getCommand
static String getCommand(String filename)
Definition: SortPSDSTask.java:21
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Member Function Documentation

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◆ getCommand()

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static String xmipp.viewer.ctf.SortPSDSTask.getCommand (String filename)
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Definition at line 21 of file SortPSDSTask.java.

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21  {
22  return String.format("xmipp_ctf_sort_psds -i %s -o %s", filename, filename);
23  }
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add(CommandTask task)xmipp.viewer.ctf.TasksEngineinline
done(CommandTask task)xmipp.viewer.ctf.TasksEngineinline
TasksEngine(iCTFGUI gui)xmipp.viewer.ctf.TasksEngineinline
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-Public Member Functions

 TasksEngine (iCTFGUI gui)
 
synchronized void add (CommandTask task)
 
synchronized void done (CommandTask task)
 
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Detailed Description

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Definition at line 13 of file TasksEngine.java.

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Constructor & Destructor Documentation

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◆ TasksEngine()

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Definition at line 18 of file TasksEngine.java.

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18  {
19  this.gui = gui;
20  }
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Definition at line 22 of file TasksEngine.java.

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22  {
23 
24  //System.out.println("running task " + Arrays.toString(task.commands.toArray()));
25 
26  gui.setRowBusy(task.row);
27  tasks++;
28  task.start();
29  }
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void setRowBusy(int row)
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Definition at line 35 of file TasksEngine.java.

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35  {
36  if (allDone()) { // In the end, sortPSDs is executed. After that it's done.
37  gui.done();
38  } else {
39  tasks--;
40  gui.setRowIdle(task.row);
41 
42  // It's done, so sortPSDS is executed in background, and after that,
43  // main GUI is updated.
44 // if (allDone()) {
45 // SortPSDSTask sortPSDS = new SortPSDSTask(gui.getFilename(), this);
46 // sortPSDS.start();
47 // }
48  }
49  }
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void setRowIdle(int row)
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ClassInfo(String name, Color c)xmipp.viewer.models.ClassInfoinline
ClassInfo(String name, Color c, int numberOfImages)xmipp.viewer.models.ClassInfoinline
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 ClassInfo (String name, Color c)
 
 ClassInfo (String name, Color c, int numberOfImages)
 
String getComment ()
 
void setComment (String value)
 
Color getColor ()
 
void setColor (Color value)
 
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String comment
 
ColorIcon icon
 
int index
 
int numberOfClasses
 
long numberOfImages
 
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Structure to store class info

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Definition at line 33 of file ClassInfo.java.

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Definition at line 41 of file ClassInfo.java.

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41  {
42  comment = name;
43  icon = new ColorIcon(c, 16, 16, 3, true, true);
44  }
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Definition at line 47 of file ClassInfo.java.

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47  {
48  comment = name;
49  icon = new ColorIcon(c, 16, 16, 3, true, true);
50  this.numberOfImages = numberOfImages;
51  }
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Definition at line 61 of file ClassInfo.java.

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61  {
62  return icon.getColor();
63  }
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Definition at line 53 of file ClassInfo.java.

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54  return comment;
55  }
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Definition at line 69 of file ClassInfo.java.

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69  {
70  return icon;
71  }
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Definition at line 65 of file ClassInfo.java.

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66  icon.setColor(value);
67  }
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Definition at line 57 of file ClassInfo.java.

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57  {
58  comment = value;
59  }
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Definition at line 34 of file ClassInfo.java.

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Definition at line 35 of file ClassInfo.java.

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Definition at line 36 of file ClassInfo.java.

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Definition at line 37 of file ClassInfo.java.

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Definition at line 38 of file ClassInfo.java.

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allowEditxmipp.viewer.models.ColumnInfo
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ColumnInfo(int label, String name, String comment, int type, boolean allowRender, boolean visible, boolean render, boolean allowEdit)xmipp.viewer.models.ColumnInfoinline
ColumnInfo(int label, String name, String comment, int type, boolean allowRender, boolean allowEdit)xmipp.viewer.models.ColumnInfoinline
ColumnInfo(int label)xmipp.viewer.models.ColumnInfoinline
ColumnInfo(int label, boolean visible)xmipp.viewer.models.ColumnInfoinline
ColumnInfo(int label, boolean visible, boolean render)xmipp.viewer.models.ColumnInfoinline
commentxmipp.viewer.models.ColumnInfo
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getLabelTypeString()xmipp.viewer.models.ColumnInfoinline
isEnable()xmipp.viewer.models.ColumnInfoinline
labelxmipp.viewer.models.ColumnInfo
labelNamexmipp.viewer.models.ColumnInfo
renderxmipp.viewer.models.ColumnInfo
toString()xmipp.viewer.models.ColumnInfoinline
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updateInfo(ColumnInfo ci)xmipp.viewer.models.ColumnInfoinline
visiblexmipp.viewer.models.ColumnInfo
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class  ColumnExtraInfo
 
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 ColumnInfo (int label, String name, String comment, int type, boolean allowRender, boolean visible, boolean render, boolean allowEdit)
 
 ColumnInfo (int label, String name, String comment, int type, boolean allowRender, boolean allowEdit)
 
 ColumnInfo (int label)
 
 ColumnInfo (int label, boolean visible)
 
 ColumnInfo (int label, boolean visible, boolean render)
 
boolean updateInfo (ColumnInfo ci)
 
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ColumnInfo clone ()
 
boolean equals (Object o)
 
boolean isEnable ()
 
String toString ()
 
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int label
 
String labelName
 
boolean visible
 
boolean render
 
boolean allowRender = false
 
boolean allowEdit = false
 
String comment
 
int type
 
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This class will store info about how to display label on gallery

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Definition at line 32 of file ColumnInfo.java.

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xmipp.viewer.models.ColumnInfo.ColumnInfo (int label,
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Definition at line 46 of file ColumnInfo.java.

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46  {
47  this.label = label;
48  this.labelName = name;
49  this.visible = visible;
50  this.render = render;
51  this.allowRender = allowRender;
52  this.comment = comment;
53  this.type = type;
54  this.allowEdit = allowEdit;
55  }
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Definition at line 58 of file ColumnInfo.java.

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58  {
59  this(label, name, comment, type, allowRender, true, allowRender, allowEdit);
60  }
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Definition at line 62 of file ColumnInfo.java.

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62  {
63  this(label, MetaData.getLabelName(label), MetaData.getLabelComment(label), MetaData.getLabelType(label), MetaData.isImage(label), true, false, true);
64  }
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Definition at line 67 of file ColumnInfo.java.

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67  {
68  this(label, MetaData.getLabelName(label), MetaData.getLabelComment(label), MetaData.getLabelType(label), MetaData.isImage(label), visible, false, true);
69  }
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Definition at line 71 of file ColumnInfo.java.

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71  {
72  this(label, MetaData.getLabelName(label), MetaData.getLabelComment(label), MetaData.getLabelType(label), MetaData.isImage(label), visible, render, true);
73  }
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Definition at line 99 of file ColumnInfo.java.

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99  {
100  return new ColumnInfo(label, labelName, comment, type, allowRender, visible, render, allowEdit);
101  }
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ColumnInfo(int label, String name, String comment, int type, boolean allowRender, boolean visible, boolean render, boolean allowEdit)
Definition: ColumnInfo.java:46
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Definition at line 104 of file ColumnInfo.java.

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104  {
105 
106  if (o == null) return false;
107  if (!getClass().equals(o.getClass())) return false;
108 
109  ColumnInfo col = (ColumnInfo)o;
110  return label == col.label &&
111  visible == col.visible &&
112  render == col.render;
113  }
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ColumnInfo(int label, String name, String comment, int type, boolean allowRender, boolean visible, boolean render, boolean allowEdit)
Definition: ColumnInfo.java:46
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Definition at line 88 of file ColumnInfo.java.

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88  {
89  try {
90 
91  return MetaData.getLabelTypeString(type);
92  }catch(Exception e){
93  e.printStackTrace();
94  }
95  return null;
96  }
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Definition at line 115 of file ColumnInfo.java.

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115  {
116  return label == MDLabel.MDL_ENABLED || labelName.equals("enabled");
117  }
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134  {
135  return labelName;
136  }
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Definition at line 78 of file ColumnInfo.java.

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78  {
79  boolean result = labelName != ci.labelName || visible != ci.visible
80  || render != ci.render || allowEdit != ci.allowEdit;
81  visible = ci.visible;
82  render = ci.render;
83  allowEdit = ci.allowEdit;
84  labelName = ci.labelName;
85  return result;
86  }
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Definition at line 40 of file ColumnInfo.java.

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Definition at line 37 of file ColumnInfo.java.

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ColumnExtraInfo(String c)xmipp.viewer.models.ColumnInfo.ColumnExtraInfoinline
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String color
 
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Definition at line 119 of file ColumnInfo.java.

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125  {
126  color = c;
127  linestyle = "solid";
128  marker = "none";
129  plot = false;
130  }
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Definition at line 123 of file ColumnInfo.java.

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addColumn(TableColumn tc)xmipp.viewer.models.GalleryColumnModelinline
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-Public Member Functions

 GalleryColumnModel (int w)
 
void addColumn (TableColumn tc)
 
void setWidth (int width)
 
void adjustColumnsWidth (JTable table)
 
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int width
 
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Detailed Description

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Definition at line 32 of file GalleryColumnModel.java.

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Constructor & Destructor Documentation

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◆ GalleryColumnModel()

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xmipp.viewer.models.GalleryColumnModel.GalleryColumnModel (int w)
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Definition at line 37 of file GalleryColumnModel.java.

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37  {
38  super();
39 
40  width = w;
41  }
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Member Function Documentation

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◆ addColumn()

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void xmipp.viewer.models.GalleryColumnModel.addColumn (TableColumn tc)
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When adding a new column set the width

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Definition at line 45 of file GalleryColumnModel.java.

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45  {
46  tc.setPreferredWidth(width);
47  super.addColumn(tc);
48  }
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◆ adjustColumnsWidth()

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void xmipp.viewer.models.GalleryColumnModel.adjustColumnsWidth (JTable table)
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Adjust the width of all the columns

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Definition at line 67 of file GalleryColumnModel.java.

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67  {
68  for (int i = 0; i < getColumnCount(); i++) {
69  getColumn(i).setPreferredWidth(width);
70  }
71  }
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void xmipp.viewer.models.GalleryColumnModel.setWidth (int width)
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Set the width

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Definition at line 61 of file GalleryColumnModel.java.

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61  {
62  this.width = width;
63  //adjustColumnsWidth();
64  }
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◆ width

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int xmipp.viewer.models.GalleryColumnModel.width
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Definition at line 35 of file GalleryColumnModel.java.

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xmipp.viewer.models.GalleryData Member List
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This is the complete list of members for xmipp.viewer.models.GalleryData, including all inherited members.

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addClass(ClassInfo ci)xmipp.viewer.models.GalleryDatainline
addObject()xmipp.viewer.models.GalleryDatainline
allowGallery()xmipp.viewer.models.GalleryDatainline
allowsVolumeMode()xmipp.viewer.models.GalleryDatainline
changeMode()xmipp.viewer.models.GalleryDatainline
checkifIsClassificationMd()xmipp.viewer.models.GalleryDatainline
ciFirstRenderxmipp.viewer.models.GalleryDataprotected
classesxmipp.viewer.models.GalleryDataprotected
classesArrayxmipp.viewer.models.GalleryDataprotected
containsBlock(String block)xmipp.viewer.models.GalleryDatainline
containsGeometryInfo()xmipp.viewer.models.GalleryDatainline
containsGeometryInfo(String type)xmipp.viewer.models.GalleryDatainline
createModel(boolean[] selection)xmipp.viewer.models.GalleryDatainline
createSortFile(String psdFile, int row)xmipp.viewer.models.GalleryDatainline
displaycisxmipp.viewer.models.GalleryDataprotected
displayLabelsxmipp.viewer.models.GalleryDataprotected
filenamexmipp.viewer.models.GalleryDataprotected
fillConstant(int label, String value)xmipp.viewer.models.GalleryDatainline
fillLinear(int label, Double start, Double step)xmipp.viewer.models.GalleryDatainline
fillRandom(int label, String mode, double op1, double op2)xmipp.viewer.models.GalleryDatainline
GalleryData(GalleryJFrame window, String fn, Params parameters)xmipp.viewer.models.GalleryDatainline
GalleryData(GalleryJFrame window, Params parameters, MetaData md)xmipp.viewer.models.GalleryDatainline
getBlock(int index)xmipp.viewer.models.GalleryDatainline
getBlocks()xmipp.viewer.models.GalleryDatainline
getChimeraProjectionCmd(int row)xmipp.viewer.models.GalleryDatainline
getClasses()xmipp.viewer.models.GalleryDatainline
getClassesImages(boolean[] selection)xmipp.viewer.models.GalleryDatainline
getClassesMd()xmipp.viewer.models.GalleryDatainline
getClassImages(int index)xmipp.viewer.models.GalleryDatainline
getClassInfo(int classNumber)xmipp.viewer.models.GalleryDatainline
getColumnInfo(String labelName)xmipp.viewer.models.GalleryDatainline
getColumnInfo(int col)xmipp.viewer.models.GalleryDatainline
getColumns()xmipp.viewer.models.GalleryDatainline
getDefaultZoom(int xdim)xmipp.viewer.models.GalleryDatainlinestatic
getDisplayLabel(long id)xmipp.viewer.models.GalleryDatainline
getEnabledClassesImages()xmipp.viewer.models.GalleryDatainline
getEnabledCount()xmipp.viewer.models.GalleryDatainline
getFileExtension()xmipp.viewer.models.GalleryDatainline
getFileInfo()xmipp.viewer.models.GalleryDatainline
getFileName()xmipp.viewer.models.GalleryDatainline
getGeometry(long id, ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
getGeometry(long id, String type, ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
getId(int i)xmipp.viewer.models.GalleryDatainline
getIds()xmipp.viewer.models.GalleryDatainline
getImages(MetaData md)xmipp.viewer.models.GalleryDatainline
getImagesMd()xmipp.viewer.models.GalleryDatainline
getImagesMd(boolean[] selection, boolean selected)xmipp.viewer.models.GalleryDatainline
getItemClassInfo(int index)xmipp.viewer.models.GalleryDatainline
getLabel(long objId, int label)xmipp.viewer.models.GalleryDatainline
getLabelFromCol(int col)xmipp.viewer.models.GalleryDatainline
getLabels()xmipp.viewer.models.GalleryDatainline
getLabelsInfo()xmipp.viewer.models.GalleryDatainline
getMd(List< Long > ids)xmipp.viewer.models.GalleryDatainline
getMd()xmipp.viewer.models.GalleryDatainline
getMdFilename()xmipp.viewer.models.GalleryDatainline
getMdSaveFileName()xmipp.viewer.models.GalleryDatainline
getMetaData(String block)xmipp.viewer.models.GalleryDatainline
getMetaDataRow()xmipp.viewer.models.GalleryDatainline
getMode()xmipp.viewer.models.GalleryDatainline
getModelColumns()xmipp.viewer.models.GalleryDatainline
getModelRows()xmipp.viewer.models.GalleryDatainline
getNormalized()xmipp.viewer.models.GalleryDatainline
getNumberOfBlocks()xmipp.viewer.models.GalleryDatainline
getOrderLabels()xmipp.viewer.models.GalleryDatainline
getPreffix()xmipp.viewer.models.GalleryDatainline
getRenderColumn()xmipp.viewer.models.GalleryDatainline
getRenderLabel()xmipp.viewer.models.GalleryDatainline
getRenderLabels()xmipp.viewer.models.GalleryDatainline
getResliceView()xmipp.viewer.models.GalleryDatainline
getSampleImage(ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
getSelectedBlock()xmipp.viewer.models.GalleryDatainline
getSelectionMd(boolean[] selection)xmipp.viewer.models.GalleryDatainline
getSelVolId()xmipp.viewer.models.GalleryDatainline
getSelVolumeFile()xmipp.viewer.models.GalleryDatainline
getSortBy()xmipp.viewer.models.GalleryDatainline
getTmpFile(String suffix)xmipp.viewer.models.GalleryDatainline
getValueFromCol(int index, int col)xmipp.viewer.models.GalleryDatainline
getValueFromCol(int index, ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
getValueFromLabel(int index, int label)xmipp.viewer.models.GalleryDatainline
getValueString(int label, long id)xmipp.viewer.models.GalleryDatainline
getVisibleColumnIndex(int col)xmipp.viewer.models.GalleryDatainline
getVisibleLabels()xmipp.viewer.models.GalleryDatainline
getVolumeAt(int index)xmipp.viewer.models.GalleryDatainline
getZoom()xmipp.viewer.models.GalleryDatainline
hasClasses()xmipp.viewer.models.GalleryDatainline
hasClassesChanges()xmipp.viewer.models.GalleryDatainline
hasDisabled()xmipp.viewer.models.GalleryDatainline
hasMdChangesxmipp.viewer.models.GalleryDataprotected
hasMdChanges()xmipp.viewer.models.GalleryDatainline
hasMicrographParticles()xmipp.viewer.models.GalleryDatainline
hasRecalculateCTF()xmipp.viewer.models.GalleryDatainline
hasRenderLabel()xmipp.viewer.models.GalleryDatainline
idsxmipp.viewer.models.GalleryDataprotected
initColumnInfo(int label)xmipp.viewer.models.GalleryDatainline
invertyxmipp.viewer.models.GalleryDataprotected
isAutoAdjust()xmipp.viewer.models.GalleryDatainline
isChimeraClient()xmipp.viewer.models.GalleryDatainline
isClassificationxmipp.viewer.models.GalleryDataprotected
isClassificationMd()xmipp.viewer.models.GalleryDatainline
isColumnFormat()xmipp.viewer.models.GalleryDatainline
isCTFMd()xmipp.viewer.models.GalleryDatainline
isDisplayLabel()xmipp.viewer.models.GalleryDatainline
isEnabled(int index)xmipp.viewer.models.GalleryDatainline
isFile(ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
isFile(int col)xmipp.viewer.models.GalleryDatainline
isGalleryMode()xmipp.viewer.models.GalleryDatainline
isImageFile(int col)xmipp.viewer.models.GalleryDatainline
isImageFile(ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
isInvertY()xmipp.viewer.models.GalleryDatainline
isMicrographsMode()xmipp.viewer.models.GalleryDatainline
isObjectCmd(String cmd)xmipp.viewer.models.GalleryDatainline
isRecalculateCTF(int row)xmipp.viewer.models.GalleryDatainline
isRenderLabel(ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
isScipionInstance()xmipp.viewer.models.GalleryDatainline
isTableMode()xmipp.viewer.models.GalleryDatainline
isVisibleLabel(ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
isVolumeMdxmipp.viewer.models.GalleryDataprotected
isVolumeMd()xmipp.viewer.models.GalleryDatainline
isVolumeMode()xmipp.viewer.models.GalleryDatainline
isWrap()xmipp.viewer.models.GalleryDatainline
labelsxmipp.viewer.models.GalleryDataprotected
loadClassesInfo()xmipp.viewer.models.GalleryDatainline
loadLabels()xmipp.viewer.models.GalleryDatainline
loadMd()xmipp.viewer.models.GalleryDatainline
MAX_SIZExmipp.viewer.models.GalleryDatastatic
mdxmipp.viewer.models.GalleryDataprotected
mdBlocksxmipp.viewer.models.GalleryDataprotected
MIN_SIZExmipp.viewer.models.GalleryDatastatic
modexmipp.viewer.models.GalleryDataprotected
normalizexmipp.viewer.models.GalleryDataprotected
orderLabelsxmipp.viewer.models.GalleryDataprotected
orderLabels()xmipp.viewer.models.GalleryDatainline
parametersxmipp.viewer.models.GalleryData
readMd()xmipp.viewer.models.GalleryDatainline
readMdParameters()xmipp.viewer.models.GalleryDatainlineprotected
recalculateCTF(int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)xmipp.viewer.models.GalleryDatainline
refLabelxmipp.viewer.models.GalleryDataprotected
removeClass(int classNumber)xmipp.viewer.models.GalleryDatainline
removeCTF(int row)xmipp.viewer.models.GalleryDatainline
removeDisabled()xmipp.viewer.models.GalleryDatainline
removeLabel(int label)xmipp.viewer.models.GalleryDatainline
removeSelection(boolean[] selection)xmipp.viewer.models.GalleryDatainline
renderImagesxmipp.viewer.models.GalleryDataprotected
renderImages()xmipp.viewer.models.GalleryDatainline
renderLabelxmipp.viewer.models.GalleryDataprotected
renderLabelsxmipp.viewer.models.GalleryDataprotected
resliceViewxmipp.viewer.models.GalleryDataprotected
rowsxmipp.viewer.models.GalleryDataprotected
runObjectCommand(int index, String objectCommand)xmipp.viewer.models.GalleryDatainline
saveAll(String path, boolean overwrite)xmipp.viewer.models.GalleryDatainline
saveClassSelection(boolean[]selection, String path)xmipp.viewer.models.GalleryDatainline
saveMd(String path, boolean saveall, boolean isoverwrite)xmipp.viewer.models.GalleryDatainline
saveSelection(boolean[] selection)xmipp.viewer.models.GalleryDatainline
saveSelection(boolean[] selection, String path, boolean overwrite)xmipp.viewer.models.GalleryDatainline
selectBlock(String block)xmipp.viewer.models.GalleryDatainline
selectedBlockxmipp.viewer.models.GalleryDataprotected
selectedVolFnxmipp.viewer.models.GalleryDataprotected
selectVolumeAt(int selectedIndex)xmipp.viewer.models.GalleryDatainline
setDisplayLabel(String key, boolean selected)xmipp.viewer.models.GalleryDatainline
setEnabled(int index, boolean value)xmipp.viewer.models.GalleryDatainline
setFileName(String file)xmipp.viewer.models.GalleryDatainline
setItemClass(int index, ClassInfo cli)xmipp.viewer.models.GalleryDatainline
setMdChanges(boolean value)xmipp.viewer.models.GalleryDatainline
setModelDim(Integer rows, Integer cols)xmipp.viewer.models.GalleryDatainline
setOrderLabels(String[] orderLabels)xmipp.viewer.models.GalleryDatainline
setRenderColumn(String key)xmipp.viewer.models.GalleryDatainline
setRenderLabel(String renderLabel)xmipp.viewer.models.GalleryDatainline
setRenderLabels(String[] renderLabels)xmipp.viewer.models.GalleryDatainline
setResliceView(int view)xmipp.viewer.models.GalleryDatainline
setRow(MDRow mdRow, long objId)xmipp.viewer.models.GalleryDatainline
setValueString(int label, String newValue, long l)xmipp.viewer.models.GalleryDatainline
setValueToCol(int index, ColumnInfo ci, String value)xmipp.viewer.models.GalleryDatainline
setVisibleLabels(String[] visibleLabels)xmipp.viewer.models.GalleryDatainline
setWindow(GalleryJFrame frame)xmipp.viewer.models.GalleryDatainline
setZoom(int zoom)xmipp.viewer.models.GalleryDatainline
showCTF(boolean profile, int row, boolean[] selection, TasksEngine ctfTasks)xmipp.viewer.models.GalleryDatainline
showLabelxmipp.viewer.models.GalleryDataprotected
size()xmipp.viewer.models.GalleryDatainline
sortbyxmipp.viewer.models.GalleryDataprotected
sortMd(ColumnInfo sortci, boolean asc)xmipp.viewer.models.GalleryDatainline
updateClassesInfo()xmipp.viewer.models.GalleryDatainline
useGeoxmipp.viewer.models.GalleryDataprotected
useGeo()xmipp.viewer.models.GalleryDatainline
visibleLabelsxmipp.viewer.models.GalleryDataprotected
windowxmipp.viewer.models.GalleryDataprotected
wrapxmipp.viewer.models.GalleryDataprotected
write(String path)xmipp.viewer.models.GalleryDatainline
zoomxmipp.viewer.models.GalleryDataprotected
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xmipp.viewer.models.GalleryData Class Reference
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-Inheritance diagram for xmipp.viewer.models.GalleryData:
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-Collaboration diagram for xmipp.viewer.models.GalleryData:
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-Classes

enum  Mode
 
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-Public Member Functions

boolean isObjectCmd (String cmd)
 
boolean isVolumeMd ()
 
Integer getModelRows ()
 
Integer getModelColumns ()
 
void runObjectCommand (int index, String objectCommand)
 
String getTmpFile (String suffix)
 
void selectVolumeAt (int selectedIndex)
 
boolean isAutoAdjust ()
 
void setModelDim (Integer rows, Integer cols)
 
boolean isScipionInstance ()
 
boolean isInvertY ()
 
String getChimeraProjectionCmd (int row)
 
 GalleryData (GalleryJFrame window, String fn, Params parameters)
 
 GalleryData (GalleryJFrame window, Params parameters, MetaData md)
 
List< ColumnInfo > getColumns ()
 
void setRenderColumn (String key)
 
ColumnInfo getRenderColumn ()
 
String getMdFilename ()
 
String getMdSaveFileName ()
 
void setFileName (String file)
 
void setDisplayLabel (String key, boolean selected)
 
void loadMd () throws Exception
 
ColumnInfo getColumnInfo (String labelName)
 
boolean isDisplayLabel ()
 
String getDisplayLabel (long id)
 
void loadLabels ()
 
String getSampleImage (ColumnInfo ci)
 
ColumnInfo initColumnInfo (int label)
 
void sortMd (ColumnInfo sortci, boolean asc)
 
void readMd ()
 
void selectBlock (String block)
 
ImageGalleryTableModel createModel (boolean[] selection)
 
int getNumberOfBlocks ()
 
Mode getMode ()
 
boolean hasRenderLabel ()
 
int getRenderLabel ()
 
boolean allowGallery ()
 
boolean isGalleryMode ()
 
boolean isVolumeMode ()
 
boolean isTableMode ()
 
boolean isColumnFormat ()
 
boolean isMicrographsMode ()
 
void changeMode ()
 
String getVolumeAt (int index)
 
boolean containsGeometryInfo ()
 
boolean containsGeometryInfo (String type)
 
boolean isEnabled (int index)
 
void setEnabled (int index, boolean value)
 
void setRow (MDRow mdRow, long objId)
 
boolean isFile (ColumnInfo ci)
 
boolean isFile (int col)
 
boolean isImageFile (int col)
 
boolean isImageFile (ColumnInfo ci)
 
boolean isClassificationMd ()
 
boolean checkifIsClassificationMd ()
 
ClassInfo getItemClassInfo (int index)
 
void setItemClass (int index, ClassInfo cli)
 
ClassInfo getClassInfo (int classNumber)
 
void updateClassesInfo ()
 
void loadClassesInfo ()
 
MetaData getSelectionMd (boolean[] selection)
 
MetaData [] getClassesMd ()
 
MetaData getClassImages (int index)
 
MetaData getClassesImages (boolean[] selection)
 
MetaData getEnabledClassesImages ()
 
boolean containsBlock (String block)
 
int getVisibleColumnIndex (int col)
 
int getLabelFromCol (int col)
 
ColumnInfo getColumnInfo (int col)
 
String getValueFromCol (int index, int col)
 
String getValueFromCol (int index, ColumnInfo ci)
 
String getValueFromLabel (int index, int label)
 
void setValueToCol (int index, ColumnInfo ci, String value)
 
void removeSelection (boolean[] selection) throws Exception
 
void addClass (ClassInfo ci)
 
void removeClass (int classNumber)
 
boolean hasMdChanges ()
 
void setMdChanges (boolean value)
 
boolean hasClassesChanges ()
 
boolean hasMicrographParticles ()
 
String getFileName ()
 
String getBlock (int index)
 
MDRow [] getImages (MetaData md)
 
String getFileInfo ()
 
void saveClassSelection (boolean[]selection, String path)
 
boolean isCTFMd ()
 
void saveSelection (boolean[] selection) throws Exception
 
void saveSelection (boolean[] selection, String path, boolean overwrite) throws Exception
 
int size ()
 
Integer getZoom ()
 
boolean useGeo ()
 
void fillConstant (int label, String value)
 
void fillLinear (int label, Double start, Double step)
 
void fillRandom (int label, String mode, double op1, double op2)
 
void removeDisabled ()
 
void removeLabel (int label)
 
long [] getIds ()
 
int [] getLabels ()
 
String getValueString (int label, long id)
 
boolean setValueString (int label, String newValue, long l)
 
Object getSelectedBlock ()
 
String getSelVolumeFile ()
 
void setResliceView (int view)
 
boolean isWrap ()
 
boolean renderImages ()
 
int getResliceView ()
 
boolean addObject ()
 
String [] getBlocks ()
 
long getId (int i)
 
String createSortFile (String psdFile, int row)
 
ArrayList< ClassInfo > getClasses ()
 
List< ColumnInfo > getLabelsInfo ()
 
MetaData getMetaDataRow ()
 
String getLabel (long objId, int label)
 
String getFileExtension ()
 
void saveAll (String path, boolean overwrite) throws Exception
 
void saveMd (String path, boolean saveall, boolean isoverwrite) throws Exception
 
MetaData getMetaData (String block)
 
boolean hasClasses ()
 
boolean getNormalized ()
 
MetaData getMd (List< Long > ids)
 
void setWindow (GalleryJFrame frame)
 
void write (String path)
 
MetaData getMd ()
 
boolean isRenderLabel (ColumnInfo ci)
 
boolean isVisibleLabel (ColumnInfo ci)
 
void orderLabels ()
 
void removeCTF (int row)
 
boolean isRecalculateCTF (int row)
 
boolean hasRecalculateCTF ()
 
void recalculateCTF (int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)
 
void showCTF (boolean profile, int row, boolean[] selection, TasksEngine ctfTasks)
 
Geometry getGeometry (long id, ColumnInfo ci)
 
Geometry getGeometry (long id, String type, ColumnInfo ci)
 
void setRenderLabels (String[] renderLabels)
 
void setVisibleLabels (String[] visibleLabels)
 
void setOrderLabels (String[] orderLabels)
 
void setRenderLabel (String renderLabel)
 
String [] getRenderLabels ()
 
String [] getVisibleLabels ()
 
String [] getOrderLabels ()
 
Long getSelVolId ()
 
MetaData getImagesMd ()
 
MetaData getImagesMd (boolean[] selection, boolean selected)
 
String [] getSortBy ()
 
boolean isChimeraClient ()
 
boolean hasDisabled ()
 
int getEnabledCount ()
 
String getPreffix ()
 
void setZoom (int zoom)
 
boolean allowsVolumeMode ()
 
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-Static Public Member Functions

static int getDefaultZoom (int xdim)
 
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-Public Attributes

final Params parameters
 
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-Static Public Attributes

static int MIN_SIZE = 16
 
static int MAX_SIZE = 256
 
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-Protected Member Functions

void readMdParameters ()
 
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-Protected Attributes

HashMap< String, ColumnInfo > displaycis
 
MetaData md
 
long [] ids
 
String [] mdBlocks = null
 
String selectedBlock
 
String selectedVolFn = ""
 
List< ColumnInfo > labels = null
 
ColumnInfo ciFirstRender = null
 
Integer zoom
 
String filename
 
int resliceView
 
Mode mode
 
boolean showLabel = false
 
boolean renderImages
 
boolean normalize = false
 
boolean useGeo
 
boolean wrap
 
boolean isClassification = false
 
int refLabel
 
ArrayList< ClassInfo > classesArray
 
ClassInfo [] classes
 
boolean hasMdChanges
 
GalleryJFrame window
 
String [] displayLabels
 
String [] sortby
 
boolean isVolumeMd
 
Integer rows
 
String [] renderLabels
 
String renderLabel = "first"
 
String [] visibleLabels
 
String [] orderLabels
 
boolean inverty
 
-

Detailed Description

-

This class will serve to store important data about the gallery

- -

Definition at line 69 of file GalleryData.java.

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Constructor & Destructor Documentation

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◆ GalleryData() [1/2]

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xmipp.viewer.models.GalleryData.GalleryData (GalleryJFrame window,
String fn,
Params parameters 
)
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Definition at line 220 of file GalleryData.java.

-
221  {
222  this(window, parameters, new MetaData(fn));
223  }
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◆ GalleryData() [2/2]

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xmipp.viewer.models.GalleryData.GalleryData (GalleryJFrame window,
Params parameters,
MetaData md 
)
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The constructor receive the filename of a metadata The metadata can also be passed, if null, it will be readed from filename

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Parameters
- - -
jFrameGallery
-
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Definition at line 231 of file GalleryData.java.

-
231  {
232  this.window = window;
233  this.parameters = parameters;
234 
235  try {
236  selectedBlock = "";
237  this.md = md;
238  setFileName(md.getPath());
239  zoom = parameters.zoom;
240  resliceView = parameters.resliceView;
241  if(parameters.rows > 0)
242  rows = parameters.rows;
243  if(parameters.columns > 0)
244  columns = parameters.columns;
245  loadMd();
246 
247  } catch (Exception e) {
248  e.printStackTrace();
249  md = null;
250  }
251 
252  }// constructor GalleryData
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-

Member Function Documentation

- -

◆ addClass()

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void xmipp.viewer.models.GalleryData.addClass (ClassInfo ci)
- 		-inline
-
-

Add a new class

- -

Definition at line 1223 of file GalleryData.java.

-
1223  {
1224  classesArray.add(ci);
1225  hasClassesChanges = true;
1226  }
-
xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
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-
-
- -

◆ addObject()

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boolean xmipp.viewer.models.GalleryData.addObject ()
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Definition at line 1461 of file GalleryData.java.

-
1461  {
1462  AddObjectJDialog dlg = new AddObjectJDialog(window);
1463  if (dlg.showDialog()) {
1464  md.unionAll(dlg.md);
1465  return true;
1466  }
1467  return false;
1468  }
-
xmipp.jni.MetaData.unionAll
native void unionAll(MetaData mdIn)
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◆ allowGallery()

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boolean xmipp.viewer.models.GalleryData.allowGallery ()
- 		-inline
-
-

Return true if the gallery mode is allowed

- -

Definition at line 722 of file GalleryData.java.

-
722  {
723  return hasRenderLabel();
724  }
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-
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◆ allowsVolumeMode()

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boolean xmipp.viewer.models.GalleryData.allowsVolumeMode ()
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-
- -

Definition at line 1940 of file GalleryData.java.

-
1941  {
1942  boolean allowsVolumeMode = !selectedVolFn.isEmpty();
1943  return allowsVolumeMode;
1944  }
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-
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◆ changeMode()

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void xmipp.viewer.models.GalleryData.changeMode ()
- 		-inline
-
- -

Definition at line 753 of file GalleryData.java.

-
753  {
754  if (isGalleryMode()) {
755  mode = Mode.TABLE_MD;
756 
757  }
758  else if ( isVolumeMd)
759  mode = Mode.GALLERY_VOL;
760  else
761  mode = Mode.GALLERY_MD;
762  }
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◆ checkifIsClassificationMd()

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boolean xmipp.viewer.models.GalleryData.checkifIsClassificationMd ()
- 		-inline
-
-

Return true if current metadata comes from 2d classification

- -

Definition at line 861 of file GalleryData.java.

-
861  {
862  try {
863  boolean valid = selectedBlock.startsWith("classes")
864  && (md.containsLabel(MDLabel.MDL_REF) || md.containsLabel(MDLabel.MDL_REF3D))
865  && md.containsLabel(MDLabel.MDL_CLASS_COUNT);
866 
867  if (!valid) {
868  return false;
869  }
870 
871  refLabel = md.containsLabel(MDLabel.MDL_REF) ? MDLabel.MDL_REF : MDLabel.MDL_REF3D;
872 
873  for (long id : ids) {
874  int ref = md.getValueInt(refLabel, id);
875  long count = md.getValueLong(MDLabel.MDL_CLASS_COUNT, id);
876  String s = Filename.getClassBlockName(ref);
877  if (count > 0 && !containsBlock(s)) {
878  DEBUG.printFormat("2Dclass: for ref: %d, no block '%s'\n", ref, s);
879  return false;
880  }
881  }
882  } catch (Exception e) {
883  // TODO Auto-generated catch block
884  e.printStackTrace();
885  }
886  return true;
887  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
-
xmipp.jni.MetaData.getValueLong
native long getValueLong(int label, long objId)
- - -
xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
- -
xmipp.viewer.models.GalleryData.containsBlock
boolean containsBlock(String block)
Definition: GalleryData.java:1132
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◆ containsBlock()

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boolean xmipp.viewer.models.GalleryData.containsBlock (String block)
- 		-inline
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-

Check if a block is present, ignore case

- -

Definition at line 1132 of file GalleryData.java.

-
1132  {
1133  if (mdBlocks != null) {
1134  for (String b : mdBlocks) {
1135  if (b.equalsIgnoreCase(block)) {
1136  return true;
1137  }
1138  }
1139  }
1140  return false;
1141  }
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boolean xmipp.viewer.models.GalleryData.containsGeometryInfo ()
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- -

Definition at line 771 of file GalleryData.java.

-
772  {
773  return containsGeometryInfo("2D");
774  }
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boolean xmipp.viewer.models.GalleryData.containsGeometryInfo (String type)
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Definition at line 777 of file GalleryData.java.

-
778  {
779  try {
780  return md.containsGeometryInfo(type);
781  } catch (Exception e) {
782  e.printStackTrace();
783  return false;
784  }
785  }
-
xmipp.jni.MetaData.containsGeometryInfo
boolean containsGeometryInfo(String type)
Definition: MetaData.java:147
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- -

◆ createModel()

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ImageGalleryTableModel xmipp.viewer.models.GalleryData.createModel (boolean [] selection)
- 		-inline
-
-

defines how each row is rendered on ImageGalleryTableModel

-
Returns
- -

Definition at line 665 of file GalleryData.java.

-
665  {
666  try {
667  switch (mode) {
668  case GALLERY_VOL:
669  return new VolumeGalleryTableModel(this);
670  case GALLERY_MD:
671  if (md.size() > 0 && hasRenderLabel()) {
672 
673  return new MetadataGalleryTableModel(this, selection);
674  }
675  // else fall in the next case
676  case TABLE_MD:
677  mode = Mode.TABLE_MD; // this is necessary when coming from
678  // previous case
679  if (!md.isColumnFormat()) {
680  return new MetadataRowTableModel(this);
681  }
682 
683  return new MetadataTableModel(this, selection);
684 
685  }
686  } catch (Exception e) {
687  e.printStackTrace();
688  }
689  return null;
690  }
-
xmipp.jni.MetaData.size
native int size()
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xmipp.jni.MetaData.isColumnFormat
native boolean isColumnFormat()
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◆ createSortFile()

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String xmipp.viewer.models.GalleryData.createSortFile (String psdFile,
int row 
)
- 		-inline
-
- -

Definition at line 1478 of file GalleryData.java.

-
1478  {
1479 
1480  MetaData mdRow = new MetaData();
1481  MDRow row2 = new MDRow();
1482  md.getRow(row2, getId(row));
1483  mdRow.setRow(row2, mdRow.addObject());
1484  String sortFn = psdFile.replace(".psd", ".xmd");
1485  mdRow.write(sortFn);
1486  mdRow.destroy();
1487  return sortFn;
1488 
1489  }
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xmipp.jni.MetaData.getRow
native void getRow(MDRow mdRow, long objId)
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◆ fillConstant()

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void xmipp.viewer.models.GalleryData.fillConstant (int label,
String value 
)
- 		-inline
-
- -

Definition at line 1399 of file GalleryData.java.

-
1399  {
1400  md.fillConstant(label, value);
1401  }
xmipp.jni.MetaData.fillConstant
native void fillConstant(int label, String value)
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◆ fillLinear()

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void xmipp.viewer.models.GalleryData.fillLinear (int label,
Double start,
Double step 
)
- 		-inline
-
- -

Definition at line 1403 of file GalleryData.java.

-
1403  {
1404  md.fillLinear(label, start, step);
1405  }
-
xmipp.jni.MetaData.fillLinear
native void fillLinear(int label, double start, double step)
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◆ fillRandom()

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void xmipp.viewer.models.GalleryData.fillRandom (int label,
String mode,
double op1,
double op2 
)
- 		-inline
-
- -

Definition at line 1407 of file GalleryData.java.

-
1407  {
1408  md.fillRandom(label, mode, op1, op2);
1409  }
- -
xmipp.jni.MetaData.fillRandom
native void fillRandom(int label, String mode, double op1, double op2)
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◆ getBlock()

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String xmipp.viewer.models.GalleryData.getBlock (int index)
- 		-inline
-
- -

Definition at line 1263 of file GalleryData.java.

-
1263  {
1264  int size = getNumberOfBlocks();
1265  if (size > 0 && index >= 0 && index < size) {
1266  return mdBlocks[index];
1267  }
1268  return null;
1269  }
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-
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- -

◆ getBlocks()

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String [] xmipp.viewer.models.GalleryData.getBlocks ()
- 		-inline
-
- -

Definition at line 1470 of file GalleryData.java.

-
1470  {
1471  return mdBlocks;
1472  }
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-
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◆ getChimeraProjectionCmd()

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String xmipp.viewer.models.GalleryData.getChimeraProjectionCmd (int row)
- 		-inline
-
- -

Definition at line 202 of file GalleryData.java.

-
202  {
203  String rot = getValueFromLabel(row, MDLabel.MDL_ANGLE_ROT);
204  String tilt = getValueFromLabel(row, MDLabel.MDL_ANGLE_TILT);
205  String psi = getValueFromLabel(row, MDLabel.MDL_ANGLE_PSI);
206  String command = String.format("rotate %s %s %s", rot, tilt, psi);
207  return command;
208  }
xmipp.viewer.models.GalleryData.getValueFromLabel
String getValueFromLabel(int index, int label)
Definition: GalleryData.java:1190
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-
-
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◆ getClasses()

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-
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ArrayList<ClassInfo> xmipp.viewer.models.GalleryData.getClasses ()
- 		-inline
-
- -

Definition at line 1491 of file GalleryData.java.

-
1491  {
1492  return classesArray;
1493  }
xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
-
-
-
- -

◆ getClassesImages()

- -
-
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MetaData xmipp.viewer.models.GalleryData.getClassesImages (boolean [] selection)
- 		-inline
-
-

Get all the images assigned to all selected classes

- -

Definition at line 1098 of file GalleryData.java.

-
1098  {
1099  MetaData mdImages = new MetaData();
1100  MetaData md;
1101  for (int i = 0; i < selection.length; i++) {
1102  if (selection[i]) {
1103  md = getClassImages(i);
1104  if (md != null) {
1105  mdImages.unionAll(md);
1106  md.destroy();
1107  }
1108  }
1109  }
1110  return mdImages;
1111  }
xmipp.viewer.models.GalleryData.getClassImages
MetaData getClassImages(int index)
Definition: GalleryData.java:1081
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-
-
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◆ getClassesMd()

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-
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MetaData [] xmipp.viewer.models.GalleryData.getClassesMd ()
- 		-inline
-
-

Compute the metadatas

- -

Definition at line 1034 of file GalleryData.java.

-
1034  {
1035  try {
1036  if (!classesArray.isEmpty()) {
1037  updateClassesInfo();
1038  // Count the number of non-empty classes
1039  MetaData[] mds = new MetaData[classesArray.size() + 1];
1040  mds[0] = new MetaData();
1041  MetaData mdAux = mds[0];
1042  int i = 0;
1043  long id;
1044  // Md for classes block
1045  for (ClassInfo cli : classesArray) {
1046  id = mdAux.addObject();
1047  mdAux.setValueInt(MDLabel.MDL_REF, ++i, id);
1048  mdAux.setValueLong(MDLabel.MDL_CLASS_COUNT,
1049  cli.numberOfImages, id);
1050  mdAux.setValueString(MDLabel.MDL_KEYWORDS,
1051  cli.getComment(), id);
1052  mds[i] = new MetaData();
1053  }
1054  i = 0;
1055  // Fill the classX_images blocks
1056  for (i = 0; i < ids.length; ++i) {
1057  ClassInfo cli = getItemClassInfo(i);
1058  if (cli != null) {
1059  id = ids[i];
1060  md.setValueInt(MDLabel.MDL_REF2, cli.index + 1, id);
1061  md.setValueString(MDLabel.MDL_KEYWORDS,
1062  cli.getComment(), id);
1063  mdAux = getClassImages(i);
1064  if (mdAux != null) {
1065  mds[cli.index + 1].unionAll(mdAux);
1066  }
1067  }
1068  }
1069  return mds;
1070  }
1071  } catch (Exception e) {
1072  // TODO Auto-generated catch block
1073  e.printStackTrace();
1074  }
1075  return null;
1076  }
xmipp.jni.MetaData.setValueString
native boolean setValueString(int label, String value, long objId)
-
xmipp.viewer.models.GalleryData.getClassImages
MetaData getClassImages(int index)
Definition: GalleryData.java:1081
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xmipp.viewer.models.GalleryData.getItemClassInfo
ClassInfo getItemClassInfo(int index)
Definition: GalleryData.java:892
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xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
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xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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◆ getClassImages()

- -
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MetaData xmipp.viewer.models.GalleryData.getClassImages (int index)
- 		-inline
-
-

Get the metadata with assigned images to this classes

- -

Definition at line 1081 of file GalleryData.java.

-
1081  {
1082  try {
1083  long id = ids[index];
1084  int ref = md.getValueInt(refLabel, id);
1085  String blockName = Filename.getClassBlockName(ref);
1086  if (containsBlock(blockName)) {
1087  return new MetaData(blockName + Filename.SEPARATOR + filename);
1088  }
1089  } catch (Exception e) {
1090  e.printStackTrace();
1091  }
1092  return null;
1093  }
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.viewer.models.GalleryData.containsBlock
boolean containsBlock(String block)
Definition: GalleryData.java:1132
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◆ getClassInfo()

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ClassInfo xmipp.viewer.models.GalleryData.getClassInfo (int classNumber)
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-
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Definition at line 930 of file GalleryData.java.

-
930  {
931  return classesArray.get(classNumber);
932  }
xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
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ColumnInfo xmipp.viewer.models.GalleryData.getColumnInfo (String labelName)
- 		-inline
-
- -

Definition at line 477 of file GalleryData.java.

-
477  {
478  for (ColumnInfo ci : labels) {
479  if (ci.labelName.equals(labelName)) {
480  return ci;
481  }
482  }
483  return null;
484  }
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Definition at line 1167 of file GalleryData.java.

-
1167  {
1168  return labels.get(col);
1169  }
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-
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◆ getColumns()

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List<ColumnInfo> xmipp.viewer.models.GalleryData.getColumns ()
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-
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Definition at line 293 of file GalleryData.java.

-
293  {
294  return labels;
295  }
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-
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◆ getDefaultZoom()

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static int xmipp.viewer.models.GalleryData.getDefaultZoom (int xdim)
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-
- -

Definition at line 469 of file GalleryData.java.

-
470  {
471  int x = Math.min(Math.max(xdim, MIN_SIZE), MAX_SIZE);
472  float scale = (float) x / xdim;
473  int zoom = (int) Math.ceil(scale * 100);
474  return zoom;
475  }
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-
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◆ getDisplayLabel()

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String xmipp.viewer.models.GalleryData.getDisplayLabel (long id)
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-
- -

Definition at line 494 of file GalleryData.java.

-
495  {
496  String label = "";
497 
498  for(ColumnInfo ci: displaycis.values())
499  label += ci.labelName + "=" + md.getValueString(ci.label, id) + ", ";
500  if(!label.isEmpty())
501  label = label.substring(0, label.length() - 2);
502  return label;
503  }
-
xmipp.viewer.models.GalleryData.displaycis
HashMap< String, ColumnInfo > displaycis
Definition: GalleryData.java:72
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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◆ getEnabledClassesImages()

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MetaData xmipp.viewer.models.GalleryData.getEnabledClassesImages ()
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- -

Definition at line 1113 of file GalleryData.java.

-
1113  {
1114  MetaData mdImages = new MetaData();
1115  MetaData md;
1116  for (int i = 0; i < ids.length; ++i) {
1117  if (isEnabled(i)) {
1118  md = getClassImages(i);
1119  if (md != null) {
1120  mdImages.unionAll(md);
1121  md.destroy();
1122  }
1123  }
1124  }
1125  return mdImages;
1126  }
xmipp.viewer.models.GalleryData.getClassImages
MetaData getClassImages(int index)
Definition: GalleryData.java:1081
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- -

◆ getEnabledCount()

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int xmipp.viewer.models.GalleryData.getEnabledCount ()
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- -

Definition at line 1922 of file GalleryData.java.

-
1923  {
1924  int count = 0;
1925  for(int i = 0; i < ids.length; i ++)
1926  if(isEnabled(i))
1927  count ++;
1928  return count;
1929  }
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-
-
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◆ getFileExtension()

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String xmipp.viewer.models.GalleryData.getFileExtension ()
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-
- -

Definition at line 1518 of file GalleryData.java.

-
1518  {
1519  if (getFileName() == null) {
1520  return "";
1521  }
1522  return XmippStringUtils.getFileExtension(filename);
1523  }
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-
-
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◆ getFileInfo()

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String xmipp.viewer.models.GalleryData.getFileInfo ()
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Definition at line 1312 of file GalleryData.java.

-
1312  {
1313  File file = new File(getFileName());
1314 
1315  String fileInfo = "Path: " + file.getAbsolutePath() + "\n";
1316 
1317  fileInfo += "Last Modified: "
1318  + new Date(file.lastModified()) + "\n"
1319  + "Size: " + Filename.humanReadableByteCount(file.length());
1320  return fileInfo;
1321  }
-
-
-
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◆ getFileName()

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String xmipp.viewer.models.GalleryData.getFileName ()
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Definition at line 1258 of file GalleryData.java.

-
1258  {
1259  return filename;
1260 
1261  }
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Geometry xmipp.viewer.models.GalleryData.getGeometry (long id,
ColumnInfo ci 
)
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- -

Definition at line 1779 of file GalleryData.java.

-
1780  {
1781  return getGeometry(id, "2D", ci);
1782  }
xmipp.viewer.models.GalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: GalleryData.java:1779
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Geometry xmipp.viewer.models.GalleryData.getGeometry (long id,
String type,
ColumnInfo ci 
)
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-
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Definition at line 1785 of file GalleryData.java.

-
1786  {
1787  if(md.containsLabel(MDLabel.MDL_IMAGE) && ci.label != MDLabel.MDL_IMAGE)
1788  return null;
1789 
1790  if(md.containsLabel(MDLabel.RLN_IMAGE_NAME) && ci.label != MDLabel.RLN_IMAGE_NAME)
1791  return null;
1792 
1793 
1794  double shiftx, shifty, psiangle, scaleFactor=1;
1795  boolean flip;
1796 
1797  if(md.containsLabel(MetaData.GEOMETRY_LABELS))
1798  {
1799  shiftx = md.getValueDouble(MDLabel.MDL_SHIFT_X, id);
1800  shifty = md.getValueDouble(MDLabel.MDL_SHIFT_Y, id);
1801  psiangle = md.getValueDouble(MDLabel.MDL_ANGLE_PSI, id);
1802  flip = md.getValueBoolean(MDLabel.MDL_FLIP, id);
1803 
1804  if(md.containsLabel(MDLabel.MDL_SCALE))
1805  scaleFactor = md.getValueDouble(MDLabel.MDL_SCALE, id);
1806  }
1807  else if(md.containsLabel(MetaData.GEOMETRY_RELION_LABELS))
1808  {
1809  shiftx = md.getValueDouble(MDLabel.RLN_ORIENT_ORIGIN_X, id);
1810  shifty = md.getValueDouble(MDLabel.RLN_ORIENT_ORIGIN_Y, id);
1811  psiangle = -1 * md.getValueDouble(MDLabel.RLN_ORIENT_PSI, id);
1812  flip = md.getValueBoolean(MDLabel.MDL_FLIP, id);
1813  }
1814  else
1815  return null;
1816 
1817  return new Geometry(shiftx, shifty, psiangle, flip, scaleFactor);
1818  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
- -
xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.jni.MetaData.getValueBoolean
native boolean getValueBoolean(int label, long objId)
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◆ getId()

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long xmipp.viewer.models.GalleryData.getId (int i)
- 		-inline
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Definition at line 1474 of file GalleryData.java.

-
1474  {
1475  return ids[i];
1476  }
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-
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◆ getIds()

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long [] xmipp.viewer.models.GalleryData.getIds ()
- 		-inline
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Definition at line 1419 of file GalleryData.java.

-
1419  {
1420  return ids;
1421  }
-
-
-
- -

◆ getImages()

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MDRow [] xmipp.viewer.models.GalleryData.getImages (MetaData md)
- 		-inline
-
- -

Definition at line 1273 of file GalleryData.java.

-
1273  {
1274  int idlabel = getRenderLabel();
1275  if (md == null) {
1276  return null;
1277  }
1278  if (!md.containsLabel(idlabel)) {
1279  return null;
1280  }
1281 
1282  MDRow mdRow = null;
1283  ArrayList<MDRow> imagesmd = new ArrayList<MDRow>();
1284  int index = 0;
1285  String imagepath;
1286 
1287  for (long id : md.findObjects()) {
1288  if (isEnabled(index)) {
1289 
1290  imagepath = md.getValueString(idlabel, id, true);
1291  if (imagepath != null && ImageGeneric.exists(imagepath)) {
1292  mdRow = new MDRow();
1293 
1294  if (useGeo) {
1295 
1296  md.getRow(mdRow, id);
1297  mdRow.setValueString(idlabel, imagepath);
1298 
1299  } else {
1300  mdRow.setValueString(MDLabel.MDL_IMAGE, imagepath);
1301  }
1302 
1303  imagesmd.add(mdRow);
1304  }
1305  }
1306  index++;
1307  }
1308 
1309  return imagesmd.toArray(new MDRow[]{});
1310  }
-
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
- -
xmipp.jni.MetaData.getRow
native void getRow(MDRow mdRow, long objId)
- -
xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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◆ getImagesMd() [1/2]

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MetaData xmipp.viewer.models.GalleryData.getImagesMd ()
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-
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Definition at line 1866 of file GalleryData.java.

-
1866  {
1867  return getImagesMd(null, false);
1868  }
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MetaData xmipp.viewer.models.GalleryData.getImagesMd (boolean [] selection,
boolean selected 
)
- 		-inline
-
- -

Definition at line 1870 of file GalleryData.java.

-
1870  {
1871  int idlabel = getRenderLabel();
1872  MDRow mdRow;
1873  MetaData imagesmd = new MetaData();
1874  int index = 0;
1875  String imagepath;
1876  long imageid;
1877  for (long id : md.findObjects()) {
1878  if (isEnabled(index) && (!selected || selection[index])) {
1879  imagepath = md.getValueString(idlabel, id, true);
1880  if (imagepath != null && ImageGeneric.exists(imagepath)) {
1881  imageid = imagesmd.addObject();
1882  if (useGeo())
1883  {
1884  Geometry geo = getGeometry(id, ciFirstRender);
1885  mdRow = new MDRow();
1886  //md.getRow(mdRow, id);//copy geo info in mdRow
1887  mdRow.setValueDouble(MDLabel.MDL_SHIFT_X, geo.shiftx);
1888  mdRow.setValueDouble(MDLabel.MDL_SHIFT_Y, geo.shifty);
1889  mdRow.setValueDouble(MDLabel.MDL_ANGLE_PSI, geo.psiangle);
1890  mdRow.setValueBoolean(MDLabel.MDL_FLIP, geo.flip);
1891  imagesmd.setRow(mdRow, imageid);
1892  }
1893  imagesmd.setValueString(MDLabel.MDL_IMAGE, imagepath, imageid);
1894  }
1895  }
1896  index++;
1897  }
1898  return imagesmd;
1899  }
- -
xmipp.viewer.models.GalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: GalleryData.java:1779
- - -
xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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◆ getItemClassInfo()

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ClassInfo xmipp.viewer.models.GalleryData.getItemClassInfo (int index)
- 		-inline
-
-

Get the assigned class of some element

- -

Definition at line 892 of file GalleryData.java.

-
892  {
893  if (isClassification && index < classes.length) {
894  return classes[index];
895  }
896  return null;
897  }
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◆ getLabel()

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String xmipp.viewer.models.GalleryData.getLabel (long objId,
int label 
)
- 		-inline
-
- -

Definition at line 1503 of file GalleryData.java.

-
1503  {
1504  try {
1505  if (isClassification) {
1506  int ref = md.getValueInt(MDLabel.MDL_REF, objId);
1507  long count = md.getValueLong(MDLabel.MDL_CLASS_COUNT, objId);
1508  return String.format("class %d (%d images)", ref, count);
1509  } else {
1510  return md.getValueString(label, objId);
1511  }
1512  } catch (Exception e) {
1513  e.printStackTrace();
1514  }
1515  return null;
1516  }
xmipp.jni.MetaData.getValueLong
native long getValueLong(int label, long objId)
- - -
xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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◆ getLabelFromCol()

- -
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int xmipp.viewer.models.GalleryData.getLabelFromCol (int col)
- 		-inline
-
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Definition at line 1163 of file GalleryData.java.

-
1163  {
1164  return labels.get(col).label;
1165  }
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◆ getLabels()

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int [] xmipp.viewer.models.GalleryData.getLabels ()
- 		-inline
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Definition at line 1423 of file GalleryData.java.

-
1423  {
1424  return md.getActiveLabels();
1425  }
-
xmipp.jni.MetaData.getActiveLabels
native int [] getActiveLabels()
-
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◆ getLabelsInfo()

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List<ColumnInfo> xmipp.viewer.models.GalleryData.getLabelsInfo ()
- 		-inline
-
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Definition at line 1495 of file GalleryData.java.

-
1495  {
1496  return labels;
1497  }
-
-
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◆ getMd() [1/2]

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- 		-inline
-
- -

Definition at line 1626 of file GalleryData.java.

-
1626  {
1627  MetaData selmd = null;
1628  try {
1629  long[] ids2 = new long[ids.size()];
1630  for (int i = 0; i < ids.size(); i++) {
1631  ids2[i] = ids.get(i);
1632  }
1633  selmd = new MetaData();
1634  selmd.importObjects(md, ids2);
1635  } catch (Exception e) {
1636  e.printStackTrace();
1637  }
1638  return selmd;
1639  }
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◆ getMd() [2/2]

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Definition at line 1652 of file GalleryData.java.

-
1652  {
1653  return md;
1654  }
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◆ getMdFilename()

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String xmipp.viewer.models.GalleryData.getMdFilename ()
- 		-inline
-
-

Return the name of the selected md block

- -

Definition at line 313 of file GalleryData.java.

-
313  {
314  if (selectedBlock.isEmpty()) {
315  return filename;
316  }
317  return String.format("%s@%s", selectedBlock, filename);
318  }// function getMdFilename
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◆ getMdSaveFileName()

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String xmipp.viewer.models.GalleryData.getMdSaveFileName ()
- 		-inline
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- -

Definition at line 320 of file GalleryData.java.

-
320  {
321  if (filename == null) {
322  return null;
323  }
324 
325  String savefn;
326  if (selectedBlock.isEmpty()) {
327  savefn = filename;
328  } else {
329  savefn = String.format("%s@%s", selectedBlock, filename);
330  }
331  String ext;
332  if (savefn.contains(".")) {
333  ext = savefn.substring(savefn.lastIndexOf("."));
334  if (ext.equals(".stk")) {
335  return savefn.replace(ext, ".xmd");
336  }
337  } else {
338  savefn = savefn + ".xmd";
339  }
340  return savefn;
341  }
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◆ getMetaData()

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MetaData xmipp.viewer.models.GalleryData.getMetaData (String block)
- 		-inline
-
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Definition at line 1612 of file GalleryData.java.

-
1612  {
1613  return new MetaData(block + "@" + filename);
1614  }
-
-
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◆ getMetaDataRow()

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MetaData xmipp.viewer.models.GalleryData.getMetaDataRow ()
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Definition at line 1499 of file GalleryData.java.

-
1499  {
1500  return md.getMetaDataRow();
1501  }
-
xmipp.jni.MetaData.getMetaDataRow
MetaData getMetaDataRow()
Definition: MetaData.java:384
-
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◆ getMode()

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Mode xmipp.viewer.models.GalleryData.getMode ()
- 		-inline
-
-

Return the mode of the gallery

- -

Definition at line 701 of file GalleryData.java.

-
701  {
702  return mode;
703  }
-
-
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◆ getModelColumns()

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Integer xmipp.viewer.models.GalleryData.getModelColumns ()
- 		-inline
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Definition at line 144 of file GalleryData.java.

-
145  {
146  return columns;
147  }
-
-
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◆ getModelRows()

- -
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Integer xmipp.viewer.models.GalleryData.getModelRows ()
- 		-inline
-
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Definition at line 139 of file GalleryData.java.

-
140  {
141  return rows;
142  }
-
-
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- -

◆ getNormalized()

- -
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boolean xmipp.viewer.models.GalleryData.getNormalized ()
- 		-inline
-
- -

Definition at line 1620 of file GalleryData.java.

-
1620  {
1621  return normalize;
1622  }
-
-
-
- -

◆ getNumberOfBlocks()

- -
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int xmipp.viewer.models.GalleryData.getNumberOfBlocks ()
- 		-inline
-
- -

Definition at line 692 of file GalleryData.java.

-
692  {
693  return mdBlocks != null ? mdBlocks.length : 0;
694  }
-
-
-
- -

◆ getOrderLabels()

- -
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String [] xmipp.viewer.models.GalleryData.getOrderLabels ()
- 		-inline
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Definition at line 1847 of file GalleryData.java.

-
1848  {
1849  return orderLabels;
1850  }
-
-
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◆ getPreffix()

- -
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String xmipp.viewer.models.GalleryData.getPreffix ()
- 		-inline
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Definition at line 1931 of file GalleryData.java.

-
1931  {
1932  return selectedBlock;
1933  }
-
-
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◆ getRenderColumn()

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ColumnInfo xmipp.viewer.models.GalleryData.getRenderColumn ()
- 		-inline
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Definition at line 306 of file GalleryData.java.

-
306  {
307  return ciFirstRender;
308  }
-
-
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◆ getRenderLabel()

- -
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int xmipp.viewer.models.GalleryData.getRenderLabel ()
- 		-inline
-
-

Return the label that is used for rendering

- -

Definition at line 715 of file GalleryData.java.

-
715  {
716  return ciFirstRender.label;
717  }
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◆ getRenderLabels()

- -
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String [] xmipp.viewer.models.GalleryData.getRenderLabels ()
- 		-inline
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Definition at line 1837 of file GalleryData.java.

-
1838  {
1839  return renderLabels;
1840  }
-
-
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- -

◆ getResliceView()

- -
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int xmipp.viewer.models.GalleryData.getResliceView ()
- 		-inline
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- -

Definition at line 1457 of file GalleryData.java.

-
1457  {
1458  return resliceView;
1459  }
-
-
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◆ getSampleImage()

- -
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String xmipp.viewer.models.GalleryData.getSampleImage (ColumnInfo ci)
- 		-inline
-
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Definition at line 580 of file GalleryData.java.

-
581  {
582  String imageFn, mddir = md.getBaseDir();
583  for (int i = 0; i < ids.length; ++i)
584  {
585  if( i == 100)
586  break;
587  imageFn = getValueFromLabel(i, ci.label);
588  if(imageFn != null)
589  {
590  imageFn = Filename.findImagePath(imageFn, mddir, true);
591  if (imageFn != null && Filename.exists(imageFn))
592  return imageFn;
593  }
594  }
595  return null;
596  }
-
xmipp.viewer.models.GalleryData.getValueFromLabel
String getValueFromLabel(int index, int label)
Definition: GalleryData.java:1190
- -
xmipp.jni.MetaData.getBaseDir
String getBaseDir()
Definition: MetaData.java:430
-
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◆ getSelectedBlock()

- -
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Object xmipp.viewer.models.GalleryData.getSelectedBlock ()
- 		-inline
-
- -

Definition at line 1435 of file GalleryData.java.

-
1435  {
1436  return selectedBlock;
1437  }
-
-
-
- -

◆ getSelectionMd()

- -
-
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- - - - - - - - -
MetaData xmipp.viewer.models.GalleryData.getSelectionMd (boolean [] selection)
- 		-inline
-
-

Create a metadata just with selected items

- -

Definition at line 1011 of file GalleryData.java.

-
1011  {
1012  MetaData selectionMd = null;
1013  if (!isVolumeMode()) {
1014  long[] selectedIds = new long[selection.length];
1015  int count = 0;
1016  for (int i = 0; i < selection.length; i++) {
1017  if (selection[i]) {
1018  selectedIds[count++] = ids[i];
1019  }
1020  }
1021  try {
1022  selectionMd = new MetaData();
1023  selectionMd.importObjects(md, selectedIds);
1024  } catch (Exception e) {
1025  e.printStackTrace();
1026  }
1027  }
1028  return selectionMd;
1029  }
- - -
-
-
- -

◆ getSelVolId()

- -
-
- - - - - -
- - - - - - - -
Long xmipp.viewer.models.GalleryData.getSelVolId ()
- 		-inline
-
- -

Definition at line 1852 of file GalleryData.java.

-
1853  {
1854  if(selectedVolFn == null || selectedVolFn.isEmpty())
1855  return null;
1856  String vol;
1857  for(Long id: ids)
1858  {
1859  vol = md.getValueString(ciFirstRender.label, id);
1860  if(vol.equals(selectedVolFn))
1861  return id;
1862  }
1863  return null;
1864  }
- - - - -
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
-
-
- -

◆ getSelVolumeFile()

- -
-
- - - - - -
- - - - - - - -
String xmipp.viewer.models.GalleryData.getSelVolumeFile ()
- 		-inline
-
- -

Definition at line 1441 of file GalleryData.java.

-
1441  {
1442  return selectedVolFn;
1443  }
-
-
-
- -

◆ getSortBy()

- -
-
- - - - - -
- - - - - - - -
String [] xmipp.viewer.models.GalleryData.getSortBy ()
- 		-inline
-
- -

Definition at line 1903 of file GalleryData.java.

-
1904  {
1905  return sortby;
1906  }
-
-
-
- -

◆ getTmpFile()

- -
-
- - - - - -
- - - - - - - - -
String xmipp.viewer.models.GalleryData.getTmpFile (String suffix)
- 		-inline
-
- -

Definition at line 158 of file GalleryData.java.

-
158  {
159  String ext = XmippStringUtils.getFileExtension(filename);
160  String ext2 = suffix + ext;
161  String tmpfile = filename;
162  if(!filename.endsWith(ext2))
163  tmpfile = filename.replace(ext, ext2);
164  return tmpfile;
165  }
-
-
-
- -

◆ getValueFromCol() [1/2]

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String xmipp.viewer.models.GalleryData.getValueFromCol (int index,
int col 
)
- 		-inline
-
- -

Definition at line 1173 of file GalleryData.java.

-
1173  {
1174  if (!isColumnFormat()) {
1175  col = index;
1176  index = 0;
1177  }
1178  return getValueFromCol(index, labels.get(col));
1179  }
-
xmipp.viewer.models.GalleryData.getValueFromCol
String getValueFromCol(int index, int col)
Definition: GalleryData.java:1173
- -
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-
- -

◆ getValueFromCol() [2/2]

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String xmipp.viewer.models.GalleryData.getValueFromCol (int index,
ColumnInfo ci 
)
- 		-inline
-
- -

Definition at line 1181 of file GalleryData.java.

-
1181  {
1182  try {
1183  return md.getValueString(ci.label, ids[index]);
1184  } catch (Exception e) {
1185  e.printStackTrace();
1186  }
1187  return null;
1188  }
- -
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
-
-
- -

◆ getValueFromLabel()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
String xmipp.viewer.models.GalleryData.getValueFromLabel (int index,
int label 
)
- 		-inline
-
- -

Definition at line 1190 of file GalleryData.java.

-
1190  {
1191  try {
1192  return md.getValueString(label, ids[index]);
1193  } catch (Exception e) {
1194  e.printStackTrace();
1195  }
1196  return null;
1197  }
- -
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
-
-
- -

◆ getValueString()

- -
-
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String xmipp.viewer.models.GalleryData.getValueString (int label,
long id 
)
- 		-inline
-
- -

Definition at line 1427 of file GalleryData.java.

-
1427  {
1428  return md.getValueString(label, id);
1429  }
-
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
-
-
- -

◆ getVisibleColumnIndex()

- -
-
- - - - - -
- - - - - - - - -
int xmipp.viewer.models.GalleryData.getVisibleColumnIndex (int col)
- 		-inline
-
-

Take an index counting only visible columns and translate into the general column index

-
Parameters
- - -
colcolumn index in visible counting
-
-
-
Returns
column index in general counting
- -

Definition at line 1150 of file GalleryData.java.

-
1150  {
1151  int visibleIndex = 0;
1152  for (int i = 0; i < labels.size(); i++) {
1153  if (labels.get(i).visible) {
1154  if (col == visibleIndex) {
1155  return i;
1156  }
1157  visibleIndex++;
1158  }
1159  }
1160  return -1;
1161  }
-
-
-
- -

◆ getVisibleLabels()

- -
-
- - - - - -
- - - - - - - -
String [] xmipp.viewer.models.GalleryData.getVisibleLabels ()
- 		-inline
-
- -

Definition at line 1842 of file GalleryData.java.

-
1843  {
1844  return visibleLabels;
1845  }
-
-
-
- -

◆ getVolumeAt()

- -
-
- - - - - -
- - - - - - - - -
String xmipp.viewer.models.GalleryData.getVolumeAt (int index)
- 		-inline
-
-

following function only should be used in VolumeGallery mode

- -

Definition at line 767 of file GalleryData.java.

-
767  {
768  return md.getValueString(ciFirstRender.label, ids[index]);
769  }
- - - -
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
-
-
-
- -

◆ getZoom()

- -
-
- - - - - -
- - - - - - - -
Integer xmipp.viewer.models.GalleryData.getZoom ()
- 		-inline
-
- -

Definition at line 1391 of file GalleryData.java.

-
1391  {
1392  return zoom;
1393  }
-
-
-
- -

◆ hasClasses()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.hasClasses ()
- 		-inline
-
- -

Definition at line 1616 of file GalleryData.java.

-
1616  {
1617  return isClassification;
1618  }
-
-
-
- -

◆ hasClassesChanges()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.hasClassesChanges ()
- 		-inline
-
- -

Definition at line 1250 of file GalleryData.java.

-
1250  {
1251  return hasClassesChanges;
1252  }
-
-
-
- -

◆ hasDisabled()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.hasDisabled ()
- 		-inline
-
- -

Definition at line 1914 of file GalleryData.java.

-
1915  {
1916  for(int i = 0; i < ids.length; i ++)
1917  if(!isEnabled(i))
1918  return true;
1919  return false;
1920  }
- -
-
-
- -

◆ hasMdChanges()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.hasMdChanges ()
- 		-inline
-
- -

Definition at line 1242 of file GalleryData.java.

-
1242  {
1243  return hasMdChanges;
1244  }
-
-
-
- -

◆ hasMicrographParticles()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.hasMicrographParticles ()
- 		-inline
-
- -

Definition at line 1254 of file GalleryData.java.

-
1254  {
1255  return md.containsMicrographParticles();
1256  }
-
xmipp.jni.MetaData.containsMicrographParticles
boolean containsMicrographParticles()
Definition: MetaData.java:206
-
-
-
- -

◆ hasRecalculateCTF()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.hasRecalculateCTF ()
- 		-inline
-
- -

Definition at line 1723 of file GalleryData.java.

-
1724  {
1725  return md.hasRecalculateCTF();
1726  }
-
xmipp.jni.MetaData.hasRecalculateCTF
boolean hasRecalculateCTF()
Definition: MetaData.java:682
-
-
-
- -

◆ hasRenderLabel()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.hasRenderLabel ()
- 		-inline
-
-

Return true if there is a renderizable label in the metadata

- -

Definition at line 708 of file GalleryData.java.

-
708  {
709  return ciFirstRender != null;
710  }
-
-
-
- -

◆ initColumnInfo()

- -
-
- - - - - -
- - - - - - - - -
ColumnInfo xmipp.viewer.models.GalleryData.initColumnInfo (int label)
- 		-inline
-
- -

Definition at line 598 of file GalleryData.java.

-
599  {
600  return new ColumnInfo(label);
601  }
-
-
- -

◆ isAutoAdjust()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isAutoAdjust ()
- 		-inline
-
- -

Definition at line 182 of file GalleryData.java.

-
183  {
184  return rows == null && columns == null;
185  }
-
-
-
- -

◆ isChimeraClient()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isChimeraClient ()
- 		-inline
-
- -

Definition at line 1909 of file GalleryData.java.

-
1910  {
1911  return parameters.getChimeraPort() != null;
1912  }
-
xmipp.utils.Params.getChimeraPort
Integer getChimeraPort()
Definition: Params.java:339
-
-
-
- -

◆ isClassificationMd()

- -
-
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- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isClassificationMd ()
- 		-inline
-
- -

Definition at line 854 of file GalleryData.java.

-
854  {
855  return isClassification;
856  }
-
-
-
- -

◆ isColumnFormat()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isColumnFormat ()
- 		-inline
-
-

Return true if the underlying metadata is in row format

- -

Definition at line 743 of file GalleryData.java.

-
743  {
744  return md.isColumnFormat();
745  }
-
xmipp.jni.MetaData.isColumnFormat
native boolean isColumnFormat()
-
-
-
- -

◆ isCTFMd()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isCTFMd ()
- 		-inline
-
- -

Definition at line 1346 of file GalleryData.java.

-
1346  {
1347  return md.isCTFMd();
1348  }
-
xmipp.jni.MetaData.isCTFMd
boolean isCTFMd()
Definition: MetaData.java:591
-
-
-
- -

◆ isDisplayLabel()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isDisplayLabel ()
- 		-inline
-
- -

Definition at line 487 of file GalleryData.java.

-
488  {
489  return displaycis != null;
490  }
xmipp.viewer.models.GalleryData.displaycis
HashMap< String, ColumnInfo > displaycis
Definition: GalleryData.java:72
-
-
-
- -

◆ isEnabled()

- -
-
- - - - - -
- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isEnabled (int index)
- 		-inline
-
-

Check if an item is enabled or not

- -

Definition at line 790 of file GalleryData.java.

-
790  {
791  try {
792  if (isVolumeMode()) {
793  return true;
794  }
795  return md.getEnabled(ids[index]);
796  } catch (Exception e) {
797  e.printStackTrace();
798  }
799  return true;
800  }
- - -
xmipp.jni.MetaData.getEnabled
boolean getEnabled(long objId)
Definition: MetaData.java:448
-
-
-
- -

◆ isFile() [1/2]

- -
-
- - - - - -
- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isFile (ColumnInfo ci)
- 		-inline
-
-

This is only needed for metadata table galleries

- -

Definition at line 827 of file GalleryData.java.

-
827  {
828  try {
829  return MetaData.isPathField(ci.label);
830  } catch (Exception e) {
831  e.printStackTrace();
832  }
833  return false;
834  }
-
-
- -

◆ isFile() [2/2]

- -
-
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- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isFile (int col)
- 		-inline
-
- -

Definition at line 836 of file GalleryData.java.

-
836  {
837  return isFile(labels.get(col));
838  }
xmipp.viewer.models.GalleryData.isFile
boolean isFile(ColumnInfo ci)
Definition: GalleryData.java:827
- -
-
-
- -

◆ isGalleryMode()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isGalleryMode ()
- 		-inline
-
- -

Definition at line 727 of file GalleryData.java.

-
727  {
728  return mode == Mode.GALLERY_MD || mode == Mode.GALLERY_VOL;
729 
730  }
- - -
-
-
- -

◆ isImageFile() [1/2]

- -
-
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- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isImageFile (int col)
- 		-inline
-
- -

Definition at line 840 of file GalleryData.java.

-
840  {
841  return isImageFile(labels.get(col));
842  }
- -
-
-
- -

◆ isImageFile() [2/2]

- -
-
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- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isImageFile (ColumnInfo ci)
- 		-inline
-
- -

Definition at line 844 of file GalleryData.java.

-
844  {
845  try {
846 
847  return ci.render;
848  } catch (Exception e) {
849  e.printStackTrace();
850  }
851  return false;
852  }
-
-
- -

◆ isInvertY()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isInvertY ()
- 		-inline
-
- -

Definition at line 198 of file GalleryData.java.

-
198  {
199  return inverty;
200  }
-
-
-
- -

◆ isMicrographsMode()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isMicrographsMode ()
- 		-inline
-
- -

Definition at line 748 of file GalleryData.java.

-
748  {
749  return md.containsMicrographsInfo();
750  }
xmipp.jni.MetaData.containsMicrographsInfo
boolean containsMicrographsInfo()
Definition: MetaData.java:218
- -
-
-
- -

◆ isObjectCmd()

- -
-
- - - - - -
- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isObjectCmd (String cmd)
- 		-inline
-
- -

Definition at line 127 of file GalleryData.java.

-
127  {
128  for(String objCmd: parameters.objectCommands)
129  if(objCmd.equals(cmd))
130  return true;
131  return false;
132  }
-
xmipp.utils.Params.objectCommands
String [] objectCommands
Definition: Params.java:88
-
-
-
- -

◆ isRecalculateCTF()

- -
-
- - - - - -
- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isRecalculateCTF (int row)
- 		-inline
-
- -

Definition at line 1714 of file GalleryData.java.

-
1714  {
1715  if(!isCTFMd())
1716  return false;
1717  long id = ids[row];
1718  if(md.containsCTF(id))
1719  return true;
1720  return false;
1721  }
- - -
xmipp.jni.MetaData.containsCTF
boolean containsCTF(long id)
Definition: MetaData.java:690
-
-
-
- -

◆ isRenderLabel()

- -
-
- - - - - -
- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isRenderLabel (ColumnInfo ci)
- 		-inline
-
- -

Definition at line 1656 of file GalleryData.java.

-
1656  {
1657  if(!renderImages)
1658  return false;
1659  if (renderLabel.equals("first") )
1660  {
1661  if(md instanceof ScipionMetaData)
1662  return ci.render && ci.visible;
1663  else
1664  return MetaData.isImage(ci.label) && ci.visible;
1665  }
1666 
1667  for (String i : getRenderLabels()) {
1668  if (i.equals(ci.labelName) && ci.visible) {
1669  return true;
1670  }
1671  }
1672  return false;
1673  }
- - - -
-
-
- -

◆ isScipionInstance()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isScipionInstance ()
- 		-inline
-
- -

Definition at line 194 of file GalleryData.java.

-
194  {
195  return this instanceof ScipionGalleryData;
196  }
-
-
- -

◆ isTableMode()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isTableMode ()
- 		-inline
-
- -

Definition at line 736 of file GalleryData.java.

-
736  {
737  return mode == Mode.TABLE_MD;
738  }
- -
-
-
- -

◆ isVisibleLabel()

- -
-
- - - - - -
- - - - - - - - -
boolean xmipp.viewer.models.GalleryData.isVisibleLabel (ColumnInfo ci)
- 		-inline
-
- -

Definition at line 1675 of file GalleryData.java.

-
1675  {
1676  if (getVisibleLabels() == null) {
1677  return true;
1678  }
1679  for (String i : getVisibleLabels()) {
1680  if (i.equals(ci.labelName)) {
1681  return true;
1682  }
1683  }
1684  return false;
1685  }
-
-
-
- -

◆ isVolumeMd()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isVolumeMd ()
- 		-inline
-
- -

Definition at line 134 of file GalleryData.java.

-
135  {
136  return isVolumeMd;
137  }
-
-
-
- -

◆ isVolumeMode()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isVolumeMode ()
- 		-inline
-
- -

Definition at line 732 of file GalleryData.java.

-
732  {
733  return mode == Mode.GALLERY_VOL;
734  }
- -
-
-
- -

◆ isWrap()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.isWrap ()
- 		-inline
-
- -

Definition at line 1449 of file GalleryData.java.

-
1449  {
1450  return wrap;
1451  }
-
-
-
- -

◆ loadClassesInfo()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.models.GalleryData.loadClassesInfo ()
- 		-inline
-
-

Load classes structure if previously stored

- -

Definition at line 968 of file GalleryData.java.

-
968  {
969  try {
970  if (md.containsLabel(MDLabel.MDL_REF2)) {
971  long id;
972  int ref2;
973  ClassInfo cli;
974 
975  for (int i = 0; i < ids.length; ++i) {
976  id = ids[i];
977  ref2 = md.getValueInt(MDLabel.MDL_REF2, id);
978 
979  if (ref2 > 0) {
980  cli = null;
981 
982  for (ClassInfo cli2 : classesArray) {
983  if (cli2.index == ref2) {
984  cli = cli2;
985  break;
986  }
987  }
988 
989  if (cli == null) {
990  String comment = md.getValueString(
991  MDLabel.MDL_KEYWORDS, id);
992  int color = md.getValueInt(MDLabel.MDL_COLOR, id);
993  cli = new ClassInfo(comment, new Color(color));
994  cli.index = ref2;
995  classesArray.add(cli);
996  }
997  classes[i] = cli;
998  }
999  }
1000  }
1001  } catch (Exception e) {
1002  e.printStackTrace();
1003  }
1004  }// function loadClassesInfo
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
- - -
xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
-
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
- -
xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
-
-
-
- -

◆ loadLabels()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.models.GalleryData.loadLabels ()
- 		-inline
-
-

Load labels info in md, try to keep previous settings of render and visible on same columns

- -

Definition at line 509 of file GalleryData.java.

-
509  {
510 
511  ColumnInfo ci;
512  try {
513  int[] labelids = md.getActiveLabels();
514  ArrayList<ColumnInfo> newLabels = new ArrayList<ColumnInfo>(
515  labelids.length);
516  ciFirstRender = null;
517  ColumnInfo ciFirstRenderVisible = null;
518  String inputRenderLabel = "";
519 
520  if (!renderLabel.equalsIgnoreCase("first")) {
521  inputRenderLabel = renderLabel;
522  }
523  String sampleImage;
524  ColumnInfo auxRender = null;
525  for (int i = 0; i < labelids.length; ++i) {
526  ci = initColumnInfo(labelids[i]);
527 
528  ci.render = isRenderLabel(ci);
529  if(ci.render)
530  auxRender = ci;
531  ci.visible = isVisibleLabel(ci);
532  newLabels.add(ci);
533  if (inputRenderLabel.equals(ci.labelName) && ci.render) {//render label specified and included on renders
534  ciFirstRender = ci;
535  if (ci.visible) {
536  ciFirstRenderVisible = ci;
537  }
538  }
539 
540 
541  if (ciFirstRender == null && ci.allowRender)
542  {
543  sampleImage = getSampleImage(ci);
544  if(sampleImage != null)
545  {
546  ciFirstRender = ci;
547  if (ciFirstRenderVisible == null && ci.visible)
548  ciFirstRenderVisible = ci;
549  }
550  }
551  }
552  if(ciFirstRender == null)
553  ciFirstRender = ciFirstRenderVisible = auxRender;//if there are no images found render none image on gallery mode
554  if (ciFirstRenderVisible != null) {
555  ciFirstRender = ciFirstRenderVisible;
556  }
557 
558  // Add MDL_ENABLED if not present
559  if (!md.containsLabel(MDLabel.MDL_ENABLED) && (md.containsLabel(MDLabel.MDL_IMAGE) || md.containsLabel(MDLabel.MDL_MICROGRAPH))) {
560  newLabels.add(0, new ColumnInfo(MDLabel.MDL_ENABLED));
561  md.addLabel(MDLabel.MDL_ENABLED);
562  for (long id : ids) {
563  md.setEnabled(true, id);
564  }
565  // hasMdChanges = true;
566  }
567 
568 
569  labels = newLabels;
570  orderLabels();
571  if(displayLabels != null)
572  for(String label: displayLabels)
573  setDisplayLabel(label, true);
575  } catch (Exception e) {
576  e.printStackTrace();
577  }
578  }// function loadLabels
xmipp.viewer.models.GalleryData.setDisplayLabel
void setDisplayLabel(String key, boolean selected)
Definition: GalleryData.java:361
-
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
- - -
xmipp.viewer.models.GalleryData.isRenderLabel
boolean isRenderLabel(ColumnInfo ci)
Definition: GalleryData.java:1656
- -
xmipp.viewer.models.GalleryData.getSampleImage
String getSampleImage(ColumnInfo ci)
Definition: GalleryData.java:580
- -
xmipp.jni.MetaData.addLabel
native void addLabel(int label)
-
xmipp.jni.MetaData.getActiveLabels
native int [] getActiveLabels()
-
xmipp.jni.MetaData.setEnabled
boolean setEnabled(boolean value, long objId)
Definition: MetaData.java:442
-
xmipp.viewer.models.GalleryData.isVisibleLabel
boolean isVisibleLabel(ColumnInfo ci)
Definition: GalleryData.java:1675
- -
xmipp.viewer.models.GalleryData.initColumnInfo
ColumnInfo initColumnInfo(int label)
Definition: GalleryData.java:598
- - -
-
-
- -

◆ loadMd()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.models.GalleryData.loadMd () throws Exception
- 		-inline
-
-

Load contents from a metadata already read

- -

Definition at line 379 of file GalleryData.java.

-
379  {
380  readMdParameters();
381  ids = md.findObjects();
382  loadLabels();
383 
384  if (!containsGeometryInfo()) {
385  useGeo = false;
386  wrap = false;
387  }
388 
389  isClassification = checkifIsClassificationMd();
390 
391  if (isClassification) {
392  classes = new ClassInfo[ids.length];
393  classesArray = new ArrayList<ClassInfo>();
394  loadClassesInfo();
395  }
396 
397 
398  if (!md.isColumnFormat() ) {
399  mode = Mode.TABLE_MD;
400  renderImages = false;
401  }
402 
403  if (isGalleryMode()) {
404  mode = Mode.GALLERY_MD;
405  }
406  isVolumeMd = false;
407  if (hasRenderLabel()) {
408  int renderLabel = ciFirstRender.label;
409  ImageGeneric image = null;
410  String imageFn = null;
411 
412 
413  // Try to find at least one image to render
414  // and take dimensions from that
415  for (int i = 0; i < ids.length && image == null; ++i) {
416  if(i == 100)//after 100 items if there is no image available break
417  break;
418  imageFn = md.getValueString(renderLabel, ids[i]);
419  if(imageFn != null)
420  imageFn = Filename.findImagePath(imageFn , filename, true);
421  if (imageFn != null) {
422  try {
423  image = new ImageGeneric(imageFn);
424  } catch (Exception e) {
425  image = null;
426  }
427  break;
428  }
429 
430  }
431  if (image != null) { // Image file was found to render
432  if (zoom == null) { // if default value, calculate zoom
433  // If in micrograph mode, reduce the
434  // MAX_SIZE constant
435  if (md.containsMicrographsInfo()) {
436  MAX_SIZE /= 2;
437  }
438  zoom = getDefaultZoom(image.getXDim());
439 
440  }
441  if (image.isVolume()) { // We are assuming all are volumes
442  // or images, don't mix it
443  if (isGalleryMode())
444  mode = Mode.GALLERY_VOL;
445 
446  isVolumeMd = true;
447  if (selectedVolFn.isEmpty()) {
448  selectedVolFn = imageFn;
449  }
450 
451  }
452  image.destroy();
453  }
454  } else {
455  // force this mode when there aren't render label
456  mode = Mode.TABLE_MD;
457  }
458  if(parameters.sortby != null && parameters.getBlock().equals(selectedBlock))
459  {
460  ColumnInfo sortci = getColumnInfo(parameters.sortby[0]);
461  boolean asc = parameters.sortby.length == 1 || parameters.sortby[1].equalsIgnoreCase("asc");
462  if(sortci != null)
463  sortMd(sortci, asc);
464  }
465 
466  }// function loadMd
- -
xmipp.utils.Params.sortby
String [] sortby
Definition: Params.java:86
- - -
xmipp.jni.MetaData.containsMicrographsInfo
boolean containsMicrographsInfo()
Definition: MetaData.java:218
- - - - -
xmipp.viewer.models.GalleryData.sortMd
void sortMd(ColumnInfo sortci, boolean asc)
Definition: GalleryData.java:624
- - - - - -
xmipp.jni.MetaData.findObjects
native long [] findObjects()
-
xmipp.utils.Params.getBlock
String getBlock()
Definition: Params.java:323
- - -
xmipp.viewer.models.GalleryData.getColumnInfo
ColumnInfo getColumnInfo(String labelName)
Definition: GalleryData.java:477
- -
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
- - - - -
xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
-
xmipp.viewer.models.GalleryData.getDefaultZoom
static int getDefaultZoom(int xdim)
Definition: GalleryData.java:469
- - - - -
xmipp.jni.MetaData.isColumnFormat
native boolean isColumnFormat()
- - - - -
-
-
- -

◆ orderLabels()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.models.GalleryData.orderLabels ()
- 		-inline
-
- -

Definition at line 1687 of file GalleryData.java.

-
1687  {
1688  String[] orderLabels = getOrderLabels();
1689  if (orderLabels == null) {
1690  return;
1691  }
1692 
1693  ColumnInfo aux;
1694  int j, k = 0;//k index added to avoid errors if some order columns are not present. This way order index is k not i
1695  for (int i = 0; i < orderLabels.length; i++) {
1696  j = 0;
1697  for (ColumnInfo ci : labels) {
1698  if (ci.labelName.equals(orderLabels[i])) {
1699 
1700  aux = labels.get(k);
1701  labels.set(k, ci);
1702  labels.set(j, aux);
1703  k ++;
1704  }
1705  j ++;
1706  }
1707  }
1708  }
- - -
-
-
- -

◆ readMd()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.models.GalleryData.readMd ()
- 		-inline
-
-

Reload current metadata from file

- -

Definition at line 645 of file GalleryData.java.

-
645  {
646  if (filename != null) {
647  readMetadata(getMdFilename());
648  }
649  }
- -
-
-
- -

◆ readMdParameters()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.models.GalleryData.readMdParameters ()
- 		-inlineprotected
-
- -

Definition at line 254 of file GalleryData.java.

-
255  {
256  renderLabels = null;
257  renderLabel = "first";
258  visibleLabels = null;
259  orderLabels = null;
260  sortby = null;
261 
262  useGeo = wrap = false;
263  displayLabels = null;
264 
265  if (mode == null)
266  mode = Mode.GALLERY_MD;
267  this.renderImages = true;
268  displaycis = new HashMap<String, ColumnInfo>();
269  this.inverty = parameters.inverty;
270 
271  if(parameters.getBlock() == null)
272  parameters.setBlock(selectedBlock);//Identifies parameters with first block loaded
273 
274  if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_METADATA))
275  mode = Mode.TABLE_MD;
276  else if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_GALLERY))
277  mode = Mode.GALLERY_MD;
278 
279  if(parameters.getBlock().equals(selectedBlock))
280  {
281  setRenderLabels(parameters.renderLabels);
282  setRenderLabel(parameters.getRenderLabel());
283  setVisibleLabels(parameters.visibleLabels);
284  setOrderLabels(parameters.orderLabels);
285  useGeo = parameters.useGeo;
286  wrap = parameters.wrap;
287  displayLabels = parameters.getDisplayLabels();
288  this.renderImages = parameters.renderImages;
289 
290  }
291  }
- -
xmipp.utils.Params.useGeo
boolean useGeo
Definition: Params.java:80
- - - -
xmipp.viewer.models.GalleryData.setRenderLabels
void setRenderLabels(String[] renderLabels)
Definition: GalleryData.java:1820
-
xmipp.viewer.models.GalleryData.displaycis
HashMap< String, ColumnInfo > displaycis
Definition: GalleryData.java:72
- - -
xmipp.utils.Params.getDisplayLabels
String [] getDisplayLabels()
Definition: Params.java:313
- - - -
xmipp.utils.Params.getBlock
String getBlock()
Definition: Params.java:323
-
xmipp.utils.Params.orderLabels
String [] orderLabels
Definition: Params.java:85
-
xmipp.utils.Params.renderImages
boolean renderImages
Definition: Params.java:92
-
xmipp.viewer.models.GalleryData.setOrderLabels
void setOrderLabels(String[] orderLabels)
Definition: GalleryData.java:1828
- -
xmipp.utils.Params.getRenderLabel
String getRenderLabel()
Definition: Params.java:308
- - -
xmipp.viewer.models.GalleryData.setVisibleLabels
void setVisibleLabels(String[] visibleLabels)
Definition: GalleryData.java:1824
- -
xmipp.viewer.models.GalleryData.setRenderLabel
void setRenderLabel(String renderLabel)
Definition: GalleryData.java:1832
-
xmipp.utils.Params.setBlock
void setBlock(String block)
Definition: Params.java:318
- -
xmipp.utils.Params.renderLabels
String [] renderLabels
Definition: Params.java:64
-
xmipp.utils.Params.inverty
boolean inverty
Definition: Params.java:91
- - -
xmipp.utils.Params.visibleLabels
String [] visibleLabels
Definition: Params.java:84
-
-
-
- -

◆ recalculateCTF()

- -
-
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void xmipp.viewer.models.GalleryData.recalculateCTF (int row,
boolean [] selection,
EllipseCTF ellipseCTF,
String sortFn 
)
- 		-inline
-
- -

Definition at line 1728 of file GalleryData.java.

-
1729  {
1730  if(isEnabled(row))
1731  {
1732  for(int i = 0; i <selection.length; i ++ )
1733  if(selection[i] && isEnabled(i))
1734  md.putCTF(ids[i], ellipseCTF);
1735  EstimateFromCTFTask estimateFromCTFTask = new EstimateFromCTFTask(
1736  ellipseCTF, 90 - ellipseCTF.getDefocusAngle(),
1737  md.getPSDFile(ids[row]), ellipseCTF.getD(), window.getTasksEngine(), row, sortFn);
1738  window.getTasksEngine().add(estimateFromCTFTask);
1739  }
1740  }
xmipp.jni.MetaData.getPSDFile
String getPSDFile(long id)
Definition: MetaData.java:633
-
xmipp.viewer.ctf.TasksEngine.add
synchronized void add(CommandTask task)
Definition: TasksEngine.java:22
- - - - -
xmipp.jni.MetaData.putCTF
void putCTF(long id, EllipseCTF ellipseCTF)
Definition: MetaData.java:694
- -
-
-
- -

◆ removeClass()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.removeClass (int classNumber)
- 		-inline
-
-

Remove a class from the selection

- -

Definition at line 1231 of file GalleryData.java.

-
1231  {
1232  ClassInfo cli = getClassInfo(classNumber);
1233  for (int i = 0; i < ids.length; ++i) {
1234  if (getItemClassInfo(i) == cli) {
1235  setItemClass(i, null);
1236  }
1237  }
1238  classesArray.remove(classNumber);
1239  hasClassesChanges = true;
1240  }
xmipp.viewer.models.GalleryData.getItemClassInfo
ClassInfo getItemClassInfo(int index)
Definition: GalleryData.java:892
- - -
xmipp.viewer.models.GalleryData.getClassInfo
ClassInfo getClassInfo(int classNumber)
Definition: GalleryData.java:930
-
xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
-
xmipp.viewer.models.GalleryData.setItemClass
void setItemClass(int index, ClassInfo cli)
Definition: GalleryData.java:923
-
-
-
- -

◆ removeCTF()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.removeCTF (int row)
- 		-inline
-
- -

Definition at line 1710 of file GalleryData.java.

-
1710  {
1711  md.removeCTF(ids[row]);
1712  }
- -
xmipp.jni.MetaData.removeCTF
void removeCTF(long id)
Definition: MetaData.java:686
-
-
-
- -

◆ removeDisabled()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.models.GalleryData.removeDisabled ()
- 		-inline
-
- -

Definition at line 1411 of file GalleryData.java.

-
1411  {
1412  md.removeDisabled();
1413  }
-
xmipp.jni.MetaData.removeDisabled
native void removeDisabled()
-
-
-
- -

◆ removeLabel()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.removeLabel (int label)
- 		-inline
-
- -

Definition at line 1415 of file GalleryData.java.

-
1415  {
1416  md.removeLabel(label);
1417  }
-
xmipp.jni.MetaData.removeLabel
native boolean removeLabel(int label)
-
-
-
- -

◆ removeSelection()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.removeSelection (boolean [] selection) throws Exception
- 		-inline
-
-

Delete from metadata selected items

- -

Definition at line 1211 of file GalleryData.java.

-
1211  {
1212  for (int i = 0; i < selection.length; i++) {
1213  if (selection[i]) {
1214  md.removeObject(ids[i]);
1215  hasMdChanges = true;
1216  }
1217  }
1218  }
- -
xmipp.jni.MetaData.removeObject
native boolean removeObject(long objId)
- -
-
-
- -

◆ renderImages()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.renderImages ()
- 		-inline
-
- -

Definition at line 1453 of file GalleryData.java.

-
1453  {
1454  return renderImages;
1455  }
-
-
-
- -

◆ runObjectCommand()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.runObjectCommand (int index,
String objectCommand 
)
- 		-inline
-
- -

Definition at line 149 of file GalleryData.java.

-
149  {
150  try {
151  String[] cmd = new String[]{objectCommand};
152  System.out.println(Arrays.toString(cmd));
153  } catch (Exception ex) {
154  Logger.getLogger(GalleryData.class.getName()).log(Level.SEVERE, null, ex);
155  }
156  }
xmipp.viewer.models.GalleryData.GalleryData
GalleryData(GalleryJFrame window, String fn, Params parameters)
Definition: GalleryData.java:220
-
-
-
- -

◆ saveAll()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.saveAll (String path,
boolean overwrite 
) throws Exception
- 		-inline
-
- -

Definition at line 1525 of file GalleryData.java.

-
1525  {
1526  String from = getFileName();
1527  String blockto = path;
1528  String to;
1529  String block;
1530  if (blockto.contains("@")) {
1531  int sep = blockto.lastIndexOf("@");
1532  block = blockto.substring(0, sep);
1533  to = blockto.substring(sep + 1, blockto.length());
1534  } else {
1535  to = blockto;
1536  blockto = selectedBlock + "@" + blockto;
1537  block = selectedBlock;
1538  }
1539 
1540  if (from != null) {
1541  MetaData md;
1542  Hashtable<String, MetaData> mds = new Hashtable<String, MetaData>();
1543  for (String blockit : getBlocks()) {
1544  mds.put(blockit, getMetaData(blockit));
1545  }
1546  File file = new File(to);
1547  if (overwrite) {
1548  file.delete();
1549  }
1550  if (!file.exists() && file.getParentFile() != null) {
1551  file.getParentFile().mkdirs();
1552  }
1553  for (String blockit : getBlocks()) {
1554  md = mds.get(blockit);
1555  if (blockit.equals(selectedBlock)) {
1556  saveMd(blockto, true, overwrite);
1557  } else {
1558  md.writeBlock(blockit + "@" + to);
1559  }
1560  md.destroy();
1561  }
1562  } else {
1563  saveMd(blockto, true, overwrite);
1564  }
1565 
1566  setMdChanges(false);
1567  setFileName(to);
1568  if (blockto.contains("@")) {
1569  selectBlock(block);
1570  }
1571  }
-
xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
- - -
xmipp.viewer.models.GalleryData.saveMd
void saveMd(String path, boolean saveall, boolean isoverwrite)
Definition: GalleryData.java:1573
-
xmipp.viewer.models.GalleryData.selectBlock
void selectBlock(String block)
Definition: GalleryData.java:654
- -
xmipp.viewer.models.GalleryData.getMetaData
MetaData getMetaData(String block)
Definition: GalleryData.java:1612
- -
-
-
- -

◆ saveClassSelection()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.saveClassSelection (boolean [] selection,
String path 
)
- 		-inline
-
- -

Definition at line 1323 of file GalleryData.java.

-
1323  {
1324  try {
1325  saveSelection(selection, "classes" + Filename.SEPARATOR + path, true);
1326  MetaData imagesmd;
1327  // Fill the classX_images blocks
1328  for (int i = 0; i < selection.length; i++) {
1329  if (selection[i]) {
1330  long id = ids[i];
1331  int ref = md.getValueInt(MDLabel.MDL_REF, id);
1332  String blockName = Filename.getClassBlockName(ref);
1333  if (containsBlock(blockName)) {
1334  imagesmd = new MetaData(blockName + Filename.SEPARATOR + filename);
1335  imagesmd.writeBlock(blockName + Filename.SEPARATOR + path);
1336  imagesmd.destroy();
1337  }
1338  }
1339  }
1340 
1341  } catch (Exception ex) {
1342  Logger.getLogger(GalleryJFrame.class.getName()).log(Level.SEVERE, null, ex);
1343  }
1344  }
- -
xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
-
xmipp.viewer.models.GalleryData.containsBlock
boolean containsBlock(String block)
Definition: GalleryData.java:1132
-
xmipp.viewer.models.GalleryData.saveSelection
void saveSelection(boolean[] selection)
Definition: GalleryData.java:1353
- -
-
-
- -

◆ saveMd()

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void xmipp.viewer.models.GalleryData.saveMd (String path,
boolean saveall,
boolean isoverwrite 
) throws Exception
- 		-inline
-
- -

Definition at line 1573 of file GalleryData.java.

-
1573  {
1574  try {
1575 
1576  if (path == null) {
1577  throw new IllegalArgumentException();
1578  }
1579 
1580  boolean overwritewithblock;
1581  String file;
1582  if (path.contains("@")) {
1583  file = path.substring(path.lastIndexOf("@") + 1);
1584  } else {
1585  file = path;
1586  path = selectedBlock + "@" + file;
1587  }
1588 
1589  File iofile = new File(file);
1590  if (!iofile.exists())// overwrite or append, save active
1591  {
1592  if (iofile.getParentFile() != null) {
1593  iofile.getParentFile().mkdirs();
1594  }
1595  md.write(path);
1596  } else {
1597 
1598  overwritewithblock = isoverwrite && !saveall;
1599  if (overwritewithblock) {
1600  md.write(path);// overwrite with active block only,
1601  } // other blocks were dismissed
1602  else {
1603  md.writeBlock(path);// either if save active block or all, save active, other blocks where already managed
1604  }
1605  }
1606 
1607  } catch (Exception e) {
1608  e.printStackTrace();
1609  }
1610  }// function saveMd
xmipp.jni.MetaData.write
native void write(String filename)
- -
xmipp.jni.MetaData.writeBlock
native void writeBlock(String filename)
- -
-
-
- -

◆ saveSelection() [1/2]

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-
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void xmipp.viewer.models.GalleryData.saveSelection (boolean [] selection) throws Exception
- 		-inline
-
-

Save selected items as a metadata

- -

Definition at line 1353 of file GalleryData.java.

-
1353  {
1354 
1355  SaveJDialog dlg = new SaveJDialog(window, "selection" + getFileExtension(), true);
1356  boolean save = dlg.showDialog();
1357  if (save) {
1358  boolean overwrite = dlg.isOverwrite();
1359  String path = dlg.getMdFilename();
1360  saveSelection(selection, path, overwrite);
1361  }
1362 
1363  }
-
xmipp.viewer.models.GalleryData.saveSelection
void saveSelection(boolean[] selection)
Definition: GalleryData.java:1353
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-
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◆ saveSelection() [2/2]

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-
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- - - - - - - - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.saveSelection (boolean [] selection,
String path,
boolean overwrite 
) throws Exception
- 		-inline
-
-

Save selected items as a metadata

- -

Definition at line 1368 of file GalleryData.java.

-
1368  {
1369  MetaData md = getSelectionMd(selection);
1370 
1371  String file = path.substring(path.lastIndexOf("@") + 1, path.length());
1372  if (!new File(file).exists())// overwrite or append, save selection
1373  {
1374  md.write(path);
1375  } else {
1376  if (overwrite) {
1377  md.write(path);// overwrite with active block only, other
1378  } // blocks were dismissed
1379  else {
1380  md.writeBlock(path);// append selection
1381  }
1382  }
1383 
1384  md.destroy();
1385  }
xmipp.viewer.models.GalleryData.getSelectionMd
MetaData getSelectionMd(boolean[] selection)
Definition: GalleryData.java:1011
- -
-
-
- -

◆ selectBlock()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.selectBlock (String block)
- 		-inline
-
-

Select one of the blocks

- -

Definition at line 654 of file GalleryData.java.

-
654  {
655  selectedBlock = block;
656  selectedVolFn = ""; // Set to empty string to get the first vol
657  readMd();
658  }
- - -
-
-
- -

◆ selectVolumeAt()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.selectVolumeAt (int selectedIndex)
- 		-inline
-
- -

Definition at line 167 of file GalleryData.java.

-
167  {
168  String vol = getVolumeAt(selectedIndex);
169  String file = vol;
170  if (vol.contains(":"))
171  file = vol.substring(0, vol.lastIndexOf(":"));
172  if (vol.contains("@"))
173  file = file.substring(file.lastIndexOf("@") + 1);
174  if(new File(file).exists())
175  {
176  selectedVolFn = vol;
177  }
178  else
179  throw new IllegalArgumentException(XmippMessage.getPathNotExistsMsg(file));
180  }
- -
-
-
- -

◆ setDisplayLabel()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.setDisplayLabel (String key,
boolean selected 
)
- 		-inline
-
- -

Definition at line 361 of file GalleryData.java.

-
361  {
362  if(!selected)
363  {
364  displaycis.remove(key);
365  return;
366  }
367 
368  for(ColumnInfo ci: labels)
369  if(ci.labelName.equals(key))
370  {
371  displaycis.put(key, ci);
372  break;
373  }
374  }
xmipp.viewer.models.GalleryData.displaycis
HashMap< String, ColumnInfo > displaycis
Definition: GalleryData.java:72
- -
-
-
- -

◆ setEnabled()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.setEnabled (int index,
boolean value 
)
- 		-inline
-
-

Set enabled state

- -

Definition at line 805 of file GalleryData.java.

-
805  {
806  try {
807  if (!isVolumeMode()) { // slices in a volume are always enabled
808  md.setEnabled(value, ids[index]);
809  hasMdChanges = true;
810  }
811  } catch (Exception e) {
812  e.printStackTrace();
813  }
814  }
- - -
xmipp.jni.MetaData.setEnabled
boolean setEnabled(boolean value, long objId)
Definition: MetaData.java:442
- -
-
-
- -

◆ setFileName()

- -
-
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- - - - - - - - -
void xmipp.viewer.models.GalleryData.setFileName (String file)
- 		-inline
-
- -

Definition at line 343 of file GalleryData.java.

-
343  {
344  filename = file;
345  if (file != null) {
346  if (Filename.hasPrefix(file)) {
347  if (Filename.isMetadata(file)) {
348  selectedBlock = Filename.getPrefix(file);
349  filename = Filename.getFilename(file);
350  }
351  }
352  if (Filename.exists(filename)) {
353  mdBlocks = MetaData.getBlocksInMetaDataFile(filename);
354  if (mdBlocks.length >= 1 && selectedBlock.isEmpty()) {
355  selectedBlock = mdBlocks[0];
356  }
357  }
358  }
359  }
- - -
-
-
- -

◆ setItemClass()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.setItemClass (int index,
ClassInfo cli 
)
- 		-inline
-
-

Set the class of an element

- -

Definition at line 923 of file GalleryData.java.

-
923  {
924  hasClassesChanges = true;
925  classes[index] = cli;
926  long id = ids[index];
927  setItemClassInfo(id, cli);
928  }
- - -
-
-
- -

◆ setMdChanges()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setMdChanges (boolean value)
- 		-inline
-
- -

Definition at line 1246 of file GalleryData.java.

-
1246  {
1247  hasMdChanges = value;
1248  }
-
-
-
- -

◆ setModelDim()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.setModelDim (Integer rows,
Integer cols 
)
- 		-inline
-
- -

Definition at line 187 of file GalleryData.java.

-
187  {
188  if(cols != null && cols == 0)
189  throw new IllegalArgumentException(XmippMessage.getIllegalValueMsg("columns", 0));
190  this.rows = rows;
191  this.columns = cols;
192  }
-
-
-
- -

◆ setOrderLabels()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setOrderLabels (String [] orderLabels)
- 		-inline
-
- -

Definition at line 1828 of file GalleryData.java.

-
1828  {
1829  this.orderLabels = orderLabels;
1830  }
-
-
-
- -

◆ setRenderColumn()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setRenderColumn (String key)
- 		-inline
-
- -

Definition at line 297 of file GalleryData.java.

-
297  {
298  if(key.equalsIgnoreCase("none"))
299  ciFirstRender = null;
300  for(ColumnInfo ci: labels)
301  if(ci.labelName.equals(key))
302  ciFirstRender = ci;
303  renderLabel = ciFirstRender.labelName;
304  }
- - - -
-
-
- -

◆ setRenderLabel()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setRenderLabel (String renderLabel)
- 		-inline
-
- -

Definition at line 1832 of file GalleryData.java.

-
1832  {
1833  this.renderLabel = renderLabel;
1834  }
-
-
-
- -

◆ setRenderLabels()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setRenderLabels (String [] renderLabels)
- 		-inline
-
- -

Definition at line 1820 of file GalleryData.java.

-
1820  {
1821  this.renderLabels = renderLabels;
1822  }
-
-
-
- -

◆ setResliceView()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setResliceView (int view)
- 		-inline
-
- -

Definition at line 1445 of file GalleryData.java.

-
1445  {
1446  resliceView = view;
1447  }
-
-
-
- -

◆ setRow()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.setRow (MDRow mdRow,
long objId 
)
- 		-inline
-
-

Set all values coming from a row md

- -

Definition at line 819 of file GalleryData.java.

-
819  {
820  md.setRow(mdRow, objId);
821  setMdChanges(true);
822  }
xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
- -
xmipp.jni.MetaData.setRow
native void setRow(MDRow mdRow, long objId)
-
-
-
- -

◆ setValueString()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - -
boolean xmipp.viewer.models.GalleryData.setValueString (int label,
String newValue,
long l 
)
- 		-inline
-
- -

Definition at line 1431 of file GalleryData.java.

-
1431  {
1432  return md.setValueString(label, newValue, l);
1433  }
xmipp.jni.MetaData.setValueString
native boolean setValueString(int label, String value, long objId)
- -
-
-
- -

◆ setValueToCol()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.setValueToCol (int index,
ColumnInfo ci,
String value 
)
- 		-inline
-
- -

Definition at line 1199 of file GalleryData.java.

-
1199  {
1200  try {
1201  md.setValueString(ci.label, value, ids[index]);
1202  setMdChanges(true);
1203  } catch (Exception e) {
1204  e.printStackTrace();
1205  }
1206  }
xmipp.jni.MetaData.setValueString
native boolean setValueString(int label, String value, long objId)
-
xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
- - -
-
-
- -

◆ setVisibleLabels()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setVisibleLabels (String [] visibleLabels)
- 		-inline
-
- -

Definition at line 1824 of file GalleryData.java.

-
1824  {
1825  this.visibleLabels = visibleLabels;
1826  }
-
-
-
- -

◆ setWindow()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setWindow (GalleryJFrame frame)
- 		-inline
-
- -

Definition at line 1642 of file GalleryData.java.

-
1642  {
1643  window = frame;
1644  }
-
-
-
- -

◆ setZoom()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.setZoom (int zoom)
- 		-inline
-
- -

Definition at line 1935 of file GalleryData.java.

-
1936  {
1937  this.zoom = zoom;
1938  }
-
-
-
- -

◆ showCTF()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.showCTF (boolean profile,
int row,
boolean [] selection,
TasksEngine ctfTasks 
)
- 		-inline
-
- -

Definition at line 1742 of file GalleryData.java.

-
1742  {
1743  try {
1744  long id = ids[row];
1745 
1746  String psd = md.getPSDFile(id);
1747  String psden = md.getPSDEnhanced(id);
1748 
1749  boolean noPsdEnhanced = (psden == null);
1750  // Use the same PSD image in case no PSD enhanced
1751 
1752  if (noPsdEnhanced)
1753  psden = psd;
1754 
1755  if (profile)
1756  {
1757  if (noPsdEnhanced)
1758  new CTFAnalyzerJFrame(psden, md.getCTFDescription(id), psd, md.getEllipseCTF(id).getSamplingRate());
1759  else
1760  new CTFAnalyzerJFrame(psden, md.getCTFFile(id), psd);
1761  }
1762  else
1763  {
1764  ImageGeneric img = new ImageGeneric(psden);
1765  ImagePlus imp = XmippImageConverter.readToImagePlus(img);
1766  img.destroy();
1767  EllipseCTF ctfparams = md.getEllipseCTF(id, imp.getWidth());
1768  String sortfn = createSortFile(psd, row);
1769  XmippUtil.showImageJ(Tool.VIEWER); // removed Toolbar.FREEROI
1770  CTFRecalculateImageWindow ctfiw = new CTFRecalculateImageWindow(this, selection, imp, psd, ctfparams,
1771  ctfTasks, row, sortfn);
1772  }
1773 
1774  } catch (Exception e) {
1775  XmippDialog.showError(window, e.getMessage());
1776  }
1777  }
xmipp.jni.MetaData.getEllipseCTF
EllipseCTF getEllipseCTF(long id)
Definition: MetaData.java:605
-
xmipp.jni.MetaData.getPSDFile
String getPSDFile(long id)
Definition: MetaData.java:633
- - - -
xmipp.jni.MetaData.getPSDEnhanced
String getPSDEnhanced(long id)
Definition: MetaData.java:637
-
xmipp.jni.MetaData.getCTFFile
String getCTFFile(long id)
Definition: MetaData.java:600
- -
xmipp.viewer.models.GalleryData.createSortFile
String createSortFile(String psdFile, int row)
Definition: GalleryData.java:1478
-
xmipp.jni.MetaData.getCTFDescription
CTFDescription getCTFDescription(long id)
Definition: MetaData.java:641
-
-
-
- -

◆ size()

- -
-
- - - - - -
- - - - - - - -
int xmipp.viewer.models.GalleryData.size ()
- 		-inline
-
- -

Definition at line 1387 of file GalleryData.java.

-
1387  {
1388  return ids.length;
1389  }
-
-
-
- -

◆ sortMd()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.models.GalleryData.sortMd (ColumnInfo sortci,
boolean asc 
)
- 		-inline
-
-

Sort the metadata by a given column. The sort could be ascending or descending

- -

Definition at line 624 of file GalleryData.java.

-
624  {
625  try {
626  if(sortby == null)
627  sortby = new String[2];
628  sortby[0] = sortci.labelName;
629  sortby[1] = (asc)? "ASC": "DESC";
630  md.sort(sortci.label, asc);
631  hasMdChanges = true;
632  ids = md.findObjects();
633  } catch (Exception e) {
634  e.printStackTrace();
635  }
636  }
-
xmipp.jni.MetaData.sort
native void sort(int sortLabel, boolean ascending)
- -
xmipp.jni.MetaData.findObjects
native long [] findObjects()
- - -
-
-
- -

◆ updateClassesInfo()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.models.GalleryData.updateClassesInfo ()
- 		-inline
-
-

Compute and update the number of classes and images assigned to this superclass

- -

Definition at line 938 of file GalleryData.java.

-
938  {
939  try {
940  int i = 0;
941  for (ClassInfo cli : classesArray) {
942  cli.numberOfClasses = 0;
943  cli.numberOfImages = 0;
944  cli.index = i++;
945  }
946  i = 0;
947  for (long id : ids) { // iterate over all references
948  long count = md.getValueLong(MDLabel.MDL_CLASS_COUNT, id);
949 
950  ClassInfo cli = getItemClassInfo(i);
951  if (cli != null) {
952  cli.numberOfClasses += 1;
953  cli.numberOfImages += count;
954  hasMdChanges = true;
955  }
956  setItemClassInfo(id, cli);
957  ++i;
958  }
959  } catch (Exception e) {
960  // TODO Auto-generated catch block
961  e.printStackTrace();
962  }
963  }// function upateClassesInfo
xmipp.jni.MetaData.getValueLong
native long getValueLong(int label, long objId)
-
xmipp.viewer.models.GalleryData.getItemClassInfo
ClassInfo getItemClassInfo(int index)
Definition: GalleryData.java:892
- - -
xmipp.viewer.models.GalleryData.classesArray
ArrayList< ClassInfo > classesArray
Definition: GalleryData.java:106
- -
-
-
- -

◆ useGeo()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.models.GalleryData.useGeo ()
- 		-inline
-
- -

Definition at line 1395 of file GalleryData.java.

-
1395  {
1396  return useGeo;
1397  }
-
-
-
- -

◆ write()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.models.GalleryData.write (String path)
- 		-inline
-
- -

Definition at line 1646 of file GalleryData.java.

-
1646  {
1647  md.write(path);
1648  }
xmipp.jni.MetaData.write
native void write(String filename)
- -
-
-
-

Member Data Documentation

- -

◆ ciFirstRender

- -
-
- - - - - -
- - - - -
ColumnInfo xmipp.viewer.models.GalleryData.ciFirstRender = null
- 		-protected
-
- -

Definition at line 83 of file GalleryData.java.

- -
-
- -

◆ classes

- -
-
- - - - - -
- - - - -
ClassInfo [] xmipp.viewer.models.GalleryData.classes
- 		-protected
-
- -

Definition at line 108 of file GalleryData.java.

- -
-
- -

◆ classesArray

- -
-
- - - - - -
- - - - -
ArrayList<ClassInfo> xmipp.viewer.models.GalleryData.classesArray
- 		-protected
-
- -

Definition at line 106 of file GalleryData.java.

- -
-
- -

◆ displaycis

- -
-
- - - - - -
- - - - -
HashMap<String, ColumnInfo> xmipp.viewer.models.GalleryData.displaycis
- 		-protected
-
- -

Definition at line 72 of file GalleryData.java.

- -
-
- -

◆ displayLabels

- -
-
- - - - - -
- - - - -
String [] xmipp.viewer.models.GalleryData.displayLabels
- 		-protected
-
- -

Definition at line 113 of file GalleryData.java.

- -
-
- -

◆ filename

- -
-
- - - - - -
- - - - -
String xmipp.viewer.models.GalleryData.filename
- 		-protected
-
- -

Definition at line 85 of file GalleryData.java.

- -
-
- -

◆ hasMdChanges

- -
-
- - - - - -
- - - - -
boolean xmipp.viewer.models.GalleryData.hasMdChanges
- 		-protected
-
- -

Definition at line 110 of file GalleryData.java.

- -
-
- -

◆ ids

- -
-
- - - - - -
- - - - -
long [] xmipp.viewer.models.GalleryData.ids
- 		-protected
-
- -

Definition at line 74 of file GalleryData.java.

- -
-
- -

◆ inverty

- -
-
- - - - - -
- - - - -
boolean xmipp.viewer.models.GalleryData.inverty
- 		-protected
-
- -

Definition at line 125 of file GalleryData.java.

- -
-
- -

◆ isClassification

- -
-
- - - - - -
- - - - -
boolean xmipp.viewer.models.GalleryData.isClassification = false
- 		-protected
-
- -

Definition at line 100 of file GalleryData.java.

- -
-
- -

◆ isVolumeMd

- -
-
- - - - - -
- - - - -
boolean xmipp.viewer.models.GalleryData.isVolumeMd
- 		-protected
-
- -

Definition at line 116 of file GalleryData.java.

- -
-
- -

◆ labels

- -
-
- - - - - -
- - - - -
List<ColumnInfo> xmipp.viewer.models.GalleryData.labels = null
- 		-protected
-
- -

Definition at line 81 of file GalleryData.java.

- -
-
- -

◆ MAX_SIZE

- -
-
- - - - - -
- - - - -
int xmipp.viewer.models.GalleryData.MAX_SIZE = 256
- 		-static
-
- -

Definition at line 218 of file GalleryData.java.

- -
-
- -

◆ md

- -
-
- - - - - -
- - - - -
MetaData xmipp.viewer.models.GalleryData.md
- 		-protected
-
- -

Definition at line 73 of file GalleryData.java.

- -
-
- -

◆ mdBlocks

- -
-
- - - - - -
- - - - -
String [] xmipp.viewer.models.GalleryData.mdBlocks = null
- 		-protected
-
- -

Definition at line 75 of file GalleryData.java.

- -
-
- -

◆ MIN_SIZE

- -
-
- - - - - -
- - - - -
int xmipp.viewer.models.GalleryData.MIN_SIZE = 16
- 		-static
-
- -

Definition at line 217 of file GalleryData.java.

- -
-
- -

◆ mode

- -
-
- - - - - -
- - - - -
Mode xmipp.viewer.models.GalleryData.mode
- 		-protected
-
- -

Definition at line 87 of file GalleryData.java.

- -
-
- -

◆ normalize

- -
-
- - - - - -
- - - - -
boolean xmipp.viewer.models.GalleryData.normalize = false
- 		-protected
-
- -

Definition at line 94 of file GalleryData.java.

- -
-
- -

◆ orderLabels

- -
-
- - - - - -
- - - - -
String [] xmipp.viewer.models.GalleryData.orderLabels
- 		-protected
-
- -

Definition at line 124 of file GalleryData.java.

- -
-
- -

◆ parameters

- -
-
- - - - -
final Params xmipp.viewer.models.GalleryData.parameters
-
- -

Definition at line 90 of file GalleryData.java.

- -
-
- -

◆ refLabel

- -
-
- - - - - -
- - - - -
int xmipp.viewer.models.GalleryData.refLabel
- 		-protected
-
- -

Definition at line 101 of file GalleryData.java.

- -
-
- -

◆ renderImages

- -
-
- - - - - -
- - - - -
boolean xmipp.viewer.models.GalleryData.renderImages
- 		-protected
-
- -

Definition at line 89 of file GalleryData.java.

- -
-
- -

◆ renderLabel

- -
-
- - - - - -
- - - - -
String xmipp.viewer.models.GalleryData.renderLabel = "first"
- 		-protected
-
- -

Definition at line 122 of file GalleryData.java.

- -
-
- -

◆ renderLabels

- -
-
- - - - - -
- - - - -
String [] xmipp.viewer.models.GalleryData.renderLabels
- 		-protected
-
- -

Definition at line 121 of file GalleryData.java.

- -
-
- -

◆ resliceView

- -
-
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Definition at line 86 of file GalleryData.java.

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Definition at line 117 of file GalleryData.java.

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Definition at line 76 of file GalleryData.java.

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Definition at line 78 of file GalleryData.java.

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Definition at line 88 of file GalleryData.java.

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Definition at line 114 of file GalleryData.java.

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Definition at line 96 of file GalleryData.java.

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Definition at line 123 of file GalleryData.java.

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Definition at line 111 of file GalleryData.java.

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Definition at line 98 of file GalleryData.java.

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Definition at line 84 of file GalleryData.java.

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The documentation for this class was generated from the following file: -
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-} diff --git a/html/classxmipp_1_1viewer_1_1models_1_1GalleryData__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1models_1_1GalleryData__coll__graph.md5 deleted file mode 100644 index 8a0773a6..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1GalleryData__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -250333957536f445aa09298d7a561388 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1models_1_1GalleryData__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1models_1_1GalleryData__inherit__graph.dot deleted file mode 100644 index bdb30cc0..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1GalleryData__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.models.GalleryData" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.models.GalleryData",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; 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xmipp.viewer.models.GalleryRowHeaderModel Member List
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This is the complete list of members for xmipp.viewer.models.GalleryRowHeaderModel, including all inherited members.

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addListDataListener(ListDataListener ll)xmipp.viewer.models.GalleryRowHeaderModelinline
GalleryRowHeaderModel(int n, int first_index)xmipp.viewer.models.GalleryRowHeaderModelinline
GalleryRowHeaderModel(int n)xmipp.viewer.models.GalleryRowHeaderModelinline
GalleryRowHeaderModel(GalleryData data)xmipp.viewer.models.GalleryRowHeaderModelinline
getElementAt(int i)xmipp.viewer.models.GalleryRowHeaderModelinline
getSize()xmipp.viewer.models.GalleryRowHeaderModelinline
removeListDataListener(ListDataListener ll)xmipp.viewer.models.GalleryRowHeaderModelinline
setSize(int n)xmipp.viewer.models.GalleryRowHeaderModelinline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1models_1_1GalleryRowHeaderModel.html b/html/classxmipp_1_1viewer_1_1models_1_1GalleryRowHeaderModel.html deleted file mode 100644 index ff0dee3a..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1GalleryRowHeaderModel.html +++ /dev/null @@ -1,359 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.models.GalleryRowHeaderModel Class Reference - - - - - - - - - -
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xmipp.viewer.models.GalleryRowHeaderModel Class Reference
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-Public Member Functions

 GalleryRowHeaderModel (int n, int first_index)
 
 GalleryRowHeaderModel (int n)
 
 GalleryRowHeaderModel (GalleryData data)
 
int getSize ()
 
void setSize (int n)
 
Object getElementAt (int i)
 
void addListDataListener (ListDataListener ll)
 
void removeListDataListener (ListDataListener ll)
 
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Detailed Description

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Definition at line 31 of file GalleryRowHeaderModel.java.

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Constructor & Destructor Documentation

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◆ GalleryRowHeaderModel() [1/3]

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xmipp.viewer.models.GalleryRowHeaderModel.GalleryRowHeaderModel (int n,
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Definition at line 36 of file GalleryRowHeaderModel.java.

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38  this.first_index = first_index;
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Definition at line 42 of file GalleryRowHeaderModel.java.

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Definition at line 46 of file GalleryRowHeaderModel.java.

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47  this.data = data;
48  }
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◆ addListDataListener()

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void xmipp.viewer.models.GalleryRowHeaderModel.addListDataListener (ListDataListener ll)
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Definition at line 66 of file GalleryRowHeaderModel.java.

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Definition at line 60 of file GalleryRowHeaderModel.java.

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61  if (data != null)
62  return data.labels.get(i).labelName;
63  return new Integer(first_index + i);
64  }
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Definition at line 50 of file GalleryRowHeaderModel.java.

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51  if (data != null)
52  return data.labels.size();
53  return n;
54  }
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Definition at line 69 of file GalleryRowHeaderModel.java.

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Definition at line 56 of file GalleryRowHeaderModel.java.

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57  this.n = n;
58  }
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xmipp.viewer.models.ImageGalleryTableModel Member List
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This is the complete list of members for xmipp.viewer.models.ImageGalleryTableModel, including all inherited members.

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adjustColumn(int width)xmipp.viewer.models.ImageGalleryTableModelinline
adjustColumnsWidth()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
adjustWidthxmipp.viewer.models.ImageGalleryTableModel
busyRowsxmipp.viewer.models.ImageGalleryTableModelprotected
cachexmipp.viewer.models.ImageGalleryTableModelprotected
calculateCellSize()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
calculateMinAndMax()xmipp.viewer.models.ImageGalleryTableModelinline
cellDimxmipp.viewer.models.ImageGalleryTableModel
clearSelection()xmipp.viewer.models.ImageGalleryTableModelinline
columnModelxmipp.viewer.models.ImageGalleryTableModelprotected
createColumnModel()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
createItem(int index, String key, ColumnInfo ci)xmipp.viewer.models.ImageGalleryTableModelprotected
dataxmipp.viewer.models.ImageGalleryTableModel
dimensionxmipp.viewer.models.ImageGalleryTableModelprotected
getCellSize()xmipp.viewer.models.ImageGalleryTableModelinline
getColumn(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getColumnClass(int c)xmipp.viewer.models.ImageGalleryTableModelinline
getColumnCount()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnModel()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnName(int column)xmipp.viewer.models.ImageGalleryTableModelinline
getColumns()xmipp.viewer.models.ImageGalleryTableModelinline
getCoords(int index)xmipp.viewer.models.ImageGalleryTableModelinline
getFirstSelectedIndex()xmipp.viewer.models.ImageGalleryTableModelinline
getId(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getImageHeight()xmipp.viewer.models.ImageGalleryTableModelinline
getImageLoader()xmipp.viewer.models.ImageGalleryTableModel
getImageWidth()xmipp.viewer.models.ImageGalleryTableModelinline
getIndex(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getItemKey(int index)xmipp.viewer.models.ImageGalleryTableModel
getItemKey(int index, int label)xmipp.viewer.models.ImageGalleryTableModelinline
getLabel(int row, int col)xmipp.viewer.models.ImageGalleryTableModel
getMinAndMax()xmipp.viewer.models.ImageGalleryTableModelprotected
getRenderer()xmipp.viewer.models.ImageGalleryTableModelinline
getRowCount()xmipp.viewer.models.ImageGalleryTableModelinline
getRows()xmipp.viewer.models.ImageGalleryTableModelinline
getSelection()xmipp.viewer.models.ImageGalleryTableModelinline
getSelectionCount()xmipp.viewer.models.ImageGalleryTableModelinline
getSelFrom()xmipp.viewer.models.ImageGalleryTableModelinline
getSelTo()xmipp.viewer.models.ImageGalleryTableModelinline
getSize()xmipp.viewer.models.ImageGalleryTableModelinline
getTableHeaderModel()xmipp.viewer.models.ImageGalleryTableModelinline
getTitle()xmipp.viewer.models.ImageGalleryTableModel
getValueAt(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
gotoItem(int i)xmipp.viewer.models.ImageGalleryTableModelinline
handleDoubleClick(int row, int col)xmipp.viewer.models.ImageGalleryTableModel
handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)xmipp.viewer.models.ImageGalleryTableModel
hasSelection()xmipp.viewer.models.ImageGalleryTableModelinline
image_widthxmipp.viewer.models.ImageGalleryTableModelprotected
ImageGalleryTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.ImageGalleryTableModelinline
isBusy(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isSelected(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isSelected(int index)xmipp.viewer.models.ImageGalleryTableModelinline
isValidIndex(int index)xmipp.viewer.models.ImageGalleryTableModelinline
loadDimension()xmipp.viewer.models.ImageGalleryTableModelprotected
nxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_calculatedxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_minxmipp.viewer.models.ImageGalleryTableModelprotected
refreshAt(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
refreshRow(int row)xmipp.viewer.models.ImageGalleryTableModelinline
removeClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
rendererxmipp.viewer.models.ImageGalleryTableModelprotected
resizeCache()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
rowsxmipp.viewer.models.ImageGalleryTableModelprotected
scalexmipp.viewer.models.ImageGalleryTableModelprotected
selectionxmipp.viewer.models.ImageGalleryTableModelprotected
selectRange(int first_index, int last_index, boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
selectRange(int first_row, int first_col, int last_row, int last_col)xmipp.viewer.models.ImageGalleryTableModelinline
setColumns(int cols)xmipp.viewer.models.ImageGalleryTableModelinline
setColumnsValue(int cols)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setInvertY(boolean itemSelected)xmipp.viewer.models.ImageGalleryTableModelinline
setNormalized(boolean normalize)xmipp.viewer.models.ImageGalleryTableModelinline
setRowBusy(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRowIdle(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRows(int rows)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int index, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int row, int col, boolean b)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionEnabled(boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
setShowLabels()xmipp.viewer.models.ImageGalleryTableModelinline
setupItem(ImageItem item)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setupTable(JTable table)xmipp.viewer.models.ImageGalleryTableModelinline
setZoom(int z)xmipp.viewer.models.ImageGalleryTableModelinline
setZoomValue(int z)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
showLabels()xmipp.viewer.models.ImageGalleryTableModel
thumb_widthxmipp.viewer.models.ImageGalleryTableModelprotected
touchItem(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
touchItem(int row, int col, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
updateTableSelection(JTable table)xmipp.viewer.models.ImageGalleryTableModelinline
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xmipp.viewer.models.ImageGalleryTableModel Class Referenceabstract
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-Classes

class  ImageItem
 
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-Public Member Functions

 ImageGalleryTableModel (GalleryData data, boolean[] selection) throws Exception
 
int getImageWidth ()
 
int getImageHeight ()
 
int getColumnCount ()
 
int getRowCount ()
 
String getColumnName (int column)
 
Class getColumnClass (int c)
 
Object getValueAt (int row, int col)
 
void refreshAt (int row, int col)
 
void setRows (int rows)
 
void setColumns (int cols)
 
boolean adjustColumn (int width)
 
int getSize ()
 
Dimension getCellSize ()
 
void setupTable (JTable table)
 
void updateTableSelection (JTable table)
 
ImageItemRenderer getRenderer ()
 
GalleryColumnModel getColumnModel ()
 
JTableHeader getTableHeaderModel ()
 
void setZoom (int z)
 
int getIndex (int row, int col)
 
long getId (int row, int col)
 
boolean isValidIndex (int index)
 
abstract String getLabel (int row, int col)
 
Point getCoords (int index)
 
void setSelectionEnabled (boolean value)
 
int getFirstSelectedIndex ()
 
void selectRange (int first_index, int last_index, boolean value)
 
void selectRange (int first_row, int first_col, int last_row, int last_col)
 
void setSelectionClass (int classNumber)
 
void removeClass (int classNumber)
 
void touchItem (int row, int col)
 
void touchItem (int row, int col, boolean isselected)
 
void gotoItem (int i)
 
void setNormalized (boolean normalize)
 
void calculateMinAndMax ()
 
abstract boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
abstract boolean handleDoubleClick (int row, int col)
 
void setShowLabels ()
 
abstract String getItemKey (int index) throws Exception
 
String getItemKey (int index, int label) throws Exception
 
abstract String getTitle ()
 
abstract ImagePlusLoader getImageLoader ()
 
boolean isSelected (int row, int col)
 
abstract boolean showLabels ()
 
void setInvertY (boolean itemSelected)
 
int getRows ()
 
int getColumns ()
 
boolean isBusy (int row, int col)
 
void setRowBusy (int row)
 
void setRowIdle (int row)
 
void refreshRow (int row)
 
void clearSelection ()
 
int getSelectionCount ()
 
boolean [] getSelection ()
 
void setSelected (int index, boolean isselected)
 
boolean isSelected (int index)
 
int getSelFrom ()
 
int getSelTo ()
 
boolean hasSelection ()
 
void setSelected (int row, int col, boolean b)
 
ColumnInfo getColumn (int row, int col)
 
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Dimension cellDim = new Dimension()
 
GalleryData data
 
boolean adjustWidth = true
 
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abstract ImageDimension loadDimension () throws Exception
 
void resizeCache ()
 
void setupItem (ImageItem item)
 
void setColumnsValue (int cols)
 
void calculateCellSize ()
 
void adjustColumnsWidth ()
 
GalleryColumnModel createColumnModel ()
 
void setZoomValue (int z)
 
abstract double [] getMinAndMax ()
 
abstract ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
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ArrayList< Integer > busyRows = new ArrayList<Integer>()
 
int rows
 
int n
 
int image_width
 
int thumb_width
 
float scale = (float) 1.
 
Cache< String, ImageItem > cache
 
ImageDimension dimension
 
ImageItemRenderer renderer = new ImageItemRenderer()
 
GalleryColumnModel columnModel
 
boolean normalize_calculated = false
 
double normalize_min = Double.POSITIVE_INFINITY
 
boolean [] selection
 
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Detailed Description

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Definition at line 51 of file ImageGalleryTableModel.java.

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Constructor & Destructor Documentation

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◆ ImageGalleryTableModel()

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xmipp.viewer.models.ImageGalleryTableModel.ImageGalleryTableModel (GalleryData data,
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Definition at line 94 of file ImageGalleryTableModel.java.

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94  {
95  this.data = data;
96  cols = 0;
97  dimension = loadDimension();
98  columnModel = createColumnModel();
99 
100  int zoom = 100;
101  if(data.getZoom() != null)
102  zoom = data.getZoom();
103  setZoomValue(zoom);
104  // This should be changed later after a call to
105  // setColumns or adjustColumns
106  if (cols < 1) {
107  cols = 1;
108  rows = n;
109  }
110  // DEBUG.printMessage(String.format("col: %d, rows: %d", cols, rows));
111  //resizeCache(); NOw this is done when setZoomValue
112  //might be that the number of items is the same and we keep selection, although it is a different metadata
113  if(selection == null)
114  this.selection = new boolean[data.ids.length];
115  else
116  this.selection = selection;
117 
118  }
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◆ adjustColumn()

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Definition at line 243 of file ImageGalleryTableModel.java.

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243  {
244  last_width = width;
245  int new_cols = Math.max(Math.min(width / cellDim.width, n), 1);
246  if (new_cols != cols) {
247  setColumnsValue(new_cols);
248  return true;
249  }
250  return false;
251  }
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void xmipp.viewer.models.ImageGalleryTableModel.adjustColumnsWidth ()
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Ajust the width of columns and headers

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Definition at line 307 of file ImageGalleryTableModel.java.

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307  {
308  // renderer.setPreferredSize(cellDim);
309  columnModel.setWidth(cellDim.width);
310  }
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void xmipp.viewer.models.ImageGalleryTableModel.calculateCellSize ()
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This function will be used to calculate all size need to render the image cell

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Definition at line 268 of file ImageGalleryTableModel.java.

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268  {
269  thumb_width = (int) (image_width * scale);
270  thumb_height = (int) (image_height * scale);
271 
272  font_height = 0;
273  if (data.isDisplayLabel()) {
274  font_height = renderer.getFontMetrics(renderer.getFont())
275  .getHeight();
276  font_height += renderer.getIconTextGap(); // Adds the extra gap.
277  // font_height -= table.getIntercellSpacing().height; // Removes
278  }
279 
280  int borderHeight = 0, borderWidth = 0;
281  Border border = renderer.getBorder();
282 
283  if (border != null) {
284  Insets insets = renderer.getBorder().getBorderInsets(renderer);
285  borderWidth = insets.left + insets.right;
286  borderHeight = insets.bottom + insets.top;
287  }
288  cellDim.setSize(thumb_width + 1 * borderWidth, thumb_height + 1
289  * borderHeight + font_height);
290  adjustColumnsWidth();
291  }
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Calculate min and max if needed for normalization

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Definition at line 500 of file ImageGalleryTableModel.java.

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500  {
501  if (!normalize_calculated) {
502  double[] mm = getMinAndMax();
503  normalize_min = mm[0];
504  normalize_max = mm[1];
505  normalize_calculated = true;
506  }
507  }
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Definition at line 742 of file ImageGalleryTableModel.java.

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742  {
743  for (int i = 0; i < selection.length; ++i) {
744  selection[i] = false;
745  }
746 
747  }
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Internal method to create the column model

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Definition at line 327 of file ImageGalleryTableModel.java.

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327  {
328  return new GalleryColumnModel(cellDim.width);
329  }
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◆ createItem()

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abstract ImageItem xmipp.viewer.models.ImageGalleryTableModel.createItem (int index,
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Function to create the image item. this should be implemented in subclasses of ImageGallery

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Definition at line 257 of file ImageGalleryTableModel.java.

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257  {
258  return cellDim;
259  }// function getCellSize
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Definition at line 816 of file ImageGalleryTableModel.java.

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817  {
818  return data.ciFirstRender;
819  }
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Definition at line 163 of file ImageGalleryTableModel.java.

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163  {
164  return ImageItem.class;
165  }
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Definition at line 148 of file ImageGalleryTableModel.java.

-
148  {
149  return cols;
150  }
-
-
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◆ getColumnModel()

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GalleryColumnModel xmipp.viewer.models.ImageGalleryTableModel.getColumnModel ()
- 		-inline
-
-

Return the column model to be used with this table model

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Definition at line 318 of file ImageGalleryTableModel.java.

-
318  {
319  return columnModel;
320  }
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◆ getColumnName()

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String xmipp.viewer.models.ImageGalleryTableModel.getColumnName (int column)
- 		-inline
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Definition at line 158 of file ImageGalleryTableModel.java.

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158  {
159  return String.format("%d", column + 1);
160  }
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◆ getColumns()

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int xmipp.viewer.models.ImageGalleryTableModel.getColumns ()
- 		-inline
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Definition at line 690 of file ImageGalleryTableModel.java.

-
691  {
692  return cols;
693  }
-
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◆ getCoords()

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Point xmipp.viewer.models.ImageGalleryTableModel.getCoords (int index)
- 		-inline
-
-

Return the row and col given an index

-
Parameters
- - -
index
-
-
-
Returns
- -

Definition at line 384 of file ImageGalleryTableModel.java.

-
384  {
385  Point p = new Point();
386  p.y = index / cols;
387  p.x = index % cols;
388  return p;
389  }
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◆ getFirstSelectedIndex()

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int xmipp.viewer.models.ImageGalleryTableModel.getFirstSelectedIndex ()
- 		-inline
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Definition at line 416 of file ImageGalleryTableModel.java.

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416  {
417  return getSelFrom();
418  }
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◆ getId()

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long xmipp.viewer.models.ImageGalleryTableModel.getId (int row,
int col 
)
- 		-inline
-
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Definition at line 364 of file ImageGalleryTableModel.java.

-
364  {
365  int index = getIndex(row, col);
366  return data.ids[index];
367 
368  }
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◆ getImageHeight()

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int xmipp.viewer.models.ImageGalleryTableModel.getImageHeight ()
- 		-inline
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Definition at line 127 of file ImageGalleryTableModel.java.

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128  {
129  return image_height;
130  }
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◆ getImageLoader()

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abstract ImagePlusLoader xmipp.viewer.models.ImageGalleryTableModel.getImageLoader ()
- 		-abstract
-
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Return the ImagePlusLoader subclass that handle the reading of the gallery representation as an ImagePlus

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◆ getImageWidth()

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int xmipp.viewer.models.ImageGalleryTableModel.getImageWidth ()
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Definition at line 122 of file ImageGalleryTableModel.java.

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123  {
124  return image_width;
125  }
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◆ getIndex()

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int xmipp.viewer.models.ImageGalleryTableModel.getIndex (int row,
int col 
)
- 		-inline
-
-

Calculate index base on x position and y position

-
Parameters
- - - -
xx position on table
yy position on table
-
-
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Returns
index of the element
- -

Definition at line 357 of file ImageGalleryTableModel.java.

-
357  {
358 
359  return row * cols + col;
360  }
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◆ getItemKey() [1/2]

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abstract String xmipp.viewer.models.ImageGalleryTableModel.getItemKey (int index) throws Exception
- 		-abstract
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-

Retrieve the image filename, return null if error Function to create the key of the item knowing the item index

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String xmipp.viewer.models.ImageGalleryTableModel.getItemKey (int index,
int label 
) throws Exception
- 		-inline
-
-

Return a key string using label

- -

Definition at line 548 of file ImageGalleryTableModel.java.

-
548  {
549  Object value = data.getValueFromLabel(index, label);
550 
551  String format = value + "_%d_%d(%d,%d)";
552  if (data.useGeo)
553  format += "_geo";
554  if (data.wrap)
555  format += "_wrap";
556  // String key = String.format(format, thumb_width, thumb_height);
557  // DEBUG.printMessage(String.format("key: %s", key));
558  String key = String.format(format, index, label, thumb_width, thumb_height);
559  return key;
560  }
- - -
xmipp.viewer.models.GalleryData.getValueFromLabel
String getValueFromLabel(int index, int label)
Definition: GalleryData.java:1190
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◆ getLabel()

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abstract String xmipp.viewer.models.ImageGalleryTableModel.getLabel (int row,
int col 
)
- 		-abstract
-
-

Return the label of the item at this position

- -
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◆ getMinAndMax()

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abstract double [] xmipp.viewer.models.ImageGalleryTableModel.getMinAndMax ()
- 		-abstractprotected
-
-

Retrieve the mininum and maximum of data

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◆ getRenderer()

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ImageItemRenderer xmipp.viewer.models.ImageGalleryTableModel.getRenderer ()
- 		-inline
-
-

Return the cell renderer to be used to draw images

- -

Definition at line 313 of file ImageGalleryTableModel.java.

-
313  {
314  return renderer;
315  }
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◆ getRowCount()

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int xmipp.viewer.models.ImageGalleryTableModel.getRowCount ()
- 		-inline
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Definition at line 153 of file ImageGalleryTableModel.java.

-
153  {
154  return rows;
155  }
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◆ getRows()

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int xmipp.viewer.models.ImageGalleryTableModel.getRows ()
- 		-inline
-
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Definition at line 684 of file ImageGalleryTableModel.java.

-
685  {
686  return rows;
687  }
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◆ getSelection()

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boolean [] xmipp.viewer.models.ImageGalleryTableModel.getSelection ()
- 		-inline
-
- -

Definition at line 765 of file ImageGalleryTableModel.java.

-
766  {
767  return selection;
768  }
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◆ getSelectionCount()

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int xmipp.viewer.models.ImageGalleryTableModel.getSelectionCount ()
- 		-inline
-
-

Return the number of selected elements

- -

Definition at line 752 of file ImageGalleryTableModel.java.

-
752  {
753  int count = 0;
754 
755  if (!data.isVolumeMode() && hasSelection()) {
756  for (int i = 0; i < selection.length; i++) {
757  if (selection[i]) {
758  count++;
759  }
760  }
761  }
762  return count;
763  }
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◆ getSelFrom()

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int xmipp.viewer.models.ImageGalleryTableModel.getSelFrom ()
- 		-inline
-
- -

Definition at line 785 of file ImageGalleryTableModel.java.

-
786  {
787  for(int i = 0; i < selection.length; i ++)
788  {
789  if(selection[i])
790  return i;
791  }
792  return -1;
793  }
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◆ getSelTo()

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int xmipp.viewer.models.ImageGalleryTableModel.getSelTo ()
- 		-inline
-
- -

Definition at line 795 of file ImageGalleryTableModel.java.

-
796  {
797  int selto = -1;
798  for(int i = 0; i < selection.length; i ++)
799  {
800  if(selection[i])
801  selto = i;
802  }
803  return selto;
804  }
-
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◆ getSize()

- -
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int xmipp.viewer.models.ImageGalleryTableModel.getSize ()
- 		-inline
-
- -

Definition at line 253 of file ImageGalleryTableModel.java.

-
253  {
254  return n;
255  }
-
-
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◆ getTableHeaderModel()

- -
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JTableHeader xmipp.viewer.models.ImageGalleryTableModel.getTableHeaderModel ()
- 		-inline
-
- -

Definition at line 322 of file ImageGalleryTableModel.java.

-
322  {
323  return new JTableHeader(columnModel);
324  }
-
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◆ getTitle()

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abstract String xmipp.viewer.models.ImageGalleryTableModel.getTitle ()
- 		-abstract
-
-

Return the main title to be used on windows

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◆ getValueAt()

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Object xmipp.viewer.models.ImageGalleryTableModel.getValueAt (int row,
int col 
)
- 		-inline
-
- -

Definition at line 168 of file ImageGalleryTableModel.java.

-
168  {
169  int index = getIndex(row, col);
170  if (isValidIndex(index)) {
171  try {
172  String key = getItemKey(index);
173  ImageItem item;
174  // If the element is on cache, just return it
175  if (cache.containsKey(key))
176  item = cache.get(key);
177  else {
178 // // If not, create the item and store it for future
179  item = createItem(index, key, getColumn(row, col));
180  cache.put(key, item);
181  }
182  setupItem(item);
183  return item;
184  } catch (Exception e) {
185  e.printStackTrace();
186  }
187  }
188 
189  return null;
190  }
- - -
xmipp.viewer.models.ImageGalleryTableModel.createItem
abstract ImageItem createItem(int index, String key, ColumnInfo ci)
- -
xmipp.viewer.models.ImageGalleryTableModel.getItemKey
abstract String getItemKey(int index)
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◆ gotoItem()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.gotoItem (int i)
- 		-inline
-
-

Goto and select specified item, if there is a selection it will be cleared

- -

Definition at line 477 of file ImageGalleryTableModel.java.

-
477  {
478  clearSelection();
479  setSelected(i, !isSelected(i));
480  Point coords = getCoords(i);
481  fireTableCellUpdated(coords.y, coords.x);
482  }
-
xmipp.viewer.models.ImageGalleryTableModel.setSelected
void setSelected(int index, boolean isselected)
Definition: ImageGalleryTableModel.java:770
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◆ handleDoubleClick()

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abstract boolean xmipp.viewer.models.ImageGalleryTableModel.handleDoubleClick (int row,
int col 
)
- 		-abstract
-
-

This function will be called when a double click is performed under the element at specified row and column

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◆ handleRightClick()

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abstract boolean xmipp.viewer.models.ImageGalleryTableModel.handleRightClick (int row,
int col,
XmippPopupMenuCreator xpopup 
)
- 		-abstract
-
-

This function will be called when a right click is fired from the UI, the col and row of cell where the event was produced and also the JPopupMenu This function will serve to personalize the menu before showing or event not show at all if the return is false

- -
-
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◆ hasSelection()

- -
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boolean xmipp.viewer.models.ImageGalleryTableModel.hasSelection ()
- 		-inline
-
- -

Definition at line 806 of file ImageGalleryTableModel.java.

-
806  {
807  if(getSelFrom() == -1)
808  return false;
809  return true;
810  }
-
-
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◆ isBusy()

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boolean xmipp.viewer.models.ImageGalleryTableModel.isBusy (int row,
int col 
)
- 		-inline
-
-

Check if the item is busy

- -

Definition at line 697 of file ImageGalleryTableModel.java.

-
697  {
698  return busyRows.contains(row);
699  }
-
-
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◆ isSelected() [1/2]

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boolean xmipp.viewer.models.ImageGalleryTableModel.isSelected (int row,
int col 
)
- 		-inline
-
- -

Definition at line 585 of file ImageGalleryTableModel.java.

-
585  {
586  int index = getIndex(row, col);
587  return isSelected(index);
588  }
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◆ isSelected() [2/2]

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boolean xmipp.viewer.models.ImageGalleryTableModel.isSelected (int index)
- 		-inline
-
- -

Definition at line 780 of file ImageGalleryTableModel.java.

-
780  {
781 
782  return selection[index];
783  }
-
-
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◆ isValidIndex()

- -
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boolean xmipp.viewer.models.ImageGalleryTableModel.isValidIndex (int index)
- 		-inline
-
-

Check if the index is inside bounds

- -

Definition at line 371 of file ImageGalleryTableModel.java.

-
371  {
372  return index >= 0 && index < n;
373  }
-
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◆ loadDimension()

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abstract ImageDimension xmipp.viewer.models.ImageGalleryTableModel.loadDimension () throws Exception
- 		-abstractprotected
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◆ refreshAt()

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void xmipp.viewer.models.ImageGalleryTableModel.refreshAt (int row,
int col 
)
- 		-inline
-
-

Function to force the refresh of some item

- -

Definition at line 193 of file ImageGalleryTableModel.java.

-
193  {
194 
195  int index = getIndex(row, col);
196 
197  if (isValidIndex(index)) {
198  try {
199  String key = getItemKey(index, data.getLabelFromCol(col));
200  // Clear cache entry
201  cache.remove(key);
202  fireTableRowsUpdated(row, row);
203  } catch (Exception e) {
204  e.printStackTrace();
205  }
206  }
207  }
- - - -
xmipp.viewer.models.ImageGalleryTableModel.getItemKey
abstract String getItemKey(int index)
- -
-
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◆ refreshRow()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.refreshRow (int row)
- 		-inline
-
-

Function to force the refresh of some row

- -

Definition at line 722 of file ImageGalleryTableModel.java.

-
722  {
723  try {
724  int n = getColumnCount();
725  int index;
726  String key;
727  ColumnInfo ci;
728  for (int col = 0; col < n; ++col) {
729  ci = data.getColumnInfo(col);
730  if (ci.allowRender){
731  key = getItemKey(row, ci.label);
732  DEBUG.printFormat("Removing item: %s from cache", key);
733  cache.remove(key);
734  }
735  }
736  fireTableRowsUpdated(row, row);
737  } catch (Exception e) {
738  e.printStackTrace();
739  }
740  }
- -
xmipp.viewer.models.GalleryData.getColumnInfo
ColumnInfo getColumnInfo(String labelName)
Definition: GalleryData.java:477
- - -
xmipp.viewer.models.ImageGalleryTableModel.getItemKey
abstract String getItemKey(int index)
-
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◆ removeClass()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.removeClass (int classNumber)
- 		-inline
-
-

Remove a class

- -

Definition at line 452 of file ImageGalleryTableModel.java.

-
452  {
453  data.removeClass(classNumber);
454  fireTableDataChanged();
455  }
xmipp.viewer.models.GalleryData.removeClass
void removeClass(int classNumber)
Definition: GalleryData.java:1231
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◆ resizeCache()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.resizeCache ()
- 		-inlineprotected
-
-

Function to create Cache of items calculate the dimension of the cache depending on images size and available memory

- -

Definition at line 139 of file ImageGalleryTableModel.java.

-
139  {
140  int limit = Cache.getLimit(thumb_width, thumb_height);
141  if(cache == null)
142  cache = new Cache(limit);
143  else
144  cache.resize(limit > 0 ? limit : 1);
145  }
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◆ selectRange() [1/2]

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void xmipp.viewer.models.ImageGalleryTableModel.selectRange (int first_index,
int last_index,
boolean value 
)
- 		-inline
-
-

Select a range of elements given the indexes

- -

Definition at line 421 of file ImageGalleryTableModel.java.

-
421  {
422  for (int i = first_index; i <= last_index; ++i)
423  setSelected(i, value);
424  int from = getCoords(first_index).y;
425  int to = getCoords(last_index).y;
426  fireTableRowsUpdated(from, to);
427  }
-
xmipp.viewer.models.ImageGalleryTableModel.setSelected
void setSelected(int index, boolean isselected)
Definition: ImageGalleryTableModel.java:770
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void xmipp.viewer.models.ImageGalleryTableModel.selectRange (int first_row,
int first_col,
int last_row,
int last_col 
)
- 		-inline
-
-

Select a range of elements given the coordinates

- -

Definition at line 430 of file ImageGalleryTableModel.java.

-
430  {
431  int i1 = getIndex(first_row, first_col);
432  int i2 = getIndex(last_row, last_col);
433  int i = Math.min(i1, i2);
434  i2 = Math.max(i1, i2);
435  for (; i <= i2; ++i)
436  setSelected(i, true);
437  fireTableRowsUpdated(first_row, last_row);
438  }
xmipp.viewer.models.ImageGalleryTableModel.setSelected
void setSelected(int index, boolean isselected)
Definition: ImageGalleryTableModel.java:770
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◆ setColumns()

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void xmipp.viewer.models.ImageGalleryTableModel.setColumns (int cols)
- 		-inline
-
- -

Definition at line 236 of file ImageGalleryTableModel.java.

-
236  {
237  if (cols != this.cols) {
238  setColumnsValue(cols);
239  }
240  }
-
-
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◆ setColumnsValue()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.setColumnsValue (int cols)
- 		-inlineprotected
-
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Definition at line 230 of file ImageGalleryTableModel.java.

-
230  {
231  this.cols = cols;
232  rows = n / cols + (n % cols == 0 ? 0 : 1);
233  fireTableStructureChanged();
234  }
- -
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◆ setInvertY()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.setInvertY (boolean itemSelected)
- 		-inline
-
- -

Definition at line 592 of file ImageGalleryTableModel.java.

-
592  {
593  data.inverty = itemSelected;
594  cache.clear();
595  fireTableDataChanged();
596  }
- - -
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◆ setNormalized()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.setNormalized (boolean normalize)
- 		-inline
-
-

Normalization utils

- -

Definition at line 487 of file ImageGalleryTableModel.java.

-
487  {
488 
489  if (normalize != data.normalize) {
490  data.normalize = normalize;
491  if (normalize)
492  calculateMinAndMax();
493  fireTableDataChanged();
494  }
495  }
- - -
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◆ setRowBusy()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.setRowBusy (int row)
- 		-inline
-
- -

Definition at line 701 of file ImageGalleryTableModel.java.

-
701  {
702  DEBUG.printFormat("setting busy row: %d", row);
703  busyRows.add(new Integer(row));
704  fireTableRowsUpdated(row, row);
705  }
-
-
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◆ setRowIdle()

- -
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void xmipp.viewer.models.ImageGalleryTableModel.setRowIdle (int row)
- 		-inline
-
- -

Definition at line 707 of file ImageGalleryTableModel.java.

-
707  {
708  DEBUG.printFormat("setting idle row: %d", row);
709  busyRows.remove(new Integer(row));
710  long objId = data.ids[row];
711  String psdFile = data.md.getValueString(MDLabel.MDL_PSD, objId);
712  String sortFn = psdFile.replace(".psd", ".xmd");
713  MetaData mdRow = new MetaData(sortFn);
714  MDRow row2 = new MDRow();
715  mdRow.getRow(row2, mdRow.firstObject());
716  data.setRow(row2, objId);
717  mdRow.destroy();
718  refreshRow(row);
719  }
- - -
xmipp.viewer.models.GalleryData.setRow
void setRow(MDRow mdRow, long objId)
Definition: GalleryData.java:819
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void xmipp.viewer.models.ImageGalleryTableModel.setRows (int rows)
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Definition at line 222 of file ImageGalleryTableModel.java.

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222  {
223  if (rows != this.rows) {
224  this.rows = rows;
225  cols = n / rows + (n % rows == 0 ? 0 : 1);
226  fireTableStructureChanged();
227  }
228  }
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void xmipp.viewer.models.ImageGalleryTableModel.setSelected (int index,
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Definition at line 770 of file ImageGalleryTableModel.java.

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770  {
771 
772 
773  selection[index] = isselected;
774 
775  if (data.isVolumeMd && data.isTableMode())
776  data.selectedVolFn = isselected? data.getVolumeAt(index): data.getVolumeAt(0);
777 
778  }
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void xmipp.viewer.models.ImageGalleryTableModel.setSelected (int row,
int col,
boolean b 
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Definition at line 812 of file ImageGalleryTableModel.java.

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812  {
813  setSelected(getIndex(row, col), b);
814  }
xmipp.viewer.models.ImageGalleryTableModel.setSelected
void setSelected(int index, boolean isselected)
Definition: ImageGalleryTableModel.java:770
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void xmipp.viewer.models.ImageGalleryTableModel.setSelectionClass (int classNumber)
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Set the class of a given selection of elements.

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Definition at line 441 of file ImageGalleryTableModel.java.

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441  {
442  ClassInfo cli = data.getClassInfo(classNumber);
443  for (int i = getSelFrom(); i <= getSelTo(); ++i)
444  if (selection[i]) {
445  data.setItemClass(i, cli);
446  }
447  clearSelection();
448  fireTableDataChanged();
449  }
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ClassInfo getClassInfo(int classNumber)
Definition: GalleryData.java:930
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Definition: GalleryData.java:923
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Definition at line 394 of file ImageGalleryTableModel.java.

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394  {
395  try {
396  int from = getSelFrom(), to = getSelTo();
397  for (int i = from; i <= to; i++)
398  if (selection[i])
399  data.setEnabled(i, value);
400 
401  if(from != -1)
402  {
403  from = getCoords(from).y;
404  to = getCoords(to).y;
405  fireTableRowsUpdated(from, to);
406  }
407 
408  } catch (Exception e) {
409  // TODO Auto-generated catch block
410  e.printStackTrace();
411  }
412  }
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void setEnabled(int index, boolean value)
Definition: GalleryData.java:805
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Whether to display the labels

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Definition at line 525 of file ImageGalleryTableModel.java.

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526 
527  calculateCellSize();
528  fireTableStructureChanged();
529 
530  }
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void xmipp.viewer.models.ImageGalleryTableModel.setupItem (ImageItem item)
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Definition at line 211 of file ImageGalleryTableModel.java.

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211  {
212  ImagePlus imp = item.getImagePlus();
213  if (imp != null && imp.getProcessor() != null) { // When image is missing this will be null
214  if (data.normalize)
215  imp.getProcessor().setMinAndMax(normalize_min, normalize_max);
216  else
217  imp.getProcessor().resetMinAndMax();
218  imp.updateImage();
219  }
220  }
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Definition at line 296 of file ImageGalleryTableModel.java.

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296  {
297  table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
298  table.setDefaultRenderer(ImageItem.class, renderer);
299  }
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Definition at line 338 of file ImageGalleryTableModel.java.

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338  {
339 
340  if (data.getZoom() != null || data.getZoom() != z) {
341  setZoomValue(z);
342  fireTableDataChanged();
343  if (data.isAutoAdjust())
344  adjustColumn(last_width);
345  }
346  }
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Definition at line 331 of file ImageGalleryTableModel.java.

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331  {
332  data.setZoom(z);
333  scale = (float) (z / 100.0);
334  calculateCellSize();
335  resizeCache();
336  }
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Set the selection state of an element give row and col

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Definition at line 458 of file ImageGalleryTableModel.java.

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458  {
459  setSelected(row, col, !isSelected(row, col));
460  adjustWidth = false;
461  fireTableCellUpdated(row, col);
462  }
xmipp.viewer.models.ImageGalleryTableModel.setSelected
void setSelected(int index, boolean isselected)
Definition: ImageGalleryTableModel.java:770
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void xmipp.viewer.models.ImageGalleryTableModel.touchItem (int row,
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boolean isselected 
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Definition at line 465 of file ImageGalleryTableModel.java.

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465  {
466 
467  setSelected(row, col, isselected);
468  adjustWidth = false;
469  fireTableCellUpdated(row, col);
470  }
xmipp.viewer.models.ImageGalleryTableModel.setSelected
void setSelected(int index, boolean isselected)
Definition: ImageGalleryTableModel.java:770
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Definition at line 302 of file ImageGalleryTableModel.java.

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302  {
303  // For now do nothing, overrided in MetadataTable
304  }
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boolean xmipp.viewer.models.ImageGalleryTableModel.adjustWidth = true
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Definition at line 90 of file ImageGalleryTableModel.java.

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ArrayList<Integer> xmipp.viewer.models.ImageGalleryTableModel.busyRows = new ArrayList<Integer>()
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Definition at line 53 of file ImageGalleryTableModel.java.

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Cache<String, ImageItem> xmipp.viewer.models.ImageGalleryTableModel.cache
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Definition at line 72 of file ImageGalleryTableModel.java.

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Definition at line 65 of file ImageGalleryTableModel.java.

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Definition at line 79 of file ImageGalleryTableModel.java.

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Definition at line 88 of file ImageGalleryTableModel.java.

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Definition at line 61 of file ImageGalleryTableModel.java.

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Definition at line 59 of file ImageGalleryTableModel.java.

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boolean xmipp.viewer.models.ImageGalleryTableModel.normalize_calculated = false
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Definition at line 84 of file ImageGalleryTableModel.java.

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double xmipp.viewer.models.ImageGalleryTableModel.normalize_min = Double.POSITIVE_INFINITY
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Definition at line 85 of file ImageGalleryTableModel.java.

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Definition at line 77 of file ImageGalleryTableModel.java.

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Definition at line 57 of file ImageGalleryTableModel.java.

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Definition at line 69 of file ImageGalleryTableModel.java.

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Definition at line 91 of file ImageGalleryTableModel.java.

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Definition at line 63 of file ImageGalleryTableModel.java.

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xmipp.viewer.models.ImageGalleryTableModel.ImageItem Member List
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This is the complete list of members for xmipp.viewer.models.ImageGalleryTableModel.ImageItem, including all inherited members.

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getCellDim()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
getClassInfo()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
getImage()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
getImagePlus()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
getIndex()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
getKey()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
getLabel()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
getShowLabel()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
imagexmipp.viewer.models.ImageGalleryTableModel.ImageItemprotected
ImageItem(int row, int col)xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
ImageItem(int index, ImagePlus imp)xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
indexxmipp.viewer.models.ImageGalleryTableModel.ImageItemprotected
isBusy()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
isEnabled()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
isSelected()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
setImagePlus(ImagePlus value)xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
toString()xmipp.viewer.models.ImageGalleryTableModel.ImageIteminline
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-Public Member Functions

 ImageItem (int row, int col)
 
 ImageItem (int index, ImagePlus imp)
 
int getIndex ()
 
ImagePlus getImagePlus ()
 
void setImagePlus (ImagePlus value)
 
Image getImage ()
 
boolean getShowLabel ()
 
Dimension getCellDim ()
 
String getLabel ()
 
String getKey ()
 
boolean isSelected ()
 
boolean isEnabled ()
 
boolean isBusy ()
 
ClassInfo getClassInfo ()
 
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-Protected Attributes

ImagePlus image = null
 
int index
 
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Detailed Description

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This class will contains basic info to be used for image rendering. It will contains an ImagePlus, label and some other useful info.

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Definition at line 604 of file ImageGalleryTableModel.java.

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◆ ImageItem() [1/2]

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First argument is the gallery to which this item belongs Constructor of ImageItem

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Definition at line 612 of file ImageGalleryTableModel.java.

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612  {
613  index = ImageGalleryTableModel.this.getIndex(row, col);
614  }
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ImageGalleryTableModel(GalleryData data, boolean[] selection)
Definition: ImageGalleryTableModel.java:94
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Definition at line 616 of file ImageGalleryTableModel.java.

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616  {
617  this.index = index;
618  this.image = imp;
619  }
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Definition at line 643 of file ImageGalleryTableModel.java.

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643  {
644  return cellDim;
645  }
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Definition at line 674 of file ImageGalleryTableModel.java.

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674  {
675  return data.getItemClassInfo(index);
676  }
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Definition at line 633 of file ImageGalleryTableModel.java.

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633  {
634  if (image != null)
635  return image.getImage();
636  return null;
637  }
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Definition at line 625 of file ImageGalleryTableModel.java.

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625  {
626  return image;
627  }
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Definition at line 621 of file ImageGalleryTableModel.java.

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621  {
622  return index;
623  }
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Definition at line 652 of file ImageGalleryTableModel.java.

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652  {
653  try {
654  return getItemKey(index);
655  } catch (Exception e) {
656  // TODO Auto-generated catch block
657  e.printStackTrace();
658  }
659  return null;
660  }
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Definition at line 647 of file ImageGalleryTableModel.java.

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647  {
648  Point coords = getCoords(index);
649  return ImageGalleryTableModel.this.getLabel(coords.y, coords.x);
650  }
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ImageGalleryTableModel(GalleryData data, boolean[] selection)
Definition: ImageGalleryTableModel.java:94
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Definition at line 639 of file ImageGalleryTableModel.java.

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639  {
640  return data.isDisplayLabel();
641  }
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Definition at line 670 of file ImageGalleryTableModel.java.

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670  {
671  return ImageGalleryTableModel.this.isBusy(index, 0);
672  }
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Definition: ImageGalleryTableModel.java:94
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Definition at line 666 of file ImageGalleryTableModel.java.

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666  {
667  return data.isEnabled(index);
668  }
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Definition at line 662 of file ImageGalleryTableModel.java.

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662  {
663  return ImageGalleryTableModel.this.isSelected(index);
664  }
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Definition: ImageGalleryTableModel.java:94
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Definition at line 629 of file ImageGalleryTableModel.java.

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629  {
630  image = value;
631  }
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String xmipp.viewer.models.ImageGalleryTableModel.ImageItem.toString ()
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Definition at line 679 of file ImageGalleryTableModel.java.

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679  {
680  return image != null ? image.getFileInfo().fileName : null;
681  }
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Member Data Documentation

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◆ image

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ImagePlus xmipp.viewer.models.ImageGalleryTableModel.ImageItem.image = null
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Definition at line 606 of file ImageGalleryTableModel.java.

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◆ index

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int xmipp.viewer.models.ImageGalleryTableModel.ImageItem.index
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Definition at line 607 of file ImageGalleryTableModel.java.

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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel_1_1ImageItem__coll__graph.dot b/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel_1_1ImageItem__coll__graph.dot deleted file mode 100644 index b730c6b4..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel_1_1ImageItem__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.models.ImageGalleryTableModel.ImageItem" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node1 [label="xmipp.viewer.models.Image\lGalleryTableModel.ImageItem",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node2 -> Node1 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" image" ,fontname="Helvetica"]; - Node2 [label="ImagePlus",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel_1_1ImageItem__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel_1_1ImageItem__coll__graph.md5 deleted file mode 100644 index fa4ce99a..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel_1_1ImageItem__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -93ee6fc5b28f84c8192338430258200f \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel__coll__graph.dot b/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel__coll__graph.dot deleted file mode 100644 index 9071d836..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel__coll__graph.dot +++ /dev/null @@ -1,110 +0,0 @@ -digraph "xmipp.viewer.models.ImageGalleryTableModel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node6 [label="xmipp.viewer.models.Image\lGalleryTableModel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node7 -> Node6 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="AbstractTableModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node6 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" columnModel" ,fontname="Helvetica"]; - Node8 [label="xmipp.viewer.models.Gallery\lColumnModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1GalleryColumnModel.html"]; - Node9 -> Node8 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node9 [label="DefaultTableColumnModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node6 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cache" ,fontname="Helvetica"]; 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xmipp.viewer.models.MetadataGalleryTableModel Member List
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This is the complete list of members for xmipp.viewer.models.MetadataGalleryTableModel, including all inherited members.

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adjustColumn(int width)xmipp.viewer.models.ImageGalleryTableModelinline
adjustColumnsWidth()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
adjustWidthxmipp.viewer.models.ImageGalleryTableModel
busyRowsxmipp.viewer.models.ImageGalleryTableModelprotected
cachexmipp.viewer.models.ImageGalleryTableModelprotected
calculateCellSize()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
calculateMinAndMax()xmipp.viewer.models.ImageGalleryTableModelinline
cellDimxmipp.viewer.models.ImageGalleryTableModel
clearSelection()xmipp.viewer.models.ImageGalleryTableModelinline
columnModelxmipp.viewer.models.ImageGalleryTableModelprotected
createColumnModel()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
createImageItem(int index, ColumnInfo renderLabel)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
createItem(int index, String key, ColumnInfo ci)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
dataxmipp.viewer.models.ImageGalleryTableModel
dimensionxmipp.viewer.models.ImageGalleryTableModelprotected
getCellSize()xmipp.viewer.models.ImageGalleryTableModelinline
getColumn(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getColumnClass(int c)xmipp.viewer.models.ImageGalleryTableModelinline
getColumnCount()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnModel()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnName(int column)xmipp.viewer.models.ImageGalleryTableModelinline
getColumns()xmipp.viewer.models.ImageGalleryTableModelinline
getCoords(int index)xmipp.viewer.models.ImageGalleryTableModelinline
getFirstSelectedIndex()xmipp.viewer.models.ImageGalleryTableModelinline
getId(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getImage(long id, String imagepath, ColumnInfo renderLabel)xmipp.viewer.models.MetadataGalleryTableModelinline
getImageFilename(int index, int label)xmipp.viewer.models.MetadataGalleryTableModelinline
getImageHeight()xmipp.viewer.models.ImageGalleryTableModelinline
getImageLoader()xmipp.viewer.models.MetadataGalleryTableModelinline
getImageWidth()xmipp.viewer.models.ImageGalleryTableModelinline
getIndex(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getItemKey(int index)xmipp.viewer.models.MetadataGalleryTableModelinline
xmipp::viewer::models::ImageGalleryTableModel.getItemKey(int index, int label)xmipp.viewer.models.ImageGalleryTableModelinline
getLabel(int row, int col)xmipp.viewer.models.MetadataGalleryTableModelinline
getMinAndMax()xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
getRenderer()xmipp.viewer.models.ImageGalleryTableModelinline
getRowCount()xmipp.viewer.models.ImageGalleryTableModelinline
getRows()xmipp.viewer.models.ImageGalleryTableModelinline
getSelection()xmipp.viewer.models.ImageGalleryTableModelinline
getSelectionCount()xmipp.viewer.models.ImageGalleryTableModelinline
getSelFrom()xmipp.viewer.models.ImageGalleryTableModelinline
getSelTo()xmipp.viewer.models.ImageGalleryTableModelinline
getSize()xmipp.viewer.models.ImageGalleryTableModelinline
getTableHeaderModel()xmipp.viewer.models.ImageGalleryTableModelinline
getTitle()xmipp.viewer.models.MetadataGalleryTableModelinline
getValueAt(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
gotoItem(int i)xmipp.viewer.models.ImageGalleryTableModelinline
handleDoubleClick(int row, int col)xmipp.viewer.models.MetadataGalleryTableModelinline
handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)xmipp.viewer.models.MetadataGalleryTableModelinline
hasSelection()xmipp.viewer.models.ImageGalleryTableModelinline
image_widthxmipp.viewer.models.ImageGalleryTableModelprotected
ImageGalleryTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.ImageGalleryTableModelinline
isBusy(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isSelected(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isSelected(int index)xmipp.viewer.models.ImageGalleryTableModelinline
isValidIndex(int index)xmipp.viewer.models.ImageGalleryTableModelinline
loadDimension()xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
MetadataGalleryTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.MetadataGalleryTableModelinline
nxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_calculatedxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_minxmipp.viewer.models.ImageGalleryTableModelprotected
openXmippImageWindow(int index, ColumnInfo ci)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
refreshAt(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
refreshRow(int row)xmipp.viewer.models.ImageGalleryTableModelinline
removeClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
rendererxmipp.viewer.models.ImageGalleryTableModelprotected
renderLabelxmipp.viewer.models.MetadataGalleryTableModelprotected
resizeCache()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
rowsxmipp.viewer.models.ImageGalleryTableModelprotected
scalexmipp.viewer.models.ImageGalleryTableModelprotected
selectionxmipp.viewer.models.ImageGalleryTableModelprotected
selectRange(int first_index, int last_index, boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
selectRange(int first_row, int first_col, int last_row, int last_col)xmipp.viewer.models.ImageGalleryTableModelinline
setColumns(int cols)xmipp.viewer.models.ImageGalleryTableModelinline
setColumnsValue(int cols)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setInvertY(boolean itemSelected)xmipp.viewer.models.ImageGalleryTableModelinline
setNormalized(boolean normalize)xmipp.viewer.models.ImageGalleryTableModelinline
setRowBusy(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRowIdle(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRows(int rows)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int index, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int row, int col, boolean b)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionEnabled(boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
setShowLabels()xmipp.viewer.models.ImageGalleryTableModelinline
setupItem(ImageItem item)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setupTable(JTable table)xmipp.viewer.models.ImageGalleryTableModelinline
setUseGeometry(boolean geo, boolean wrap)xmipp.viewer.models.MetadataGalleryTableModelinline
setZoom(int z)xmipp.viewer.models.ImageGalleryTableModelinline
setZoomValue(int z)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
showLabels()xmipp.viewer.models.MetadataGalleryTableModelinline
thumb_widthxmipp.viewer.models.ImageGalleryTableModelprotected
touchItem(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
touchItem(int row, int col, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
updateColumnInfo(List< ColumnInfo > newInfo)xmipp.viewer.models.MetadataGalleryTableModelinline
updateTableSelection(JTable table)xmipp.viewer.models.ImageGalleryTableModelinline
visibleLabelsxmipp.viewer.models.MetadataGalleryTableModel
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xmipp.viewer.models.MetadataGalleryTableModel Class Reference
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-Public Member Functions

 MetadataGalleryTableModel (GalleryData data, boolean[] selection) throws Exception
 
void updateColumnInfo (List< ColumnInfo > newInfo)
 
ImagePlus getImage (long id, String imagepath, ColumnInfo renderLabel)
 
String getLabel (int row, int col)
 
String getItemKey (int index) throws Exception
 
String getTitle ()
 
String getImageFilename (int index, int label)
 
boolean handleDoubleClick (int row, int col)
 
void setUseGeometry (boolean geo, boolean wrap)
 
ImagePlusLoader getImageLoader ()
 
boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
boolean showLabels ()
 
- Public Member Functions inherited from xmipp.viewer.models.ImageGalleryTableModel
 ImageGalleryTableModel (GalleryData data, boolean[] selection) throws Exception
 
int getImageWidth ()
 
int getImageHeight ()
 
int getColumnCount ()
 
int getRowCount ()
 
String getColumnName (int column)
 
Class getColumnClass (int c)
 
Object getValueAt (int row, int col)
 
void refreshAt (int row, int col)
 
void setRows (int rows)
 
void setColumns (int cols)
 
boolean adjustColumn (int width)
 
int getSize ()
 
Dimension getCellSize ()
 
void setupTable (JTable table)
 
void updateTableSelection (JTable table)
 
ImageItemRenderer getRenderer ()
 
GalleryColumnModel getColumnModel ()
 
JTableHeader getTableHeaderModel ()
 
void setZoom (int z)
 
int getIndex (int row, int col)
 
long getId (int row, int col)
 
boolean isValidIndex (int index)
 
abstract String getLabel (int row, int col)
 
Point getCoords (int index)
 
void setSelectionEnabled (boolean value)
 
int getFirstSelectedIndex ()
 
void selectRange (int first_index, int last_index, boolean value)
 
void selectRange (int first_row, int first_col, int last_row, int last_col)
 
void setSelectionClass (int classNumber)
 
void removeClass (int classNumber)
 
void touchItem (int row, int col)
 
void touchItem (int row, int col, boolean isselected)
 
void gotoItem (int i)
 
void setNormalized (boolean normalize)
 
void calculateMinAndMax ()
 
abstract boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
abstract boolean handleDoubleClick (int row, int col)
 
void setShowLabels ()
 
abstract String getItemKey (int index) throws Exception
 
String getItemKey (int index, int label) throws Exception
 
abstract String getTitle ()
 
abstract ImagePlusLoader getImageLoader ()
 
boolean isSelected (int row, int col)
 
abstract boolean showLabels ()
 
void setInvertY (boolean itemSelected)
 
int getRows ()
 
int getColumns ()
 
boolean isBusy (int row, int col)
 
void setRowBusy (int row)
 
void setRowIdle (int row)
 
void refreshRow (int row)
 
void clearSelection ()
 
int getSelectionCount ()
 
boolean [] getSelection ()
 
void setSelected (int index, boolean isselected)
 
boolean isSelected (int index)
 
int getSelFrom ()
 
int getSelTo ()
 
boolean hasSelection ()
 
void setSelected (int row, int col, boolean b)
 
ColumnInfo getColumn (int row, int col)
 
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-Public Attributes

ArrayList< ColumnInfo > visibleLabels
 
- Public Attributes inherited from xmipp.viewer.models.ImageGalleryTableModel
Dimension cellDim = new Dimension()
 
GalleryData data
 
boolean adjustWidth = true
 
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-Protected Member Functions

void openXmippImageWindow (int index, ColumnInfo ci)
 
ImageDimension loadDimension () throws Exception
 
ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
ImageItem createImageItem (int index, ColumnInfo renderLabel) throws Exception
 
double [] getMinAndMax ()
 
- Protected Member Functions inherited from xmipp.viewer.models.ImageGalleryTableModel
abstract ImageDimension loadDimension () throws Exception
 
void resizeCache ()
 
void setupItem (ImageItem item)
 
void setColumnsValue (int cols)
 
void calculateCellSize ()
 
void adjustColumnsWidth ()
 
GalleryColumnModel createColumnModel ()
 
void setZoomValue (int z)
 
abstract double [] getMinAndMax ()
 
abstract ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
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-Protected Attributes

ColumnInfo renderLabel
 
- Protected Attributes inherited from xmipp.viewer.models.ImageGalleryTableModel
ArrayList< Integer > busyRows = new ArrayList<Integer>()
 
int rows
 
int n
 
int image_width
 
int thumb_width
 
float scale = (float) 1.
 
Cache< String, ImageItem > cache
 
ImageDimension dimension
 
ImageItemRenderer renderer = new ImageItemRenderer()
 
GalleryColumnModel columnModel
 
boolean normalize_calculated = false
 
double normalize_min = Double.POSITIVE_INFINITY
 
boolean [] selection
 
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Detailed Description

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Definition at line 44 of file MetadataGalleryTableModel.java.

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Constructor & Destructor Documentation

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◆ MetadataGalleryTableModel()

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xmipp.viewer.models.MetadataGalleryTableModel.MetadataGalleryTableModel (GalleryData data,
boolean [] selection 
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Definition at line 53 of file MetadataGalleryTableModel.java.

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54  {
55  super(data, selection);
56  data.normalize = false;
57  }
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Member Function Documentation

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◆ createImageItem()

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ImageItem xmipp.viewer.models.MetadataGalleryTableModel.createImageItem (int index,
ColumnInfo renderLabel 
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Function to create an image item

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Definition at line 221 of file MetadataGalleryTableModel.java.

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222  {
223  String imageFn = getImageFilename(index, renderLabel.label);
224  long objId = data.ids[index];
225  ImagePlus imp = getImage(objId, imageFn, renderLabel);
226  ImageItem item = new ImageItem(index, imp);
227  return item;
228  }
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xmipp.viewer.models.MetadataGalleryTableModel.getImage
ImagePlus getImage(long id, String imagepath, ColumnInfo renderLabel)
Definition: MetadataGalleryTableModel.java:104
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◆ createItem()

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ImageItem xmipp.viewer.models.MetadataGalleryTableModel.createItem (int index,
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Definition at line 195 of file MetadataGalleryTableModel.java.

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196  {
197  return createImageItem(index, ci);
198  }
xmipp.viewer.models.MetadataGalleryTableModel.createImageItem
ImageItem createImageItem(int index, ColumnInfo renderLabel)
Definition: MetadataGalleryTableModel.java:221
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◆ getImage()

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ImagePlus xmipp.viewer.models.MetadataGalleryTableModel.getImage (long id,
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Definition at line 104 of file MetadataGalleryTableModel.java.

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105  {
106  ImagePlus imp = null;
107  if (imagepath != null && Filename.exists(imagepath))
108  {
109  try
110  {
111  ImagePlusLoader loader;
112  if(Filename.isStackOrVolume(imagepath))
113  loader = new ImagePlusLoader(imagepath, null, null, data.useGeo, data.wrap, data.inverty, ImageGeneric.MID_SLICE);
114  else
115  loader = new ImagePlusLoader(imagepath, data.useGeo, data.wrap, data.inverty);
116  loader.setGeometry(data.getGeometry(id, renderLabel));
117  loader.setInvertY(data.inverty);
118  loader.setDimension(thumb_width, thumb_height);
119  return loader.getImagePlus();
120  }
121  catch (Exception ex)
122  {
123  imp = null;
124  }
125  }
126  return imp;
127  }
xmipp.viewer.models.GalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: GalleryData.java:1779
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String xmipp.viewer.models.MetadataGalleryTableModel.getImageFilename (int index,
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Definition at line 249 of file MetadataGalleryTableModel.java.

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250  {
251  try
252  {
253  String file = data.getValueFromLabel(index, label);
254  String mddir = data.md.getBaseDir();
255  file = Filename.findImagePath(file, mddir, true);
256  return file;
257  }
258  catch (Exception e)
259  {
260  e.printStackTrace();
261  }
262  return null;
263  }// function getImageFilename
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String getValueFromLabel(int index, int label)
Definition: GalleryData.java:1190
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String getBaseDir()
Definition: MetaData.java:430
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ImagePlusLoader xmipp.viewer.models.MetadataGalleryTableModel.getImageLoader ()
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Definition at line 318 of file MetadataGalleryTableModel.java.

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319  {
320  try
321  {
322  ImagePlus imp = XmippImageConverter.readMetadataToImagePlus(renderLabel.label, data.md, data.useGeo, data.wrap, data.inverty);
323  return new ImagePlusLoader(imp, data.inverty);
324  }
325  catch (Exception e)
326  {
327  e.printStackTrace();
328  }
329  return null;
330  }// function getImageLoader
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Definition at line 231 of file MetadataGalleryTableModel.java.

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232  {
233  return getItemKey(index, renderLabel.label);
234 
235  }
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Definition at line 202 of file MetadataGalleryTableModel.java.

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203  {
204  try
205  {
206  int index = getIndex(row, col);
207  long objId = data.ids[index];
208  return data.getDisplayLabel(objId);
209 
210  }
211  catch (Exception e)
212  {
213  e.printStackTrace();
214  }
215  return null;
216  }
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Definition at line 292 of file MetadataGalleryTableModel.java.

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293  {
294  try
295  {
296  return data.md.getStatistics(false, data.ciFirstRender.label);
297  }
298  catch (Exception ex)
299  {
300  DEBUG.printException(ex);
301  }
302  return null;
303  }// function getMinAndMax
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Definition at line 238 of file MetadataGalleryTableModel.java.

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239  {
240  String title = "Metadata: " + (data.getFileName() != null ? Filename.getBaseName(data.getFileName()) : "");
241  if (n > 1)
242  title += String.format(" %d items", n);
243  if (data.hasRenderLabel())
244  title += String.format(" (%d x %d)", image_width, image_height);
245 
246  return title;
247  }// function getTitle
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Definition at line 272 of file MetadataGalleryTableModel.java.

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273  {
274  try
275  {
276  if (data.isImageFile(renderLabel))
277  {
278  int index = getIndex(row, col);
279  openXmippImageWindow(index, getColumn(row, col));
280  return true;
281  }
282  }
283  catch (Exception e)
284  {
285  e.printStackTrace();
286  }
287  return false;
288  }// function handleDoubleClick
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Definition at line 333 of file MetadataGalleryTableModel.java.

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334  {
335  return true;
336  }// function handleRightClick
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Definition at line 146 of file MetadataGalleryTableModel.java.

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147  {
148  // Set information about columns
149  visibleLabels = new ArrayList<ColumnInfo>();
150  // data.globalRender = false;
151 
152  for (ColumnInfo ci : data.labels)
153  {
154  if (ci.visible)
155  visibleLabels.add(ci);
156  // if (ci.render)
157  // data.globalRender = true;
158  }
159  ImageDimension dim = null;
160  int width = 50, height = 50;
161  if (data.hasRenderLabel() && data.renderImages)
162  {
163  renderLabel = data.ciFirstRender;
164  // if (renderLabels) {
165  String imageFn = data.getSampleImage(renderLabel);
166  if(imageFn != null)
167  {
168  ImagePlusLoader loader;
169  if(Filename.isStackOrVolume(imageFn))
170  loader = new ImagePlusLoader(imageFn, null, null, false, false, false, ImageGeneric.MID_SLICE);
171  else
172  loader = new ImagePlusLoader(imageFn);
173  ImagePlus image = loader.getImagePlus();
174  if(image != null && image.getWidth() > 0)
175  {
176  width = image.getWidth();
177  height = image.getHeight();
178  dim = new ImageDimension(width, height);
179  }
180  }
181 
182  }
183 
184  if (dim == null)
185  dim = new ImageDimension(width);
186  // Zdim will always be used as number of elements to display
187  dim.setZDim(data.ids.length);
188  n = dim.getZDim();
189  image_width = dim.getXDim();
190  image_height = dim.getYDim();
191  return dim;
192  }
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String getSampleImage(ColumnInfo ci)
Definition: GalleryData.java:580
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Definition at line 130 of file MetadataGalleryTableModel.java.

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131  {
132  String file = getImageFilename(index, ci.label);
133  if(file == null)
134  throw new IllegalArgumentException(XmippMessage.getPathNotExistsMsg(data.getValueFromLabel(index, ci.label)));
135  ImagePlusLoader loader = new ImagePlusLoader(file, data.useGeo, data.wrap, data.inverty);
136  if(data.containsGeometryInfo())
137  loader.setGeometry(data.getGeometry(data.ids[index], ci));
138  if (data.getNormalized())
139  loader.setNormalize(normalize_min, normalize_max);
140  ImagesWindowFactory.openXmippImageWindow(loader, data.parameters);
141  }
xmipp.viewer.models.GalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: GalleryData.java:1779
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String getValueFromLabel(int index, int label)
Definition: GalleryData.java:1190
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void xmipp.viewer.models.MetadataGalleryTableModel.setUseGeometry (boolean geo,
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Change the use of geometry info

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Definition at line 306 of file MetadataGalleryTableModel.java.

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307  {
308  if (!geo)
309  wrap = false;
310  boolean changed = data.useGeo != geo || data.wrap != wrap;
311  data.useGeo = geo;
312  data.wrap = wrap;
313  if (changed)
314  fireTableDataChanged();
315  }// function setUseGeometry
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Definition at line 341 of file MetadataGalleryTableModel.java.

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341  {
342  return true;
343  }
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void xmipp.viewer.models.MetadataGalleryTableModel.updateColumnInfo (List< ColumnInfo > newInfo)
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Update the columns display information

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Definition at line 60 of file MetadataGalleryTableModel.java.

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61  {
62  int n = newInfo.size();
63  boolean changed = false;
64  data.renderImages = false;
65  data.ciFirstRender = null;
66 
67  for (int i = 0; i < n; ++i)
68  for (int j = 0; j < n; ++j)
69  {
70  ColumnInfo ci1 = data.labels.get(i);
71  ColumnInfo ci2 = newInfo.get(j);
72  if (ci1.label == ci2.label)
73  {
74  if (ci1.updateInfo(ci2))
75  changed = true;
76 
77  if (ci1.visible)
78  {
79  visibleLabels.add(ci1);
80  if (data.ciFirstRender == null && ci1.allowRender)
81  data.ciFirstRender = ci1;
82  }
83  if (ci1.render)
84  data.renderImages = true;
85  if (i != j)
86  changed = true;
87  }
88  }
89 
90  if (changed)
91  {
92  data.labels = newInfo;
93  visibleLabels.clear();
94  for (ColumnInfo ci : data.labels)
95  if (ci.visible)
96  visibleLabels.add(ci);
97  calculateCellSize();
98  cols = visibleLabels.size();
99  // fireTableDataChanged();
100  fireTableStructureChanged();
101  }
102  }
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Member Data Documentation

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◆ renderLabel

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ColumnInfo xmipp.viewer.models.MetadataGalleryTableModel.renderLabel
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Definition at line 49 of file MetadataGalleryTableModel.java.

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◆ visibleLabels

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ArrayList<ColumnInfo> xmipp.viewer.models.MetadataGalleryTableModel.visibleLabels
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Definition at line 51 of file MetadataGalleryTableModel.java.

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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__coll__graph.dot b/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__coll__graph.dot deleted file mode 100644 index 5e63df01..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__coll__graph.dot +++ /dev/null @@ -1,113 +0,0 @@ -digraph "xmipp.viewer.models.MetadataGalleryTableModel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node5 [label="xmipp.viewer.models.Metadata\lGalleryTableModel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="xmipp.viewer.models.Image\lGalleryTableModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel.html"]; - Node7 -> Node6 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="AbstractTableModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node6 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" columnModel" ,fontname="Helvetica"]; - Node8 [label="xmipp.viewer.models.Gallery\lColumnModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1GalleryColumnModel.html"]; - Node9 -> Node8 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node9 [label="DefaultTableColumnModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node6 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cache" ,fontname="Helvetica"]; - Node10 [label="xmipp.utils.Cache\<\l String, xmipp.viewer.models.\lImageGalleryTableModel.ImageItem \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1Cache.html"]; 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- Node26 [label="xmipp.viewer.ctf.TasksEngine",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1ctf_1_1TasksEngine.html"]; - Node27 -> Node26 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node27 [label="xmipp.viewer.ctf.iTaskCompletion\lListener",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$interfacexmipp_1_1viewer_1_1ctf_1_1iTaskCompletionListener.html"]; - Node28 -> Node19 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" jcbBlocks\njcbVolumes" ,fontname="Helvetica"]; - Node28 [label="JComboBox",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node29 -> Node19 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" jlBlocks\njlVolumes" ,fontname="Helvetica"]; - Node29 [label="JLabel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node30 -> Node19 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cbPanel\nbuttonspn\njpBottom" ,fontname="Helvetica"]; - Node30 [label="JPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node17 -> Node19 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" data" ,fontname="Helvetica"]; - Node31 -> Node19 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" menu" ,fontname="Helvetica"]; - Node31 [label="xmipp.viewer.windows.Gallery\lJFrame.GalleryMenu",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu.html"]; - Node32 -> Node31 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node32 [label="xmipp.utils.XmippMenuBar\lCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuBarCreator.html"]; - Node33 -> Node32 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node33 [label="xmipp.utils.XmippMenuCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuCreator.html"]; 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- Node53 [label="Options",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node54 -> Node52 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cmdLine" ,fontname="Helvetica"]; - Node54 [label="CommandLine",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node55 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" visibleLabels" ,fontname="Helvetica"]; - Node55 [label="ArrayList\< xmipp.viewer.models.\lColumnInfo \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node43 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" renderLabel" ,fontname="Helvetica"]; -} diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__coll__graph.md5 deleted file mode 100644 index 92a58781..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -6739e8c2f4b7987b2ac750892f22c061 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__inherit__graph.dot deleted file mode 100644 index 6f65daa2..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__inherit__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.viewer.models.MetadataGalleryTableModel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.models.Metadata\lGalleryTableModel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.models.Image\lGalleryTableModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="AbstractTableModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node0 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.models.Metadata\lTableModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1MetadataTableModel.html"]; - Node3 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="xmipp.viewer.models.Metadata\lRowTableModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1MetadataRowTableModel.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__inherit__graph.md5 deleted file mode 100644 index 547e7ce3..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataGalleryTableModel__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -c439c64aa105922fc3158aea911ce7b3 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataRowTableModel-members.html b/html/classxmipp_1_1viewer_1_1models_1_1MetadataRowTableModel-members.html deleted file mode 100644 index c5ccabbd..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataRowTableModel-members.html +++ /dev/null @@ -1,187 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.models.MetadataRowTableModel Member List
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- -

This is the complete list of members for xmipp.viewer.models.MetadataRowTableModel, including all inherited members.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
adjustColumn(int width)xmipp.viewer.models.MetadataTableModelinline
adjustColumnsWidth()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
adjustWidthxmipp.viewer.models.ImageGalleryTableModel
busyRowsxmipp.viewer.models.ImageGalleryTableModelprotected
cachexmipp.viewer.models.ImageGalleryTableModelprotected
calculateCellSize()xmipp.viewer.models.MetadataTableModelinlineprotected
calculateMinAndMax()xmipp.viewer.models.ImageGalleryTableModelinline
cellDimxmipp.viewer.models.ImageGalleryTableModel
clearSelection()xmipp.viewer.models.ImageGalleryTableModelinline
columnModelxmipp.viewer.models.ImageGalleryTableModelprotected
createColumnModel()xmipp.viewer.models.MetadataRowTableModelinline
createImageItem(int index, ColumnInfo renderLabel)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
createItem(int index, String key, ColumnInfo ci)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
dataxmipp.viewer.models.ImageGalleryTableModel
dimensionxmipp.viewer.models.ImageGalleryTableModelprotected
getCellSize()xmipp.viewer.models.ImageGalleryTableModelinline
getColumn(int row, int col)xmipp.viewer.models.MetadataRowTableModelinline
getColumnClass(int column)xmipp.viewer.models.MetadataRowTableModelinline
getColumnCount()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnModel()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnName(int column)xmipp.viewer.models.MetadataRowTableModelinline
getColumns()xmipp.viewer.models.ImageGalleryTableModelinline
getCoords(int index)xmipp.viewer.models.MetadataTableModelinline
getFirstSelectedIndex()xmipp.viewer.models.ImageGalleryTableModelinline
getId(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getImage(long id, String imagepath, ColumnInfo renderLabel)xmipp.viewer.models.MetadataGalleryTableModelinline
getImageFilename(int index, int label)xmipp.viewer.models.MetadataGalleryTableModelinline
getImageHeight()xmipp.viewer.models.ImageGalleryTableModelinline
getImageLoader()xmipp.viewer.models.MetadataGalleryTableModelinline
getImageWidth()xmipp.viewer.models.ImageGalleryTableModelinline
getIndex(int row, int col)xmipp.viewer.models.MetadataRowTableModelinline
getItemKey(int index)xmipp.viewer.models.MetadataGalleryTableModelinline
xmipp::viewer::models::ImageGalleryTableModel.getItemKey(int index, int label)xmipp.viewer.models.ImageGalleryTableModelinline
getLabel(int row, int col)xmipp.viewer.models.MetadataGalleryTableModelinline
getMinAndMax()xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
getRenderer()xmipp.viewer.models.ImageGalleryTableModelinline
getRowCount()xmipp.viewer.models.ImageGalleryTableModelinline
getRows()xmipp.viewer.models.ImageGalleryTableModelinline
getSelection()xmipp.viewer.models.ImageGalleryTableModelinline
getSelectionCount()xmipp.viewer.models.ImageGalleryTableModelinline
getSelFrom()xmipp.viewer.models.ImageGalleryTableModelinline
getSelTo()xmipp.viewer.models.ImageGalleryTableModelinline
getSize()xmipp.viewer.models.ImageGalleryTableModelinline
getTableHeaderModel()xmipp.viewer.models.MetadataTableModelinline
getTitle()xmipp.viewer.models.MetadataGalleryTableModelinline
getValueAt(int row, int column)xmipp.viewer.models.MetadataRowTableModelinline
gotoItem(int i)xmipp.viewer.models.ImageGalleryTableModelinline
handleDoubleClick(int row, int col)xmipp.viewer.models.MetadataTableModelinline
handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)xmipp.viewer.models.MetadataRowTableModelinline
hasSelection()xmipp.viewer.models.ImageGalleryTableModelinline
idxmipp.viewer.models.MetadataRowTableModelprotected
image_widthxmipp.viewer.models.ImageGalleryTableModelprotected
ImageGalleryTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.ImageGalleryTableModelinline
isBusy(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isCellEditable(int row, int column)xmipp.viewer.models.MetadataTableModelinline
isSelected(int row, int col)xmipp.viewer.models.MetadataRowTableModelinline
xmipp::viewer::models::MetadataTableModel.isSelected(int index)xmipp.viewer.models.ImageGalleryTableModelinline
isValidIndex(int index)xmipp.viewer.models.ImageGalleryTableModelinline
loadDimension()xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
MetadataGalleryTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.MetadataGalleryTableModelinline
MetadataRowTableModel(GalleryJFrame window, MetaData md)xmipp.viewer.models.MetadataRowTableModelinline
MetadataRowTableModel(GalleryData data)xmipp.viewer.models.MetadataRowTableModelinline
MetadataTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.MetadataTableModelinline
nxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_calculatedxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_minxmipp.viewer.models.ImageGalleryTableModelprotected
openXmippImageWindow(int index, ColumnInfo ci)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
refreshAt(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
refreshRow(int row)xmipp.viewer.models.ImageGalleryTableModelinline
removeClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
rendererxmipp.viewer.models.ImageGalleryTableModelprotected
renderLabelxmipp.viewer.models.MetadataGalleryTableModelprotected
resizeCache()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
rowsxmipp.viewer.models.ImageGalleryTableModelprotected
scalexmipp.viewer.models.ImageGalleryTableModelprotected
selectionxmipp.viewer.models.ImageGalleryTableModelprotected
selectRange(int first_row, int first_col, int last_row, int last_col)xmipp.viewer.models.MetadataRowTableModelinline
xmipp::viewer::models::MetadataTableModel.selectRange(int first_index, int last_index, boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
setColumns(int cols)xmipp.viewer.models.MetadataTableModelinline
setColumnsValue(int cols)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setInvertY(boolean itemSelected)xmipp.viewer.models.ImageGalleryTableModelinline
setMdValueAt(Object value, int row, int column, ColumnInfo ci, long id)xmipp.viewer.models.MetadataTableModelinlineprotected
setNormalized(boolean normalize)xmipp.viewer.models.ImageGalleryTableModelinline
setRenderImages(boolean value)xmipp.viewer.models.MetadataTableModelinline
setRowBusy(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRowIdle(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRows(int rows)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int row, int col, boolean b)xmipp.viewer.models.MetadataRowTableModelinline
xmipp::viewer::models::MetadataTableModel.setSelected(int index, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionEnabled(boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
setShowLabels()xmipp.viewer.models.ImageGalleryTableModelinline
setupItem(ImageItem item)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setupTable(JTable table)xmipp.viewer.models.MetadataRowTableModelinline
setUseGeometry(boolean geo, boolean wrap)xmipp.viewer.models.MetadataGalleryTableModelinline
setValueAt(Object value, int row, int column)xmipp.viewer.models.MetadataRowTableModelinline
setZoom(int z)xmipp.viewer.models.ImageGalleryTableModelinline
setZoomValue(int z)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
showLabels()xmipp.viewer.models.MetadataRowTableModelinline
thumb_widthxmipp.viewer.models.ImageGalleryTableModelprotected
touchItem(int row, int col)xmipp.viewer.models.MetadataRowTableModelinline
xmipp::viewer::models::MetadataTableModel.touchItem(int row, int col, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
updateColumnInfo(List< ColumnInfo > newInfo)xmipp.viewer.models.MetadataGalleryTableModelinline
updateTableSelection(JTable table)xmipp.viewer.models.MetadataTableModelinline
visibleLabelsxmipp.viewer.models.MetadataGalleryTableModel
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-Public Member Functions

 MetadataRowTableModel (GalleryJFrame window, MetaData md) throws Exception
 
 MetadataRowTableModel (GalleryData data) throws Exception
 
String getColumnName (int column)
 
Class getColumnClass (int column)
 
Object getValueAt (int row, int column)
 
void setValueAt (Object value, int row, int column)
 
GalleryColumnModel createColumnModel ()
 
void setupTable (JTable table)
 
boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
int getIndex (int row, int col)
 
ColumnInfo getColumn (int row, int col)
 
void touchItem (int row, int col)
 
boolean isSelected (int row, int col)
 
void setSelected (int row, int col, boolean b)
 
void selectRange (int first_row, int first_col, int last_row, int last_col)
 
boolean showLabels ()
 
- Public Member Functions inherited from xmipp.viewer.models.MetadataTableModel
 MetadataTableModel (GalleryData data, boolean[] selection) throws Exception
 
String getColumnName (int column)
 
Class getColumnClass (int column)
 
Object getValueAt (int row, int column)
 
void setValueAt (Object value, int row, int column)
 
boolean isCellEditable (int row, int column)
 
boolean handleDoubleClick (int row, int col)
 
void setColumns (int cols)
 
boolean adjustColumn (int width)
 
void setRenderImages (boolean value)
 
boolean showLabels ()
 
void setupTable (JTable table)
 
JTableHeader getTableHeaderModel ()
 
void updateTableSelection (JTable table)
 
boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
GalleryColumnModel createColumnModel ()
 
int getIndex (int row, int col)
 
ColumnInfo getColumn (int row, int col)
 
Point getCoords (int index)
 
- Public Member Functions inherited from xmipp.viewer.models.MetadataGalleryTableModel
 MetadataGalleryTableModel (GalleryData data, boolean[] selection) throws Exception
 
void updateColumnInfo (List< ColumnInfo > newInfo)
 
ImagePlus getImage (long id, String imagepath, ColumnInfo renderLabel)
 
String getLabel (int row, int col)
 
String getItemKey (int index) throws Exception
 
String getTitle ()
 
String getImageFilename (int index, int label)
 
boolean handleDoubleClick (int row, int col)
 
void setUseGeometry (boolean geo, boolean wrap)
 
ImagePlusLoader getImageLoader ()
 
boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
boolean showLabels ()
 
- Public Member Functions inherited from xmipp.viewer.models.ImageGalleryTableModel
 ImageGalleryTableModel (GalleryData data, boolean[] selection) throws Exception
 
int getImageWidth ()
 
int getImageHeight ()
 
int getColumnCount ()
 
int getRowCount ()
 
String getColumnName (int column)
 
Class getColumnClass (int c)
 
Object getValueAt (int row, int col)
 
void refreshAt (int row, int col)
 
void setRows (int rows)
 
void setColumns (int cols)
 
boolean adjustColumn (int width)
 
int getSize ()
 
Dimension getCellSize ()
 
void setupTable (JTable table)
 
void updateTableSelection (JTable table)
 
ImageItemRenderer getRenderer ()
 
GalleryColumnModel getColumnModel ()
 
JTableHeader getTableHeaderModel ()
 
void setZoom (int z)
 
int getIndex (int row, int col)
 
long getId (int row, int col)
 
boolean isValidIndex (int index)
 
abstract String getLabel (int row, int col)
 
Point getCoords (int index)
 
void setSelectionEnabled (boolean value)
 
int getFirstSelectedIndex ()
 
void selectRange (int first_index, int last_index, boolean value)
 
void selectRange (int first_row, int first_col, int last_row, int last_col)
 
void setSelectionClass (int classNumber)
 
void removeClass (int classNumber)
 
void touchItem (int row, int col)
 
void touchItem (int row, int col, boolean isselected)
 
void gotoItem (int i)
 
void setNormalized (boolean normalize)
 
void calculateMinAndMax ()
 
abstract boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
abstract boolean handleDoubleClick (int row, int col)
 
void setShowLabels ()
 
abstract String getItemKey (int index) throws Exception
 
String getItemKey (int index, int label) throws Exception
 
abstract String getTitle ()
 
abstract ImagePlusLoader getImageLoader ()
 
boolean isSelected (int row, int col)
 
abstract boolean showLabels ()
 
void setInvertY (boolean itemSelected)
 
int getRows ()
 
int getColumns ()
 
boolean isBusy (int row, int col)
 
void setRowBusy (int row)
 
void setRowIdle (int row)
 
void refreshRow (int row)
 
void clearSelection ()
 
int getSelectionCount ()
 
boolean [] getSelection ()
 
void setSelected (int index, boolean isselected)
 
boolean isSelected (int index)
 
int getSelFrom ()
 
int getSelTo ()
 
boolean hasSelection ()
 
void setSelected (int row, int col, boolean b)
 
ColumnInfo getColumn (int row, int col)
 
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-Protected Attributes

long id
 
- Protected Attributes inherited from xmipp.viewer.models.MetadataGalleryTableModel
ColumnInfo renderLabel
 
- Protected Attributes inherited from xmipp.viewer.models.ImageGalleryTableModel
ArrayList< Integer > busyRows = new ArrayList<Integer>()
 
int rows
 
int n
 
int image_width
 
int thumb_width
 
float scale = (float) 1.
 
Cache< String, ImageItem > cache
 
ImageDimension dimension
 
ImageItemRenderer renderer = new ImageItemRenderer()
 
GalleryColumnModel columnModel
 
boolean normalize_calculated = false
 
double normalize_min = Double.POSITIVE_INFINITY
 
boolean [] selection
 
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- Public Attributes inherited from xmipp.viewer.models.MetadataGalleryTableModel
ArrayList< ColumnInfo > visibleLabels
 
- Public Attributes inherited from xmipp.viewer.models.ImageGalleryTableModel
Dimension cellDim = new Dimension()
 
GalleryData data
 
boolean adjustWidth = true
 
- Protected Member Functions inherited from xmipp.viewer.models.MetadataTableModel
void setMdValueAt (Object value, int row, int column, ColumnInfo ci, long id) throws Exception
 
void calculateCellSize ()
 
- Protected Member Functions inherited from xmipp.viewer.models.MetadataGalleryTableModel
void openXmippImageWindow (int index, ColumnInfo ci)
 
ImageDimension loadDimension () throws Exception
 
ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
ImageItem createImageItem (int index, ColumnInfo renderLabel) throws Exception
 
double [] getMinAndMax ()
 
- Protected Member Functions inherited from xmipp.viewer.models.ImageGalleryTableModel
abstract ImageDimension loadDimension () throws Exception
 
void resizeCache ()
 
void setupItem (ImageItem item)
 
void setColumnsValue (int cols)
 
void calculateCellSize ()
 
void adjustColumnsWidth ()
 
GalleryColumnModel createColumnModel ()
 
void setZoomValue (int z)
 
abstract double [] getMinAndMax ()
 
abstract ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
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Detailed Description

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This is a data model designed for Row metadatas

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Definition at line 38 of file MetadataRowTableModel.java.

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Constructor & Destructor Documentation

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◆ MetadataRowTableModel() [1/2]

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xmipp.viewer.models.MetadataRowTableModel.MetadataRowTableModel (GalleryJFrame window,
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Constructor using a metadata row

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Definition at line 42 of file MetadataRowTableModel.java.

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42  {
43  this(new GalleryData(window, new Params(), md));
44  }
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Definition at line 46 of file MetadataRowTableModel.java.

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46  {
47  super(data, null);
48  cols = 1;
49  rows = visibleLabels.size();
50  id = data.md.firstObject();
51  // TODO Auto-generated constructor stub
52  selection = new boolean[rows];
53  }
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◆ createColumnModel()

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GalleryColumnModel xmipp.viewer.models.MetadataRowTableModel.createColumnModel ()
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Return the column model to be used with this table model

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Definition at line 77 of file MetadataRowTableModel.java.

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77  {
78  return new GalleryColumnModel(cellDim.width);
79  }//function createColumnModel
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Definition at line 103 of file MetadataRowTableModel.java.

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104  {
105  return visibleLabels.get(row);
106  }
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Definition at line 61 of file MetadataRowTableModel.java.

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61  {
62  return String.class;
63  }
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Definition at line 56 of file MetadataRowTableModel.java.

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56  {
57  return "Value";
58  }
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Definition at line 97 of file MetadataRowTableModel.java.

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97  {
98 
99  return 0;
100 
101  }
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Definition at line 66 of file MetadataRowTableModel.java.

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67  return super.getValueAt(0, row);
68  }
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Definition at line 88 of file MetadataRowTableModel.java.

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88  {
89  boolean result = super.handleRightClick(0, row, xpopup);
90  xpopup.setItemVisible(XmippPopupMenuCreator.SELECT, false);
91  xpopup.setItemVisible(XmippPopupMenuCreator.ENABLED, false);
92  xpopup.setItemVisible(XmippPopupMenuCreator.DISABLED, false);
93  return result;
94  }
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Definition at line 116 of file MetadataRowTableModel.java.

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118  return isSelected(row);
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Definition at line 127 of file MetadataRowTableModel.java.

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127  {
128  int min = Math.min(first_row, last_row);
129  int max = Math.max(first_row, last_row);
130  for (int i = min; i <= max; i++)
131  if(!isSelected(i))
132  {
133  setSelected(i, true);
134  fireTableCellUpdated(i, 0);
135  }
136  }
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Definition at line 121 of file MetadataRowTableModel.java.

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122  setSelected(row, b);
123  }
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82  {
83  super.setupTable(table);
84  table.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
85  }
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Definition at line 71 of file MetadataRowTableModel.java.

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71  {
72  data.setValueToCol(0, data.getColumnInfo(row), value.toString());
73  }// function setValueAt
xmipp.viewer.models.GalleryData.getColumnInfo
ColumnInfo getColumnInfo(String labelName)
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139  {
140  return false;
141  }
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Definition at line 110 of file MetadataRowTableModel.java.

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110  {
111  setSelected(row, !isSelected(row));
112  adjustWidth = false;
113  //fireTableCellUpdated(row, col);//item was clicked
114  }
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Definition at line 39 of file MetadataRowTableModel.java.

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The documentation for this class was generated from the following file: -
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xmipp.viewer.models.MetadataTableModel Member List
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This is the complete list of members for xmipp.viewer.models.MetadataTableModel, including all inherited members.

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adjustColumn(int width)xmipp.viewer.models.MetadataTableModelinline
adjustColumnsWidth()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
adjustWidthxmipp.viewer.models.ImageGalleryTableModel
busyRowsxmipp.viewer.models.ImageGalleryTableModelprotected
cachexmipp.viewer.models.ImageGalleryTableModelprotected
calculateCellSize()xmipp.viewer.models.MetadataTableModelinlineprotected
calculateMinAndMax()xmipp.viewer.models.ImageGalleryTableModelinline
cellDimxmipp.viewer.models.ImageGalleryTableModel
clearSelection()xmipp.viewer.models.ImageGalleryTableModelinline
columnModelxmipp.viewer.models.ImageGalleryTableModelprotected
createColumnModel()xmipp.viewer.models.MetadataTableModelinline
createImageItem(int index, ColumnInfo renderLabel)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
createItem(int index, String key, ColumnInfo ci)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
dataxmipp.viewer.models.ImageGalleryTableModel
dimensionxmipp.viewer.models.ImageGalleryTableModelprotected
getCellSize()xmipp.viewer.models.ImageGalleryTableModelinline
getColumn(int row, int col)xmipp.viewer.models.MetadataTableModelinline
getColumnClass(int column)xmipp.viewer.models.MetadataTableModelinline
getColumnCount()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnModel()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnName(int column)xmipp.viewer.models.MetadataTableModelinline
getColumns()xmipp.viewer.models.ImageGalleryTableModelinline
getCoords(int index)xmipp.viewer.models.MetadataTableModelinline
getFirstSelectedIndex()xmipp.viewer.models.ImageGalleryTableModelinline
getId(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getImage(long id, String imagepath, ColumnInfo renderLabel)xmipp.viewer.models.MetadataGalleryTableModelinline
getImageFilename(int index, int label)xmipp.viewer.models.MetadataGalleryTableModelinline
getImageHeight()xmipp.viewer.models.ImageGalleryTableModelinline
getImageLoader()xmipp.viewer.models.MetadataGalleryTableModelinline
getImageWidth()xmipp.viewer.models.ImageGalleryTableModelinline
getIndex(int row, int col)xmipp.viewer.models.MetadataTableModelinline
getItemKey(int index)xmipp.viewer.models.MetadataGalleryTableModelinline
xmipp::viewer::models::ImageGalleryTableModel.getItemKey(int index, int label)xmipp.viewer.models.ImageGalleryTableModelinline
getLabel(int row, int col)xmipp.viewer.models.MetadataGalleryTableModelinline
getMinAndMax()xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
getRenderer()xmipp.viewer.models.ImageGalleryTableModelinline
getRowCount()xmipp.viewer.models.ImageGalleryTableModelinline
getRows()xmipp.viewer.models.ImageGalleryTableModelinline
getSelection()xmipp.viewer.models.ImageGalleryTableModelinline
getSelectionCount()xmipp.viewer.models.ImageGalleryTableModelinline
getSelFrom()xmipp.viewer.models.ImageGalleryTableModelinline
getSelTo()xmipp.viewer.models.ImageGalleryTableModelinline
getSize()xmipp.viewer.models.ImageGalleryTableModelinline
getTableHeaderModel()xmipp.viewer.models.MetadataTableModelinline
getTitle()xmipp.viewer.models.MetadataGalleryTableModelinline
getValueAt(int row, int column)xmipp.viewer.models.MetadataTableModelinline
gotoItem(int i)xmipp.viewer.models.ImageGalleryTableModelinline
handleDoubleClick(int row, int col)xmipp.viewer.models.MetadataTableModelinline
handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)xmipp.viewer.models.MetadataTableModelinline
hasSelection()xmipp.viewer.models.ImageGalleryTableModelinline
image_widthxmipp.viewer.models.ImageGalleryTableModelprotected
ImageGalleryTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.ImageGalleryTableModelinline
isBusy(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isCellEditable(int row, int column)xmipp.viewer.models.MetadataTableModelinline
isSelected(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isSelected(int index)xmipp.viewer.models.ImageGalleryTableModelinline
isValidIndex(int index)xmipp.viewer.models.ImageGalleryTableModelinline
loadDimension()xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
MetadataGalleryTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.MetadataGalleryTableModelinline
MetadataTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.MetadataTableModelinline
nxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_calculatedxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_minxmipp.viewer.models.ImageGalleryTableModelprotected
openXmippImageWindow(int index, ColumnInfo ci)xmipp.viewer.models.MetadataGalleryTableModelinlineprotected
refreshAt(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
refreshRow(int row)xmipp.viewer.models.ImageGalleryTableModelinline
removeClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
rendererxmipp.viewer.models.ImageGalleryTableModelprotected
renderLabelxmipp.viewer.models.MetadataGalleryTableModelprotected
resizeCache()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
rowsxmipp.viewer.models.ImageGalleryTableModelprotected
scalexmipp.viewer.models.ImageGalleryTableModelprotected
selectionxmipp.viewer.models.ImageGalleryTableModelprotected
selectRange(int first_index, int last_index, boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
selectRange(int first_row, int first_col, int last_row, int last_col)xmipp.viewer.models.ImageGalleryTableModelinline
setColumns(int cols)xmipp.viewer.models.MetadataTableModelinline
setColumnsValue(int cols)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setInvertY(boolean itemSelected)xmipp.viewer.models.ImageGalleryTableModelinline
setMdValueAt(Object value, int row, int column, ColumnInfo ci, long id)xmipp.viewer.models.MetadataTableModelinlineprotected
setNormalized(boolean normalize)xmipp.viewer.models.ImageGalleryTableModelinline
setRenderImages(boolean value)xmipp.viewer.models.MetadataTableModelinline
setRowBusy(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRowIdle(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRows(int rows)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int index, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int row, int col, boolean b)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionEnabled(boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
setShowLabels()xmipp.viewer.models.ImageGalleryTableModelinline
setupItem(ImageItem item)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setupTable(JTable table)xmipp.viewer.models.MetadataTableModelinline
setUseGeometry(boolean geo, boolean wrap)xmipp.viewer.models.MetadataGalleryTableModelinline
setValueAt(Object value, int row, int column)xmipp.viewer.models.MetadataTableModelinline
setZoom(int z)xmipp.viewer.models.ImageGalleryTableModelinline
setZoomValue(int z)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
showLabels()xmipp.viewer.models.MetadataTableModelinline
thumb_widthxmipp.viewer.models.ImageGalleryTableModelprotected
touchItem(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
touchItem(int row, int col, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
updateColumnInfo(List< ColumnInfo > newInfo)xmipp.viewer.models.MetadataGalleryTableModelinline
updateTableSelection(JTable table)xmipp.viewer.models.MetadataTableModelinline
visibleLabelsxmipp.viewer.models.MetadataGalleryTableModel
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xmipp.viewer.models.MetadataTableModel Class Reference
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-Classes

class  MetadataColumnListener
 
class  MetadataColumnModel
 
class  MetadataTableHeader
 
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-Public Member Functions

 MetadataTableModel (GalleryData data, boolean[] selection) throws Exception
 
String getColumnName (int column)
 
Class getColumnClass (int column)
 
Object getValueAt (int row, int column)
 
void setValueAt (Object value, int row, int column)
 
boolean isCellEditable (int row, int column)
 
boolean handleDoubleClick (int row, int col)
 
void setColumns (int cols)
 
boolean adjustColumn (int width)
 
void setRenderImages (boolean value)
 
boolean showLabels ()
 
void setupTable (JTable table)
 
JTableHeader getTableHeaderModel ()
 
void updateTableSelection (JTable table)
 
boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
GalleryColumnModel createColumnModel ()
 
int getIndex (int row, int col)
 
ColumnInfo getColumn (int row, int col)
 
Point getCoords (int index)
 
- Public Member Functions inherited from xmipp.viewer.models.MetadataGalleryTableModel
 MetadataGalleryTableModel (GalleryData data, boolean[] selection) throws Exception
 
void updateColumnInfo (List< ColumnInfo > newInfo)
 
ImagePlus getImage (long id, String imagepath, ColumnInfo renderLabel)
 
String getLabel (int row, int col)
 
String getItemKey (int index) throws Exception
 
String getTitle ()
 
String getImageFilename (int index, int label)
 
boolean handleDoubleClick (int row, int col)
 
void setUseGeometry (boolean geo, boolean wrap)
 
ImagePlusLoader getImageLoader ()
 
boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
boolean showLabels ()
 
- Public Member Functions inherited from xmipp.viewer.models.ImageGalleryTableModel
 ImageGalleryTableModel (GalleryData data, boolean[] selection) throws Exception
 
int getImageWidth ()
 
int getImageHeight ()
 
int getColumnCount ()
 
int getRowCount ()
 
String getColumnName (int column)
 
Class getColumnClass (int c)
 
Object getValueAt (int row, int col)
 
void refreshAt (int row, int col)
 
void setRows (int rows)
 
void setColumns (int cols)
 
boolean adjustColumn (int width)
 
int getSize ()
 
Dimension getCellSize ()
 
void setupTable (JTable table)
 
void updateTableSelection (JTable table)
 
ImageItemRenderer getRenderer ()
 
GalleryColumnModel getColumnModel ()
 
JTableHeader getTableHeaderModel ()
 
void setZoom (int z)
 
int getIndex (int row, int col)
 
long getId (int row, int col)
 
boolean isValidIndex (int index)
 
abstract String getLabel (int row, int col)
 
Point getCoords (int index)
 
void setSelectionEnabled (boolean value)
 
int getFirstSelectedIndex ()
 
void selectRange (int first_index, int last_index, boolean value)
 
void selectRange (int first_row, int first_col, int last_row, int last_col)
 
void setSelectionClass (int classNumber)
 
void removeClass (int classNumber)
 
void touchItem (int row, int col)
 
void touchItem (int row, int col, boolean isselected)
 
void gotoItem (int i)
 
void setNormalized (boolean normalize)
 
void calculateMinAndMax ()
 
abstract boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
abstract boolean handleDoubleClick (int row, int col)
 
void setShowLabels ()
 
abstract String getItemKey (int index) throws Exception
 
String getItemKey (int index, int label) throws Exception
 
abstract String getTitle ()
 
abstract ImagePlusLoader getImageLoader ()
 
boolean isSelected (int row, int col)
 
abstract boolean showLabels ()
 
void setInvertY (boolean itemSelected)
 
int getRows ()
 
int getColumns ()
 
boolean isBusy (int row, int col)
 
void setRowBusy (int row)
 
void setRowIdle (int row)
 
void refreshRow (int row)
 
void clearSelection ()
 
int getSelectionCount ()
 
boolean [] getSelection ()
 
void setSelected (int index, boolean isselected)
 
boolean isSelected (int index)
 
int getSelFrom ()
 
int getSelTo ()
 
boolean hasSelection ()
 
void setSelected (int row, int col, boolean b)
 
ColumnInfo getColumn (int row, int col)
 
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-Protected Member Functions

void setMdValueAt (Object value, int row, int column, ColumnInfo ci, long id) throws Exception
 
void calculateCellSize ()
 
- Protected Member Functions inherited from xmipp.viewer.models.MetadataGalleryTableModel
void openXmippImageWindow (int index, ColumnInfo ci)
 
ImageDimension loadDimension () throws Exception
 
ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
ImageItem createImageItem (int index, ColumnInfo renderLabel) throws Exception
 
double [] getMinAndMax ()
 
- Protected Member Functions inherited from xmipp.viewer.models.ImageGalleryTableModel
abstract ImageDimension loadDimension () throws Exception
 
void resizeCache ()
 
void setupItem (ImageItem item)
 
void setColumnsValue (int cols)
 
void calculateCellSize ()
 
void adjustColumnsWidth ()
 
GalleryColumnModel createColumnModel ()
 
void setZoomValue (int z)
 
abstract double [] getMinAndMax ()
 
abstract ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
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-Additional Inherited Members

- Public Attributes inherited from xmipp.viewer.models.MetadataGalleryTableModel
ArrayList< ColumnInfo > visibleLabels
 
- Public Attributes inherited from xmipp.viewer.models.ImageGalleryTableModel
Dimension cellDim = new Dimension()
 
GalleryData data
 
boolean adjustWidth = true
 
- Protected Attributes inherited from xmipp.viewer.models.MetadataGalleryTableModel
ColumnInfo renderLabel
 
- Protected Attributes inherited from xmipp.viewer.models.ImageGalleryTableModel
ArrayList< Integer > busyRows = new ArrayList<Integer>()
 
int rows
 
int n
 
int image_width
 
int thumb_width
 
float scale = (float) 1.
 
Cache< String, ImageItem > cache
 
ImageDimension dimension
 
ImageItemRenderer renderer = new ImageItemRenderer()
 
GalleryColumnModel columnModel
 
boolean normalize_calculated = false
 
double normalize_min = Double.POSITIVE_INFINITY
 
boolean [] selection
 
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Detailed Description

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Definition at line 52 of file MetadataTableModel.java.

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Constructor & Destructor Documentation

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◆ MetadataTableModel()

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xmipp.viewer.models.MetadataTableModel.MetadataTableModel (GalleryData data,
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Definition at line 59 of file MetadataTableModel.java.

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59  {
60  super(data, selection);
61  cols = visibleLabels.size();
62  rows = n;
63  renderer.hackBorders = false;
64 
65  }
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◆ adjustColumn()

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boolean xmipp.viewer.models.MetadataTableModel.adjustColumn (int width)
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Definition at line 270 of file MetadataTableModel.java.

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270  {
271  return false;
272  }
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◆ calculateCellSize()

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void xmipp.viewer.models.MetadataTableModel.calculateCellSize ()
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Definition at line 307 of file MetadataTableModel.java.

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307  {
308  //System.out.println(String.format("MetadataTable:calculateSize renderLabel %s hasRenderLabel %s", data.renderImages, data.hasRenderLabel()));
309  if (data.renderImages && data.hasRenderLabel()) {
310  super.calculateCellSize();
311  //System.out.println(String.format("MetadataTable:calculateSize w:%d, h:%d", cellDim.width, cellDim.height));
312 
313  } else {
314  int font_height;
315  font_height = renderer.getFontMetrics(renderer.getFont())
316  .getHeight();
317  font_height += renderer.getIconTextGap(); // Adds the extra gap.
318  cellDim.setSize(200, font_height + 5);
319  }
320  }
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◆ createColumnModel()

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GalleryColumnModel xmipp.viewer.models.MetadataTableModel.createColumnModel ()
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Return the column model to be used with this table model

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Definition at line 371 of file MetadataTableModel.java.

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371  {
372  return new MetadataColumnModel();
373  }
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◆ getColumn()

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ColumnInfo xmipp.viewer.models.MetadataTableModel.getColumn (int row,
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Definition at line 543 of file MetadataTableModel.java.

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544  {
545  return visibleLabels.get(col);
546  }
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Class xmipp.viewer.models.MetadataTableModel.getColumnClass (int column)
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Definition at line 73 of file MetadataTableModel.java.

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73  {
74  ColumnInfo ci = visibleLabels.get(column);
75  Class c = null;
76  try {
77  if (ci.render)
78  c = ImageItem.class;
79  else if (ci.isEnable())
80  c = Boolean.class;//This way a JCheckBox is rendered
81  else
82  c = MetaData.getClassForType(ci.type);
83 
84  } catch (Exception e) {
85  e.printStackTrace();
86  }
87  return c;
88  }
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String xmipp.viewer.models.MetadataTableModel.getColumnName (int column)
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Definition at line 68 of file MetadataTableModel.java.

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68  {
69  return visibleLabels.get(column).labelName;
70  }
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Point xmipp.viewer.models.MetadataTableModel.getCoords (int index)
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Definition at line 549 of file MetadataTableModel.java.

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549  {
550 
551  Point p = new Point();
552  p.x = 0;
553  p.y = index;
554  return p;
555  }
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Definition at line 539 of file MetadataTableModel.java.

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539  {
540  return row;
541  }
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◆ getTableHeaderModel()

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JTableHeader xmipp.viewer.models.MetadataTableModel.getTableHeaderModel ()
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Definition at line 338 of file MetadataTableModel.java.

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338  {
339  return new MetadataTableHeader(columnModel);
340  }
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Object xmipp.viewer.models.MetadataTableModel.getValueAt (int row,
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Returns metadata value with java type

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Definition at line 95 of file MetadataTableModel.java.

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95  {
96  // DEBUG.printMessage(String.format("MetadataTable.getValueAt(%d, %d)",
97  // row, column));
98  try {
99 
100  ColumnInfo ci = visibleLabels.get(column);
101  if (ci.render) {
102 
103  String key = getItemKey(row, ci.label);
104  ImageItem item;
105  // If the element is on cache, just return it
106  if (cache.containsKey(key))
107  item = cache.get(key);
108  else {
109  // If not, create the item and store it for future
110  item = createImageItem(row, ci);
111  cache.put(key, item);
112  }
113  setupItem(item);
114  return item;
115  }
116  int label = ci.label;
117  long id = data.ids[row];
118 
119  int type = ci.type;
120  MetaData md = data.md;
121  switch (type) {
122  case MetaData.LABEL_INT:
123 
124  int value = md.getValueInt(label, id);
125  // treat special case of MDL_ENABLED
126  if (ci.isEnable())
127  return (value > 0);
128  return value;
129  case MetaData.LABEL_BOOL:
130  return md.getValueBoolean(label, id);
131  case MetaData.LABEL_DOUBLE:
132  return md.getValueDouble(label, id);
133  case MetaData.LABEL_SIZET:
134  return md.getValueLong(label, id);
135  case MetaData.LABEL_STRING:
136  String str = md.getValueString(label, data.ids[row]);
137  if (ci.labelName.contains("_transform._matrix"))
138  return String.format("<html>%s</html>", XmippUtil.formatNumbers(str).replace("],", "]<br>"));
139 
140  return str;
141  case MetaData.LABEL_VECTOR_DOUBLE:
142  case MetaData.LABEL_VECTOR_SIZET:
143  return md.getValueString(label, data.ids[row]);
144 
145  }
146  return null;
147 
148  } catch (Exception e) {
149  e.printStackTrace();
150 
151  }
152  return null;
153  }// function getValueAt
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xmipp.viewer.models.MetadataGalleryTableModel.createImageItem
ImageItem createImageItem(int index, ColumnInfo renderLabel)
Definition: MetadataGalleryTableModel.java:221
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static final int LABEL_INT
Definition: MetaData.java:45
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Definition at line 233 of file MetadataTableModel.java.

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233  {
234  try {
235 
236  ColumnInfo ci = visibleLabels.get(col);
237  if (ci.allowRender && data.isImageFile(ci)) {
238  int index = getIndex(row, col);
239  String file = getImageFilename(index, ci.label);
240  if(Filename.isVolume(file))
241  {
242  Params params = XmippApplication.isScipion()? ((ScipionParams)data.parameters).getScipionParams(): new Params();
243  ImagesWindowFactory.openMetadata(file, params, Params.OPENING_MODE_GALLERY);
244  }
245  else
246  openXmippImageWindow(index, ci);
247  return true;
248  }
249  if(data.isChimeraClient())//
250  {
251  String cmd = data.getChimeraProjectionCmd(row);
252  XmippWindowUtil.runCommand(cmd, data.parameters.getChimeraPort());
253  }
254  } catch (Exception e) {
255  if(e.getMessage() == null)
256  e.printStackTrace();
257  else
258  XmippDialog.showError(null, e.getMessage());
259 
260  }
261  return false;
262  }// function handleDoubleClick
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Integer getChimeraPort()
Definition: Params.java:339
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Definition: GalleryData.java:202
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boolean xmipp.viewer.models.MetadataTableModel.handleRightClick (int row,
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Definition at line 353 of file MetadataTableModel.java.

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354  {
355  if (isBusy(row, col))
356  return false;
357  xpopup.initItems();
358 
359  if (data.isFile(visibleLabels.get(col))) {
360 
361  xpopup.setItemVisible(XmippPopupMenuCreator.OPEN, true);
362  if (!data.isImageFile(visibleLabels.get(col)))
363  xpopup.setItemVisible(XmippPopupMenuCreator.OPEN_ASTEXT, true);
364  }
365 
366  return true;
367  }
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boolean isFile(ColumnInfo ci)
Definition: GalleryData.java:827
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boolean xmipp.viewer.models.MetadataTableModel.isCellEditable (int row,
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Definition at line 216 of file MetadataTableModel.java.

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216  {
217  ColumnInfo ci = visibleLabels.get(column);
218  if(ci.isEnable())
219  return ci.allowEdit;//maybe on metadatas sometimes is disabled
220  if(data.isScipionInstance() || data.isChimeraClient())
221  return false;
222 
223  return ci.allowEdit && !ci.render;
224  }
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Definition at line 265 of file MetadataTableModel.java.

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265  {
266 
267  }
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void xmipp.viewer.models.MetadataTableModel.setMdValueAt (Object value,
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ColumnInfo ci,
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Helper function to set the value of a cell

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Definition at line 181 of file MetadataTableModel.java.

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182  {
183  if (!ci.render) {
184  int label = ci.label;
185  int type = ci.type;
186  MetaData md = data.md;
187  switch (type) {
188  case MetaData.LABEL_BOOL:
189  md.setValueBoolean(label, (Boolean) value, id);
190  break;
191  case MetaData.LABEL_INT:
192  if (ci.isEnable()) {
193  md.setEnabled((Boolean) value, id);
194  } else
195  md.setValueInt(label, ((Integer) value).intValue(), id);
196  break;
197  case MetaData.LABEL_DOUBLE:
198  md.setValueDouble(label, ((Double) value).doubleValue(), id);
199  break;
200  case MetaData.LABEL_SIZET:
201  md.setValueLong(label, ((Long) value).longValue(), id);
202  break;
203  case MetaData.LABEL_STRING:
204  case MetaData.LABEL_VECTOR_DOUBLE:
205  case MetaData.LABEL_VECTOR_SIZET:
206  // TODO: Implement a better editor for vectors
207  md.setValueString(label, value.toString(), id);
208  break;
209  }
210  adjustWidth = false;
211  fireTableRowsUpdated(row, row);
212  }
213  }
xmipp.jni.MetaData.LABEL_BOOL
static final int LABEL_BOOL
Definition: MetaData.java:46
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void xmipp.viewer.models.MetadataTableModel.setRenderImages (boolean value)
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Whether to display the labels

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Definition at line 275 of file MetadataTableModel.java.

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275  {
276  boolean changed = false;
277  for (ColumnInfo ci : data.labels)
278  if (ci.allowRender && ci.render != value) {
279  ci.render = value;
280  changed = true;
281  if(data.ciFirstRender == null && value)
282  data.ciFirstRender = ci;
283  }
284  try
285  {
286  if (changed) {
287  data.renderImages = value;
288  loadDimension();
289  calculateCellSize();
290  fireTableDataChanged();
291  }
292 
293  }
294  catch (Exception e)
295  {
296  // TODO Auto-generated catch block
297  e.printStackTrace();
298  }
299  }
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void xmipp.viewer.models.MetadataTableModel.setupTable (JTable table)
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Definition at line 323 of file MetadataTableModel.java.

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323  {
324  table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
325  table.setDefaultRenderer(ImageItem.class, renderer);
326  table.setDefaultRenderer(Double.class, new FloatRenderer());
327  // MetadataTableHeader header = new MetadataTableHeader(columnModel);
328  // JTableHeader header = new JTableHeader(table.getColumnModel());
329  // table.setTableHeader(header);
330  JTableHeader header = table.getTableHeader();
331  header.setUpdateTableInRealTime(true);
332  header.addMouseListener(new MetadataColumnListener(table));
333  // header.setReorderingAllowed(true);
334  updateTableSelection(table);
335  }
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Definition at line 158 of file MetadataTableModel.java.

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158  {
159 
160  ColumnInfo ci = visibleLabels.get(column);
161  if (value == null || value.equals("")) {
162  XmippDialog.showError(null,
163  XmippMessage.getEmptyFieldMsg(ci.labelName));
164  return;// empty values are not allowed
165  }
166  try {
167  long id = data.ids[row];
168  setMdValueAt(value, row, column, ci, id);
169  data.setMdChanges(true);
170  } catch (Exception e) {
171  e.printStackTrace();
172  }
173 
174  }// function setValueAt
xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
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void setMdValueAt(Object value, int row, int column, ColumnInfo ci, long id)
Definition: MetadataTableModel.java:181
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Definition at line 302 of file MetadataTableModel.java.

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302  {
303  return data.renderImages;
304  }
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Definition at line 344 of file MetadataTableModel.java.

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344  {
345  table.clearSelection();
346  for (int i = 0; i < selection.length; ++i)
347  if (selection[i]) {
348  table.addRowSelectionInterval(i, i);
349  }
350  }
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This is the complete list of members for xmipp.viewer.models.MetadataTableModel.MetadataColumnListener, including all inherited members.

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ASCENDING_PREFIXxmipp.viewer.models.MetadataTableModel.MetadataColumnListenerstatic
DESCENDING_PREFIXxmipp.viewer.models.MetadataTableModel.MetadataColumnListenerstatic
MetadataColumnListener(JTable t)xmipp.viewer.models.MetadataTableModel.MetadataColumnListenerinline
mouseClicked(MouseEvent e)xmipp.viewer.models.MetadataTableModel.MetadataColumnListenerinline
removePreviousSortingIcon()xmipp.viewer.models.MetadataTableModel.MetadataColumnListenerinlineprotected
tablexmipp.viewer.models.MetadataTableModel.MetadataColumnListenerprotected
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-Public Member Functions

 MetadataColumnListener (JTable t)
 
void mouseClicked (MouseEvent e)
 
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static final String ASCENDING_PREFIX = "\u25B2 "
 
static final String DESCENDING_PREFIX = "\u25BC "
 
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void removePreviousSortingIcon ()
 
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JTable table
 
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Definition at line 455 of file MetadataTableModel.java.

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◆ MetadataColumnListener()

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xmipp.viewer.models.MetadataTableModel.MetadataColumnListener.MetadataColumnListener (JTable t)
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Definition at line 460 of file MetadataTableModel.java.

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460  {
461  table = t;
462  }
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◆ mouseClicked()

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void xmipp.viewer.models.MetadataTableModel.MetadataColumnListener.mouseClicked (MouseEvent e)
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Definition at line 464 of file MetadataTableModel.java.

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464  {
465 
466  TableColumnModel colModel = table.getColumnModel();
467  // Get the clicked column index
468  int columnModelIndex = colModel.getColumnIndexAtX(e.getX());
469 
470  // Get the column
471  final TableColumn column = colModel.getColumn(columnModelIndex);
472 
473  // Take into account a possible reordering of columns
474  int modelIndex = column.getModelIndex();
475 
476  // Take into account possible invisible columns indexing
477  modelIndex = data.getVisibleColumnIndex(modelIndex);
478  if (modelIndex < 0)
479  return;
480  if (sortColumnIndex == modelIndex)
481  ascending = !ascending;
482  else
483 
484  // Remove previous sorting icon
485  removePreviousSortingIcon();
486  sortColumnIndex = modelIndex;
487 
488 
489  final String columnName = data.labels.get(sortColumnIndex).labelName;
490 
491  column.setHeaderValue( "\u231B " + columnName);
492  Runnable sort = new Runnable() {
493  @Override
494  public void run() {
495 
496  data.sortMd(data.labels.get(sortColumnIndex), ascending);
497  column.setHeaderValue((ascending? ASCENDING_PREFIX : DESCENDING_PREFIX)+columnName);
498  table.getTableHeader().repaint();
499  clearSelection();
500  updateTableSelection(table);
501  cache.clear();
502  table.repaint();
503 
504  }
505  };
506 
507  SwingUtilities.invokeLater(sort);
508 
509  }
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void sortMd(ColumnInfo sortci, boolean asc)
Definition: GalleryData.java:624
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void xmipp.viewer.models.MetadataTableModel.MetadataColumnListener.removePreviousSortingIcon ()
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Definition at line 511 of file MetadataTableModel.java.

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511  {
512 
513  // If there is a previous column sorted
514  if (sortColumnIndex != NO_COLUMN_INDEX){
515  // Get the column model
516  TableColumnModel colModel = table.getColumnModel();
517 
518  // For each column
519  for (int i=0; i<colModel.getColumnCount();i++){
520  TableColumn col = colModel.getColumn(i);
521  String header = col.getHeaderValue().toString();
522 
523  // If it has the ascending prefix
524  if (header.startsWith(ASCENDING_PREFIX) ){
525  // remove it
526  col.setHeaderValue(header.replaceFirst(ASCENDING_PREFIX, ""));
527  return;
528  } else if (header.startsWith(DESCENDING_PREFIX)) {
529  // remove it
530  col.setHeaderValue(header.replaceFirst(DESCENDING_PREFIX, ""));
531  return;
532  }
533  }
534  }
535  }
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◆ ASCENDING_PREFIX

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final String xmipp.viewer.models.MetadataTableModel.MetadataColumnListener.ASCENDING_PREFIX = "\u25B2 "
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Definition at line 456 of file MetadataTableModel.java.

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final String xmipp.viewer.models.MetadataTableModel.MetadataColumnListener.DESCENDING_PREFIX = "\u25BC "
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Definition at line 457 of file MetadataTableModel.java.

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◆ table

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Definition at line 458 of file MetadataTableModel.java.

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- - diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__coll__graph.dot b/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__coll__graph.dot deleted file mode 100644 index e71bda71..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.viewer.models.MetadataTableModel.MetadataColumnListener" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.models.Metadata\lTableModel.MetadataColumnListener",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="MouseAdapter",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node4 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" table" ,fontname="Helvetica"]; - Node4 [label="JTable",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__coll__graph.md5 deleted file mode 100644 index cd3e426d..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -4a095d2681c0c02a6fc7bd3e60d45842 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__inherit__graph.dot deleted file mode 100644 index 7718be0b..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.models.MetadataTableModel.MetadataColumnListener" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.models.Metadata\lTableModel.MetadataColumnListener",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="MouseAdapter",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__inherit__graph.md5 deleted file mode 100644 index 9278ff2c..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnListener__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ffcb55049b7efa508e629702039379d5 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnModel-members.html b/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnModel-members.html deleted file mode 100644 index 3bbbf34d..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1MetadataTableModel_1_1MetadataColumnModel-members.html +++ /dev/null @@ -1,88 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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addColumn(TableColumn tc)xmipp.viewer.models.GalleryColumnModelinline
adjustColumnsWidth(JTable table)xmipp.viewer.models.MetadataTableModel.MetadataColumnModelinline
GalleryColumnModel(int w)xmipp.viewer.models.GalleryColumnModelinline
MetadataColumnModel()xmipp.viewer.models.MetadataTableModel.MetadataColumnModelinline
setWidth(int width)xmipp.viewer.models.GalleryColumnModelinline
widthxmipp.viewer.models.GalleryColumnModelprotected
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 MetadataColumnModel ()
 
void adjustColumnsWidth (JTable table)
 
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 GalleryColumnModel (int w)
 
void addColumn (TableColumn tc)
 
void setWidth (int width)
 
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Definition at line 375 of file MetadataTableModel.java.

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◆ MetadataColumnModel()

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Definition at line 376 of file MetadataTableModel.java.

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376  {
377  super(0);
378  }
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Definition at line 381 of file MetadataTableModel.java.

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381  {
382  try {
383  if (visibleLabels.size() != getColumnCount())
384  return;
385 
386  //DEBUG.printStackTrace();
387 
388  calculateCellSize();
389  // String[] row = md.getRowValues(data.ids[0]);
390  // table.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
391  int width = 0;
392  TableCellRenderer rend;
393  Component comp;
394  boolean non_empty = data.md.size() > 0;
395  TableColumn tc;
396  ColumnInfo col;
397  for (int i = 0; i < visibleLabels.size(); i++) {
398  col = visibleLabels.get(i);
399  tc = getColumn(i);
400  width = 0;
401  // Calculate width of the cell
402  if (col.render) {
403  width = cellDim.width;
404  } else if (non_empty) {
405  // else {
406 
407  rend = table.getCellRenderer(0, i);
408  if(rend != null)
409  {
410  Object value = table.getValueAt(0, i);
411  //If columns are reordered Renderer may be related to column according to visual order but value is related to real order
412  comp = rend.getTableCellRendererComponent(table, value, false, false, 0, i);
413  width = comp.getPreferredSize().width + 10;
414  }
415  }
416  // Calculate width of the header
417  rend = tc.getHeaderRenderer();
418  if (rend == null)
419  rend = table.getTableHeader().getDefaultRenderer();
420  Object value = tc.getHeaderValue();
421  comp = rend.getTableCellRendererComponent(table, value,
422  false, false, 0, i);
423  // Take max width
424  width = Math.max(width, comp.getPreferredSize().width);
425  getColumn(i).setPreferredWidth(width + 10);
426  // DEBUG.printMessage(String.format("col: %d, width: %d", i,
427  // width));
428  }
429  } catch (Exception e) {
430  // TODO Auto-generated catch block
431  e.printStackTrace();
432  }
433  }// function adjustColumnsWidth
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xmipp.viewer.models.MetadataTableModel.getColumn
ColumnInfo getColumn(int row, int col)
Definition: MetadataTableModel.java:543
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xmipp.viewer.models.MetadataTableModel.MetadataTableHeader Member List
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This is the complete list of members for xmipp.viewer.models.MetadataTableModel.MetadataTableHeader, including all inherited members.

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getToolTipText(MouseEvent e)xmipp.viewer.models.MetadataTableModel.MetadataTableHeaderinline
MetadataTableHeader(TableColumnModel columnModel)xmipp.viewer.models.MetadataTableModel.MetadataTableHeaderinline
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xmipp.viewer.models.MetadataTableModel.MetadataTableHeader Class Reference
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-Public Member Functions

 MetadataTableHeader (TableColumnModel columnModel)
 
String getToolTipText (MouseEvent e)
 
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Detailed Description

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Definition at line 437 of file MetadataTableModel.java.

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Constructor & Destructor Documentation

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◆ MetadataTableHeader()

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xmipp.viewer.models.MetadataTableModel.MetadataTableHeader.MetadataTableHeader (TableColumnModel columnModel)
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Definition at line 438 of file MetadataTableModel.java.

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438  {
439  super(columnModel);
440  }
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◆ getToolTipText()

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String xmipp.viewer.models.MetadataTableModel.MetadataTableHeader.getToolTipText (MouseEvent e)
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Show tooltips on columns header

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Definition at line 443 of file MetadataTableModel.java.

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443  {
444  java.awt.Point p = e.getPoint();
445  int index = columnModel.getColumnIndexAtX(p.x);
446  if (index > -1){
447  int col = table.convertColumnIndexToModel(index);
448  return visibleLabels.get(col).comment;
449  }
450 
451  return null;
452  }
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xmipp.viewer.models.VolumeGalleryTableModel Member List
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This is the complete list of members for xmipp.viewer.models.VolumeGalleryTableModel, including all inherited members.

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adjustColumn(int width)xmipp.viewer.models.ImageGalleryTableModelinline
adjustColumnsWidth()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
adjustWidthxmipp.viewer.models.ImageGalleryTableModel
busyRowsxmipp.viewer.models.ImageGalleryTableModelprotected
cachexmipp.viewer.models.ImageGalleryTableModelprotected
calculateCellSize()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
calculateMinAndMax()xmipp.viewer.models.ImageGalleryTableModelinline
cellDimxmipp.viewer.models.ImageGalleryTableModel
clearSelection()xmipp.viewer.models.ImageGalleryTableModelinline
columnModelxmipp.viewer.models.ImageGalleryTableModelprotected
createColumnModel()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
createItem(int index, String key, ColumnInfo ci)xmipp.viewer.models.VolumeGalleryTableModelinlineprotected
dataxmipp.viewer.models.ImageGalleryTableModel
dimensionxmipp.viewer.models.ImageGalleryTableModelprotected
getCellSize()xmipp.viewer.models.ImageGalleryTableModelinline
getColumn(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getColumnClass(int c)xmipp.viewer.models.ImageGalleryTableModelinline
getColumnCount()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnModel()xmipp.viewer.models.ImageGalleryTableModelinline
getColumnName(int column)xmipp.viewer.models.ImageGalleryTableModelinline
getColumns()xmipp.viewer.models.ImageGalleryTableModelinline
getCoords(int index)xmipp.viewer.models.ImageGalleryTableModelinline
getFirstSelectedIndex()xmipp.viewer.models.ImageGalleryTableModelinline
getId(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getImageHeight()xmipp.viewer.models.ImageGalleryTableModelinline
getImageLoader()xmipp.viewer.models.VolumeGalleryTableModelinline
getImageWidth()xmipp.viewer.models.ImageGalleryTableModelinline
getIndex(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
getItemKey(int index)xmipp.viewer.models.VolumeGalleryTableModelinline
xmipp::viewer::models::ImageGalleryTableModel.getItemKey(int index, int label)xmipp.viewer.models.ImageGalleryTableModelinline
getLabel(int row, int col)xmipp.viewer.models.VolumeGalleryTableModelinline
getMinAndMax()xmipp.viewer.models.VolumeGalleryTableModelinlineprotected
getRenderer()xmipp.viewer.models.ImageGalleryTableModelinline
getRowCount()xmipp.viewer.models.ImageGalleryTableModelinline
getRows()xmipp.viewer.models.ImageGalleryTableModelinline
getSelection()xmipp.viewer.models.ImageGalleryTableModelinline
getSelectionCount()xmipp.viewer.models.ImageGalleryTableModelinline
getSelFrom()xmipp.viewer.models.ImageGalleryTableModelinline
getSelTo()xmipp.viewer.models.ImageGalleryTableModelinline
getSize()xmipp.viewer.models.ImageGalleryTableModelinline
getTableHeaderModel()xmipp.viewer.models.ImageGalleryTableModelinline
getTitle()xmipp.viewer.models.VolumeGalleryTableModelinline
getValueAt(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
gotoItem(int i)xmipp.viewer.models.ImageGalleryTableModelinline
handleDoubleClick(int row, int col)xmipp.viewer.models.VolumeGalleryTableModelinline
handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)xmipp.viewer.models.VolumeGalleryTableModelinline
hasSelection()xmipp.viewer.models.ImageGalleryTableModelinline
image_widthxmipp.viewer.models.ImageGalleryTableModelprotected
ImageGalleryTableModel(GalleryData data, boolean[] selection)xmipp.viewer.models.ImageGalleryTableModelinline
isBusy(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isSelected(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
isSelected(int index)xmipp.viewer.models.ImageGalleryTableModelinline
isValidIndex(int index)xmipp.viewer.models.ImageGalleryTableModelinline
loadDimension()xmipp.viewer.models.VolumeGalleryTableModelinlineprotected
nxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_calculatedxmipp.viewer.models.ImageGalleryTableModelprotected
normalize_minxmipp.viewer.models.ImageGalleryTableModelprotected
refreshAt(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
refreshRow(int row)xmipp.viewer.models.ImageGalleryTableModelinline
removeClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
rendererxmipp.viewer.models.ImageGalleryTableModelprotected
resizeCache()xmipp.viewer.models.ImageGalleryTableModelinlineprotected
rowsxmipp.viewer.models.ImageGalleryTableModelprotected
scalexmipp.viewer.models.ImageGalleryTableModelprotected
selectionxmipp.viewer.models.ImageGalleryTableModelprotected
selectRange(int first_index, int last_index, boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
selectRange(int first_row, int first_col, int last_row, int last_col)xmipp.viewer.models.ImageGalleryTableModelinline
setColumns(int cols)xmipp.viewer.models.ImageGalleryTableModelinline
setColumnsValue(int cols)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setInvertY(boolean itemSelected)xmipp.viewer.models.ImageGalleryTableModelinline
setNormalized(boolean normalize)xmipp.viewer.models.ImageGalleryTableModelinline
setRowBusy(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRowIdle(int row)xmipp.viewer.models.ImageGalleryTableModelinline
setRows(int rows)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int index, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
setSelected(int row, int col, boolean b)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionClass(int classNumber)xmipp.viewer.models.ImageGalleryTableModelinline
setSelectionEnabled(boolean value)xmipp.viewer.models.ImageGalleryTableModelinline
setShowLabels()xmipp.viewer.models.ImageGalleryTableModelinline
setupItem(ImageItem item)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
setupTable(JTable table)xmipp.viewer.models.ImageGalleryTableModelinline
setZoom(int z)xmipp.viewer.models.ImageGalleryTableModelinline
setZoomValue(int z)xmipp.viewer.models.ImageGalleryTableModelinlineprotected
showLabels()xmipp.viewer.models.VolumeGalleryTableModelinline
thumb_widthxmipp.viewer.models.ImageGalleryTableModelprotected
touchItem(int row, int col)xmipp.viewer.models.ImageGalleryTableModelinline
touchItem(int row, int col, boolean isselected)xmipp.viewer.models.ImageGalleryTableModelinline
updateTableSelection(JTable table)xmipp.viewer.models.ImageGalleryTableModelinline
volFnxmipp.viewer.models.VolumeGalleryTableModelprotected
volNumberxmipp.viewer.models.VolumeGalleryTableModelprotected
VolumeGalleryTableModel(GalleryData data)xmipp.viewer.models.VolumeGalleryTableModelinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1models_1_1VolumeGalleryTableModel.html b/html/classxmipp_1_1viewer_1_1models_1_1VolumeGalleryTableModel.html deleted file mode 100644 index 7f49554a..00000000 --- a/html/classxmipp_1_1viewer_1_1models_1_1VolumeGalleryTableModel.html +++ /dev/null @@ -1,763 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.models.VolumeGalleryTableModel Class Reference - - - - - - - - - -
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-Public Member Functions | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.viewer.models.VolumeGalleryTableModel Class Reference
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-Inheritance diagram for xmipp.viewer.models.VolumeGalleryTableModel:
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-Public Member Functions

 VolumeGalleryTableModel (GalleryData data) throws Exception
 
String getItemKey (int index) throws Exception
 
String getTitle ()
 
boolean handleDoubleClick (int row, int col)
 
String getLabel (int row, int col)
 
ImagePlusLoader getImageLoader ()
 
boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
boolean showLabels ()
 
- Public Member Functions inherited from xmipp.viewer.models.ImageGalleryTableModel
 ImageGalleryTableModel (GalleryData data, boolean[] selection) throws Exception
 
int getImageWidth ()
 
int getImageHeight ()
 
int getColumnCount ()
 
int getRowCount ()
 
String getColumnName (int column)
 
Class getColumnClass (int c)
 
Object getValueAt (int row, int col)
 
void refreshAt (int row, int col)
 
void setRows (int rows)
 
void setColumns (int cols)
 
boolean adjustColumn (int width)
 
int getSize ()
 
Dimension getCellSize ()
 
void setupTable (JTable table)
 
void updateTableSelection (JTable table)
 
ImageItemRenderer getRenderer ()
 
GalleryColumnModel getColumnModel ()
 
JTableHeader getTableHeaderModel ()
 
void setZoom (int z)
 
int getIndex (int row, int col)
 
long getId (int row, int col)
 
boolean isValidIndex (int index)
 
abstract String getLabel (int row, int col)
 
Point getCoords (int index)
 
void setSelectionEnabled (boolean value)
 
int getFirstSelectedIndex ()
 
void selectRange (int first_index, int last_index, boolean value)
 
void selectRange (int first_row, int first_col, int last_row, int last_col)
 
void setSelectionClass (int classNumber)
 
void removeClass (int classNumber)
 
void touchItem (int row, int col)
 
void touchItem (int row, int col, boolean isselected)
 
void gotoItem (int i)
 
void setNormalized (boolean normalize)
 
void calculateMinAndMax ()
 
abstract boolean handleRightClick (int row, int col, XmippPopupMenuCreator xpopup)
 
abstract boolean handleDoubleClick (int row, int col)
 
void setShowLabels ()
 
abstract String getItemKey (int index) throws Exception
 
String getItemKey (int index, int label) throws Exception
 
abstract String getTitle ()
 
abstract ImagePlusLoader getImageLoader ()
 
boolean isSelected (int row, int col)
 
abstract boolean showLabels ()
 
void setInvertY (boolean itemSelected)
 
int getRows ()
 
int getColumns ()
 
boolean isBusy (int row, int col)
 
void setRowBusy (int row)
 
void setRowIdle (int row)
 
void refreshRow (int row)
 
void clearSelection ()
 
int getSelectionCount ()
 
boolean [] getSelection ()
 
void setSelected (int index, boolean isselected)
 
boolean isSelected (int index)
 
int getSelFrom ()
 
int getSelTo ()
 
boolean hasSelection ()
 
void setSelected (int row, int col, boolean b)
 
ColumnInfo getColumn (int row, int col)
 
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-Protected Member Functions

ImageDimension loadDimension () throws Exception
 
double [] getMinAndMax ()
 
ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
- Protected Member Functions inherited from xmipp.viewer.models.ImageGalleryTableModel
abstract ImageDimension loadDimension () throws Exception
 
void resizeCache ()
 
void setupItem (ImageItem item)
 
void setColumnsValue (int cols)
 
void calculateCellSize ()
 
void adjustColumnsWidth ()
 
GalleryColumnModel createColumnModel ()
 
void setZoomValue (int z)
 
abstract double [] getMinAndMax ()
 
abstract ImageItem createItem (int index, String key, ColumnInfo ci) throws Exception
 
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-Protected Attributes

String volFn
 
long volNumber
 
- Protected Attributes inherited from xmipp.viewer.models.ImageGalleryTableModel
ArrayList< Integer > busyRows = new ArrayList<Integer>()
 
int rows
 
int n
 
int image_width
 
int thumb_width
 
float scale = (float) 1.
 
Cache< String, ImageItem > cache
 
ImageDimension dimension
 
ImageItemRenderer renderer = new ImageItemRenderer()
 
GalleryColumnModel columnModel
 
boolean normalize_calculated = false
 
double normalize_min = Double.POSITIVE_INFINITY
 
boolean [] selection
 
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-Additional Inherited Members

- Public Attributes inherited from xmipp.viewer.models.ImageGalleryTableModel
Dimension cellDim = new Dimension()
 
GalleryData data
 
boolean adjustWidth = true
 
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Detailed Description

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Definition at line 40 of file VolumeGalleryTableModel.java.

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Constructor & Destructor Documentation

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◆ VolumeGalleryTableModel()

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xmipp.viewer.models.VolumeGalleryTableModel.VolumeGalleryTableModel (GalleryData data) throws Exception
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Definition at line 46 of file VolumeGalleryTableModel.java.

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46  {
47  super(data, null);
48  data.normalize = true; // volumes are displayed with global
49  // normalization by default
50  selection = new boolean[n];
51  calculateMinAndMax();
52  }
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◆ createItem()

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ImageItem xmipp.viewer.models.VolumeGalleryTableModel.createItem (int index,
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Definition at line 108 of file VolumeGalleryTableModel.java.

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108  {
109  ImageGeneric preview = new ImageGeneric();
110  volume.getPreview(preview, thumb_width, thumb_height, index + 1,
111  ImageGeneric.FIRST_IMAGE);
112  ImagePlus imp = new ImagePlusLoader(preview, data.inverty).getImagePlus();
113  ImageItem item = new ImageItem(index, imp);
114  //item.setImagePlus(imp);
115  return item;
116  }
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ImagePlusLoader xmipp.viewer.models.VolumeGalleryTableModel.getImageLoader ()
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Definition at line 139 of file VolumeGalleryTableModel.java.

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139  {
140  try {
141  ImagePlusLoader loader = new ImagePlusLoader(data.selectedVolFn, data.inverty);
142  if(data.normalize)
143  loader.setNormalize(normalize_min, normalize_max);
144  return loader;
145  } catch (Exception e) {
146  e.printStackTrace();
147  }
148  return null;
149  }
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◆ getItemKey()

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String xmipp.viewer.models.VolumeGalleryTableModel.getItemKey (int index) throws Exception
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Definition at line 97 of file VolumeGalleryTableModel.java.

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97  {
98  return String.format("%d_(%d,%d)", index, thumb_width, thumb_height);
99  }
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String xmipp.viewer.models.VolumeGalleryTableModel.getLabel (int row,
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Definition at line 133 of file VolumeGalleryTableModel.java.

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133  {
134  int index = getIndex(row, col);
135  return String.format("slice %d", index + 1);
136  }
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◆ getMinAndMax()

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Definition at line 83 of file VolumeGalleryTableModel.java.

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83  {
84  try {
85  // ImageGeneric image = new ImageGeneric(volFn);
86  // image.read(volNumber);
87  double[] stats = volume.getStatistics();
88  // image.destroy();
89  return stats;
90  } catch (Exception ex) {
91  ex.printStackTrace();
92  }
93  return null;
94  }
xmipp.jni.ImageGeneric.getStatistics
native double [] getStatistics()
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◆ getTitle()

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String xmipp.viewer.models.VolumeGalleryTableModel.getTitle ()
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Definition at line 102 of file VolumeGalleryTableModel.java.

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102  {
103  return String.format("Volume: %s (%d x %d x %d)", data.selectedVolFn,
104  image_width, image_height, n);
105  }
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◆ handleDoubleClick()

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boolean xmipp.viewer.models.VolumeGalleryTableModel.handleDoubleClick (int row,
int col 
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Definition at line 119 of file VolumeGalleryTableModel.java.

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119  {
120  try {
121  int index = getIndex(row, col);
122  //ImagePlus imp = XmippImageConverter.convertToImagePlus(volume, ImageGeneric.FIRST_IMAGE, index + 1);
123  ImagePlusLoader loader = new ImagePlusLoader(index + 1, volume, data.inverty);
124  ImagesWindowFactory.openXmippImageWindow(loader, data.parameters);
125  return true;
126  } catch (Exception e) {
127  e.printStackTrace();
128  }
129  return false;
130  }// function handleDoubleClick
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boolean xmipp.viewer.models.VolumeGalleryTableModel.handleRightClick (int row,
int col,
XmippPopupMenuCreator xpopup 
)
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Definition at line 152 of file VolumeGalleryTableModel.java.

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153  {
154  return false;
155  }
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◆ loadDimension()

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ImageDimension xmipp.viewer.models.VolumeGalleryTableModel.loadDimension () throws Exception
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Definition at line 57 of file VolumeGalleryTableModel.java.

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57  {
58  volFn = Filename.getFilename(data.selectedVolFn);
59  DEBUG.printFormat("loading volFn: %s", volFn);
60  volNumber = Filename.getNimage(data.selectedVolFn);
61  volume = new ImageGeneric(data.selectedVolFn); // read image header
62  volume.read(volNumber);
63  if (data.resliceView != ImageGeneric.Z_NEG)
64  volume.reslice(data.resliceView);
65  ImageDimension dim = new ImageDimension(volume);
66  n = dim.getZDim();
67  image_width = dim.getXDim();
68  image_height = dim.getYDim();
69  return dim;
70  }
xmipp.jni.ImageGeneric.reslice
native void reslice(int view)
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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Definition at line 158 of file VolumeGalleryTableModel.java.

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158  {
159  return false;
160  }
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Member Data Documentation

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◆ volFn

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String xmipp.viewer.models.VolumeGalleryTableModel.volFn
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Definition at line 42 of file VolumeGalleryTableModel.java.

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◆ volNumber

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Definition at line 43 of file VolumeGalleryTableModel.java.

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The documentation for this class was generated from the following file: -
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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.ColorHelper Member List
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This is the complete list of members for xmipp.viewer.particlepicker.ColorHelper, including all inherited members.

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ColorHelper(int id, String name, Color color, MetaData md)xmipp.viewer.particlepicker.ColorHelperinline
ColorHelper(int id, String name, MetaData md)xmipp.viewer.particlepicker.ColorHelperinline
getColor(double score)xmipp.viewer.particlepicker.ColorHelperinline
getColorMap()xmipp.viewer.particlepicker.ColorHelperinlinestatic
getId()xmipp.viewer.particlepicker.ColorHelperinline
getMax()xmipp.viewer.particlepicker.ColorHelperinline
getMin()xmipp.viewer.particlepicker.ColorHelperinline
getName()xmipp.viewer.particlepicker.ColorHelperinline
getNextColor()xmipp.viewer.particlepicker.ColorHelperinlinestatic
getSampleColors()xmipp.viewer.particlepicker.ColorHelperinlinestatic
numberToColor(final double value)xmipp.viewer.particlepicker.ColorHelperinlinestatic
numberToColorPercentage(final double value)xmipp.viewer.particlepicker.ColorHelperinlinestatic
toString()xmipp.viewer.particlepicker.ColorHelperinline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ColorHelper.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ColorHelper.html deleted file mode 100644 index 090fd304..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ColorHelper.html +++ /dev/null @@ -1,534 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.ColorHelper Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Static Public Member Functions | -List of all members
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xmipp.viewer.particlepicker.ColorHelper Class Reference
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-Public Member Functions

 ColorHelper (int id, String name, Color color, MetaData md)
 
 ColorHelper (int id, String name, MetaData md)
 
String toString ()
 
String getName ()
 
int getId ()
 
Color getColor (double score)
 
double getMin ()
 
double getMax ()
 
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static Color getNextColor ()
 
static Color [] getSampleColors ()
 
static Color numberToColor (final double value)
 
static Color numberToColorPercentage (final double value)
 
static JPanel getColorMap ()
 
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Definition at line 22 of file ColorHelper.java.

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Definition at line 39 of file ColorHelper.java.

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40  {
41  this.id = id;
42  this.name = name;
43  max = Math.rint(md.getColumnMax(id) * 100)/100;
44  min = Math.rint(md.getColumnMin(id) * 100)/100;
45  range = max - min;
46  }
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Definition at line 48 of file ColorHelper.java.

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49  {
50  this(id, name, getNextColor(), md);
51  }
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Definition at line 87 of file ColorHelper.java.

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88  {
89 
90  double percent = 1;
91  if(range > 0)
92  percent = (score - min)/range;
93  Color scorecolor = numberToColorPercentage(percent);
94  return scorecolor;
95  }
xmipp.viewer.particlepicker.ColorHelper.numberToColorPercentage
static Color numberToColorPercentage(final double value)
Definition: ColorHelper.java:116
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129  {
130  JPanel mappn = new JPanel(new FlowLayout(FlowLayout.LEFT, 0, 0));
131  for(int i = 0; i < map.size(); i += 10)
132  mappn.add(new JLabel(new ColorIcon(map.get(i), 1, 20, 0, false, false)));
133  return mappn;
134  }
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84  return id;
85  }
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216  return max;
217  }
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211  return min;
212  }
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79  return name;
80  }
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Definition at line 57 of file ColorHelper.java.

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58  {
59  Color next = colors[nextcolor];
60  nextcolor++;
61  if (nextcolor == colors.length)
62  nextcolor = 0;
63  return next;
64  }
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67  return colors;
68  }
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Definition at line 104 of file ColorHelper.java.

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104  {
105  if (value < 0 || value > 100) {
106  return null;
107  }
108  return numberToColorPercentage(value / 100);
109  }
xmipp.viewer.particlepicker.ColorHelper.numberToColorPercentage
static Color numberToColorPercentage(final double value)
Definition: ColorHelper.java:116
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Definition at line 116 of file ColorHelper.java.

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116  {
117  if (value < 0 || value > 1) {
118  return null;
119  }
120  Double d = value * factor;
121  int index = d.intValue();
122  if (index == factor) {
123  index--;
124  }
125  return map.get(index);
126  }
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Definition at line 70 of file ColorHelper.java.

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71  {
72  return name;
73  }
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ctfxmipp.viewer.particlepicker.CtfInfo
defocusUxmipp.viewer.particlepicker.CtfInfo
fitQualityxmipp.viewer.particlepicker.CtfInfo
psdxmipp.viewer.particlepicker.CtfInfo
resolutionxmipp.viewer.particlepicker.CtfInfo
voltagexmipp.viewer.particlepicker.CtfInfo
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String psd
 
String ctf
 
Float voltage
 
Float defocusU
 
Float resolution
 
Float fitQuality
 
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Definition at line 3 of file CtfInfo.java.

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◆ ctf

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String xmipp.viewer.particlepicker.CtfInfo.ctf
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Definition at line 6 of file CtfInfo.java.

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Definition at line 7 of file CtfInfo.java.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
browsebtxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
browseDirectory(JTextField sourcetf)xmipp.viewer.particlepicker.ImportParticlesJDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.particlepicker.ImportParticlesJDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
formatxmipp.viewer.particlepicker.ImportParticlesJDialog
formatsListxmipp.viewer.particlepicker.ImportParticlesJDialogstatic
formatsStringxmipp.viewer.particlepicker.ImportParticlesJDialogstatic
handleActionPerformed(ActionEvent evt)xmipp.viewer.particlepicker.ImportParticlesJDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.viewer.particlepicker.ImportParticlesJDialoginline
importParticles()xmipp.viewer.particlepicker.ImportParticlesJDialoginlineprotected
ImportParticlesJDialog(ParticlePickerJFrame parent)xmipp.viewer.particlepicker.ImportParticlesJDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
invertxcbxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
invertycbxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
jcbFormatxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
pathxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
scaletfxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
sourcetfxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
xfcxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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 ImportParticlesJDialog (ParticlePickerJFrame parent)
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
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boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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Format format = Format.Auto
 
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-Static Public Attributes

static final String [] formatsString = new String[]{Format.Auto.toString(), Format.Xmipp24.toString(), Format.Xmipp30.toString(), Format.Xmipp301.toString(), Format.Eman.toString(), Format.Relion.toString()}
 
static final Format [] formatsList
 
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void createContent (JPanel panel)
 
void browseDirectory (JTextField sourcetf)
 
String importParticles ()
 
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void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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ParticlePickerJFrame parent
 
JTextField sourcetf
 
JButton browsebt
 
JComboBox jcbFormat
 
XmippFileChooser xfc = null
 
String path
 
JFormattedTextField scaletf
 
JCheckBox invertxcb
 
JCheckBox invertycb
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
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Definition at line 29 of file ImportParticlesJDialog.java.

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Definition at line 48 of file ImportParticlesJDialog.java.

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48  {
49  super(parent, "Import Particles", true);
50  this.parent = parent;
51  xfc = new XmippFileChooser();
52  if(parent instanceof SupervisedPickerJFrame)
53  xfc.setFileSelectionMode(XmippFileChooser.FILES_AND_DIRECTORIES);
54  else if (this instanceof ImportParticlesFromFilesTiltPairJDialog)
55  xfc.setFileSelectionMode(XmippFileChooser.FILES_ONLY);
56  else
57  xfc.setFileSelectionMode(XmippFileChooser.DIRECTORIES_ONLY);
58 
59  xfc.setMultiSelectionEnabled(false);
60  initComponents();
61  }// constructor
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Definition at line 152 of file ImportParticlesJDialog.java.

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152  {
153  int returnVal = xfc.showOpenDialog(this);
154  try {
155  if (returnVal == XmippFileChooser.APPROVE_OPTION) {
156  path = xfc.getSelectedPath();
157  sourcetf.setText(path);
158  preffixtf.setEnabled(xfc.getSelectedFile().isDirectory());
159  suffixtf.setEnabled(xfc.getSelectedFile().isDirectory());
160 
161  }
162  } catch (Exception ex) {
163  showException(ex);
164  }
165 
166  }
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Definition at line 66 of file ImportParticlesJDialog.java.

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66  {
67  setResizable(false);
68  panel.setLayout(new GridBagLayout());
69  GridBagConstraints gbc = new GridBagConstraints();
70  gbc.insets = new Insets(5, 5, 5, 5);
71 
72  gbc.anchor = GridBagConstraints.WEST;
73  panel.add(new JLabel("Format:"),
74  XmippWindowUtil.getConstraints(gbc, 0, 0));
75  panel.add(new JLabel("Source:"),
76  XmippWindowUtil.getConstraints(gbc, 0, 1));
77 
78 
80  jcbFormat = new JComboBox(formatsString);
81  jcbFormat.addActionListener(new ActionListener() {
82 
83  @Override
84  public void actionPerformed(ActionEvent arg0) {
85  int index = jcbFormat.getSelectedIndex();
86  format = formatsList[index];
87  suffixtf.setText(parent.getParticlePicker().emextensions.get(formatsList[index]));
88 
89  }
90  });
91  panel.add(jcbFormat, XmippWindowUtil.getConstraints(gbc, 1, 0));
92 
93  sourcetf = new JTextField(20);
94  panel.add(sourcetf, XmippWindowUtil.getConstraints(gbc, 1, 1));
95 
96  browsebt = XmippWindowUtil.getIconButton("folderopen.gif", this);
97  panel.add(browsebt, XmippWindowUtil.getConstraints(gbc, 2, 1));
98 
99  String tooltip = "Preffix added to micrograph name in coordinates file";
100  JLabel preffixlb = new JLabel("Preffix:");
101  preffixlb.setToolTipText(tooltip);
102  panel.add(preffixlb, XmippWindowUtil.getConstraints(gbc, 0, 2));
103  preffixtf = new JTextField(20);
104  preffixtf.setToolTipText(tooltip);
105  panel.add(preffixtf, XmippWindowUtil.getConstraints(gbc, 1, 2));
106  tooltip = "Suffix added to micrograph name in coordinates file (eg:_filt.pos)";
107  JLabel suffixlb = new JLabel("Suffix:");
108  panel.add(suffixlb, XmippWindowUtil.getConstraints(gbc, 0, 3));
109  suffixlb.setToolTipText(tooltip);
110  suffixtf = new JTextField(20);
111  suffixtf.setToolTipText(tooltip);
112  panel.add(suffixtf, XmippWindowUtil.getConstraints(gbc, 1, 3));
113 
114  panel.add(new JLabel("Scale To:"), XmippWindowUtil.getConstraints(gbc, 0, 4));
115  scaletf = new JFormattedTextField(NumberFormat.getNumberInstance(Locale.ENGLISH));
116  scaletf.setColumns(3);
117  scaletf.setValue(1);
118  panel.add(scaletf, XmippWindowUtil.getConstraints(gbc, 1, 4));
119 
120  panel.add(new JLabel("Invert X:"),
121  XmippWindowUtil.getConstraints(gbc, 0, 5));
122  invertxcb = new JCheckBox();
123  panel.add(invertxcb, XmippWindowUtil.getConstraints(gbc, 1, 5));
124 
125  panel.add(new JLabel("Invert Y:"),
126  XmippWindowUtil.getConstraints(gbc, 0, 6));
127  invertycb = new JCheckBox();
128  panel.add(invertycb, XmippWindowUtil.getConstraints(gbc, 1, 6));
129 
130  sourcetf.addActionListener(new ActionListener()
131  {
132 
133  @Override
134  public void actionPerformed(ActionEvent e)
135  {
136  String path = sourcetf.getText();
137  boolean isDir = new File(path).isDirectory();
138  preffixtf.setEnabled(isDir);
139  suffixtf.setEnabled(isDir);
140 
141  }
142  });
143 
144  }// function createContent
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xmipp.viewer.particlepicker.ParticlePicker.emextensions
final HashMap< Format, String > emextensions
Definition: ParticlePicker.java:60
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xmipp.utils.XmippDialog.actionPerformed
void actionPerformed(ActionEvent evt)
Definition: XmippDialog.java:163
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void xmipp.viewer.particlepicker.ImportParticlesJDialog.handleActionPerformed (ActionEvent evt)
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Definition at line 147 of file ImportParticlesJDialog.java.

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147  {
148  browseDirectory(sourcetf);
149 
150  }// function actionPerformed
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Definition at line 169 of file ImportParticlesJDialog.java.

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169  {
170 
171  path = sourcetf.getText().trim();
172 
173  if (path == null || path.equals(""))
174  showError(XmippMessage.getEmptyFieldMsg("source"));
175  else if (!existsSelectedPath())
176  showError(XmippMessage.getPathNotExistsMsg(path));
177  else
178  {
179  String result = importParticles();
180  if(result != null && !result.equals(""))
181  XmippDialog.showInfo(this.parent, result);
182 
183  }
184 
185  }
xmipp.utils.XmippDialog.XmippDialog
XmippDialog(JFrame parent, String title, boolean modal)
Definition: XmippDialog.java:61
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boolean showError(String message)
Definition: XmippDialog.java:211
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String xmipp.viewer.particlepicker.ImportParticlesJDialog.importParticles ()
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Definition at line 187 of file ImportParticlesJDialog.java.

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188  {
189  try {
190  return parent.importParticles(format, path, preffixtf.getText(), suffixtf.getText(), ((Number)scaletf.getValue()).floatValue(), invertxcb.isSelected(), invertycb.isSelected());
191  } catch (Exception e) {
192  XmippDialog.showInfo(parent, e.getMessage());
193  }
194  return null;
195 
196  }
xmipp.utils.XmippDialog.XmippDialog
XmippDialog(JFrame parent, String title, boolean modal)
Definition: XmippDialog.java:61
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xmipp.viewer.particlepicker.ParticlePickerJFrame.importParticles
abstract String importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
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Definition at line 33 of file ImportParticlesJDialog.java.

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Definition at line 35 of file ImportParticlesJDialog.java.

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final Format [] xmipp.viewer.particlepicker.ImportParticlesJDialog.formatsList
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Format.Xmipp30, Format.Xmipp301, Format.Eman, Format.Relion }
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Definition at line 43 of file ImportParticlesJDialog.java.

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final String [] xmipp.viewer.particlepicker.ImportParticlesJDialog.formatsString = new String[]{Format.Auto.toString(), Format.Xmipp24.toString(), Format.Xmipp30.toString(), Format.Xmipp301.toString(), Format.Eman.toString(), Format.Relion.toString()}
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Definition at line 42 of file ImportParticlesJDialog.java.

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Definition at line 39 of file ImportParticlesJDialog.java.

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Definition at line 40 of file ImportParticlesJDialog.java.

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Definition at line 34 of file ImportParticlesJDialog.java.

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◆ parent

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Definition at line 31 of file ImportParticlesJDialog.java.

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Definition at line 37 of file ImportParticlesJDialog.java.

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Definition at line 38 of file ImportParticlesJDialog.java.

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Definition at line 32 of file ImportParticlesJDialog.java.

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Definition at line 36 of file ImportParticlesJDialog.java.

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The documentation for this class was generated from the following file: -
- -
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xmipp.viewer.particlepicker.Micrograph Member List
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This is the complete list of members for xmipp.viewer.particlepicker.Micrograph, including all inherited members.

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extxmipp.viewer.particlepicker.Micrographstatic
fits(int x, int y, int size)xmipp.viewer.particlepicker.Micrographinline
getCTF()xmipp.viewer.particlepicker.Micrographinline
getCTFIcon()xmipp.viewer.particlepicker.Micrographinline
getCtfInfo()xmipp.viewer.particlepicker.Micrographinline
getFile()xmipp.viewer.particlepicker.Micrographinline
getHeigth()xmipp.viewer.particlepicker.Micrographinline
getImagePlus()xmipp.viewer.particlepicker.Micrographinline
getImagePlus(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
getName(String file, int level)xmipp.viewer.particlepicker.Micrographinlinestatic
getName()xmipp.viewer.particlepicker.Micrographinline
getNoImageIcon()xmipp.viewer.particlepicker.Micrographinlinestatic
getParticleList()xmipp.viewer.particlepicker.Micrographinline
getPosFile()xmipp.viewer.particlepicker.Micrographinline
getPosFileFromXmipp24()xmipp.viewer.particlepicker.Micrographinline
getPSD()xmipp.viewer.particlepicker.Micrographinline
getPSDImage()xmipp.viewer.particlepicker.Micrographinline
getWidth()xmipp.viewer.particlepicker.Micrographinline
hasData()xmipp.viewer.particlepicker.Micrograph
loadDimensions()xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
releaseImage()xmipp.viewer.particlepicker.Micrographinline
runImageJFilters(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
setPosFileFromXmipp24(String posfile)xmipp.viewer.particlepicker.Micrographinline
toString()xmipp.viewer.particlepicker.Micrographinline
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html deleted file mode 100644 index eda47194..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html +++ /dev/null @@ -1,1000 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.Micrograph Class Reference - - - - - - - - - -
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xmipp.viewer.particlepicker.Micrograph Class Referenceabstract
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-Inheritance diagram for xmipp.viewer.particlepicker.Micrograph:
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-Public Member Functions

void setPosFileFromXmipp24 (String posfile)
 
String getPosFileFromXmipp24 ()
 
 Micrograph (String file)
 
 Micrograph (String file, String name)
 
 Micrograph (String file, CtfInfo ctfInfo)
 
 Micrograph (String file, String name, CtfInfo ctfInfo)
 
String getPSD ()
 
ImagePlus getPSDImage ()
 
Icon getCTFIcon ()
 
String getCTF ()
 
CtfInfo getCtfInfo ()
 
boolean fits (int x, int y, int size)
 
String getPosFile ()
 
void loadDimensions ()
 
ImagePlus getImagePlus ()
 
ImagePlus getImagePlus (List< IJCommand > filters)
 
void runImageJFilters (List< IJCommand > filters)
 
String getFile ()
 
String getName ()
 
String toString ()
 
abstract boolean hasData ()
 
int getWidth ()
 
int getHeigth ()
 
void releaseImage ()
 
List<? extends PickerParticle > getParticleList ()
 
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-Static Public Member Functions

static Icon getNoImageIcon ()
 
static String getName (String file, int level)
 
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static final String ext = ".pos"
 
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Definition at line 23 of file Micrograph.java.

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◆ Micrograph() [1/4]

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xmipp.viewer.particlepicker.Micrograph.Micrograph (String file)
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Definition at line 44 of file Micrograph.java.

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44  {
45  this(file, getName(file, 1), null);
46  }
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xmipp.viewer.particlepicker.Micrograph.Micrograph (String file,
String name 
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Definition at line 48 of file Micrograph.java.

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48  {
49  this(file, name, null);
50  }
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xmipp.viewer.particlepicker.Micrograph.Micrograph (String file,
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Definition at line 52 of file Micrograph.java.

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52  {
53  this(file, getName(file, 1), ctfInfo);
54  }
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xmipp.viewer.particlepicker.Micrograph.Micrograph (String file,
String name,
CtfInfo ctfInfo 
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Definition at line 56 of file Micrograph.java.

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56  {
57  this.file = file;
58  this.ctfInfo = ctfInfo;
59  String path = file;
60  if(Filename.hasPrefix(file))
61  path = Filename.removePrefix(file);
62  if (!new File(path).exists())
63  {
64  System.out.printf("path %s selfile %s\n", path, ParticlePicker.getPicker().selfile);
65  file = Filename.findImagePath(path, ParticlePicker.getPicker().selfile, true);
66  if(file == null)
67  throw new IllegalArgumentException(XmippMessage.getNoSuchFieldValueMsg("micrograph", path));
68  }
69 
70  this.name = name;
71  this.posfile = name + ext;
72  //loadDimensions(); // ensure width and height get updated
73 
74  }
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◆ fits()

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boolean xmipp.viewer.particlepicker.Micrograph.fits (int x,
int y,
int size 
)
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Definition at line 129 of file Micrograph.java.

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129  {
130  if (x < 0 || y < 0)
131  return false;
132 
133  int radius = size / 2;
134  if (x - radius < 0 || x + radius > getWidth() || y - radius < 0
135  || y + radius > getHeigth())
136  return false;
137  return true;
138  }
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Definition at line 121 of file Micrograph.java.

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121  {
122  return ctfInfo == null ? null : ctfInfo.ctf;
123  }
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Definition at line 89 of file Micrograph.java.

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89  {
90  String file;
91  if (ctficon == null) {
92  String psd = getPSD();
93  if (psd == null || !(new File(psd).exists()))
94  file = (Filename.getXmippPath("resources" + File.separator
95  + "no-image.jpg"));
96  else
97  file = psd;
98  ImagePlus imp = XmippUtil.getImagePlus(file);
99  Image image = imp.getImage().getScaledInstance(120, 110,
100  Image.SCALE_SMOOTH);
101  ctficon = new ImageIcon(image);
102 
103  }
104  return ctficon;
105  }
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Definition at line 125 of file Micrograph.java.

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125  {
126  return ctfInfo;
127  }
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Definition at line 245 of file Micrograph.java.

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245  {
246  return file;
247  }
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Definition at line 266 of file Micrograph.java.

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267  {
268  if(height == 0)
269  loadDimensions();
270  return height;
271  }
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Definition at line 188 of file Micrograph.java.

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188  {
189  try {
190 
191  if (imp == null) {
192  imp = XmippImageConverter.loadImage(file);
193  if (imp == null)
194  imp = new ImagePlus(file);
195 
196  }
197  return imp;
198  } catch (Exception e) {
199  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
200  throw new IllegalArgumentException(e.getMessage());
201  }
202  }
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Definition at line 204 of file Micrograph.java.

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204  {
205  try {
206  if (filters.isEmpty())
207  return getImagePlus();
208 
209  if (imp == null) {
210  ImageGeneric ig = new ImageGeneric(file);
211  ig.read(ImageGeneric.FIRST_IMAGE);
212 
213  // Smooth filter should be the first one
214  // because it is applied in Xmipp
215  for (IJCommand f : filters)
216  if (f.getCommand().equals(ParticlePicker.xmippsmoothfilter)) {
217  ig.convert2Datatype(ImageGeneric.UChar);
218  ImageGeneric igsmooth = new ImageGeneric(
219  ImageGeneric.UChar);
220  igsmooth.resize(ig.getXDim(), ig.getYDim());
221  ig.smooth(igsmooth);
222  break;
223  }
224  imp = XmippImageConverter.convertToImagePlus(ig);
225  ig.destroy();
226 
227  }
228  return imp;
229  } catch (Exception e) {
230  throw new IllegalArgumentException(e.getMessage());
231  }
232  }
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static String xmipp.viewer.particlepicker.Micrograph.getName (String file,
int level 
)
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Definition at line 140 of file Micrograph.java.

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140  {
141  if (file == null)
142  return null;
143  // level can start at 1 for file name, 2 is for parent directory name
144  String[] tokens = file.split(File.separator);
145  if (tokens.length < level)
146  throw new IllegalArgumentException(
147  String.format(
148  "Name for micrograph is taken from level %s, invalid path ",
149  level, file));
150  String name = tokens[tokens.length - level];
151  if (level == 1) {
152  int pos = name.lastIndexOf('.');
153  if (pos != -1)
154  name = name.substring(0, pos);
155 
156  pos = tokens[0].lastIndexOf('@');
157  if (pos != -1) {
158  name = tokens[0].substring(0, pos) + "_at_" + name;
159  }
160  }
161  return name;
162  }
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Definition at line 249 of file Micrograph.java.

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249  {
250  return name;
251  }
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Definition at line 107 of file Micrograph.java.

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107  {
108  String file;
109  if (noimageicon == null) {
110  file = (Filename.getXmippPath("resources" + File.separator
111  + "no-image.jpg"));
112  ImagePlus imp = XmippUtil.getImagePlus(file);
113  Image image = imp.getImage().getScaledInstance(120, 110,
114  Image.SCALE_SMOOTH);
115  noimageicon = new ImageIcon(image);
116 
117  }
118  return noimageicon;
119  }
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Definition at line 279 of file Micrograph.java.

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279  {
280  return null;
281  };
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Definition at line 164 of file Micrograph.java.

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164  {
165  return posfile;
166  }
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Definition at line 40 of file Micrograph.java.

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40  {
41  return pos24file;
42  }
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Definition at line 76 of file Micrograph.java.

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76  {
77  return ctfInfo == null ? null : ctfInfo.psd;
78  }
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Definition at line 80 of file Micrograph.java.

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80  {
81  String psd = getPSD();
82 
83  if (psd == null || !(new File(psd).exists()))
84  return null;
85  return XmippUtil.getImagePlus(psd);
86 
87  }
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Definition at line 259 of file Micrograph.java.

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260  {
261  if(width == 0)
262  loadDimensions();
263  return width;
264  }
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Definition at line 169 of file Micrograph.java.

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169  {
170 
171  if (imp != null) {
172  width = imp.getWidth();
173  height = imp.getHeight();
174  } else {
175  try {
176  ImageGeneric img = new ImageGeneric(file); // this reads the header
177  width = img.getXDim();
178  height = img.getYDim();
179  img.destroy();
180  } catch (Exception e) {
181  e.printStackTrace();
182  }
183  }
184  }
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void xmipp.viewer.particlepicker.Micrograph.releaseImage ()
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Definition at line 273 of file Micrograph.java.

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274  {
275  imp = null;
276 
277  }
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void xmipp.viewer.particlepicker.Micrograph.runImageJFilters (List< IJCommand > filters)
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Definition at line 234 of file Micrograph.java.

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234  {
235  for (IJCommand f : filters)
236  // this filter was applied
237  if (!f.getCommand().equals(ParticlePicker.xmippsmoothfilter))
238  {
239  IJ.run(imp, f.getCommand(), f.getOptions());
240  }
241  }
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void xmipp.viewer.particlepicker.Micrograph.setPosFileFromXmipp24 (String posfile)
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Definition at line 36 of file Micrograph.java.

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36  {
37  this.pos24file = posfile;
38  }
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Definition at line 253 of file Micrograph.java.

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253  {
254  return name;
255  }
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◆ ext

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final String xmipp.viewer.particlepicker.Micrograph.ext = ".pos"
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Definition at line 30 of file Micrograph.java.

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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph__inherit__graph.dot deleted file mode 100644 index 244c1ae4..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph__inherit__graph.dot +++ /dev/null @@ -1,15 +0,0 @@ -digraph "xmipp.viewer.particlepicker.Micrograph" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node0 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node0 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.extract.\lExtractMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph.html"]; - Node0 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.viewer.particlepicker.tiltpair.model.\lTiltedMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph.html"]; - Node0 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.particlepicker.tiltpair.model.\lUntiltedMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph.html"]; - Node0 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="xmipp.viewer.particlepicker.training.model.\lSupervisedPickerMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedPickerMicrograph.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph__inherit__graph.md5 deleted file mode 100644 index 2cf53a70..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -741b02aba6bccd4ab47977eb327e24fe \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas-members.html deleted file mode 100644 index c97ef742..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas-members.html +++ /dev/null @@ -1,87 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.ParticleCanvas Member List
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This is the complete list of members for xmipp.viewer.particlepicker.ParticleCanvas, including all inherited members.

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mouseDragged(MouseEvent e)xmipp.viewer.particlepicker.ParticleCanvasinline
mousePressed(MouseEvent e)xmipp.viewer.particlepicker.ParticleCanvasinline
mouseReleased(MouseEvent e)xmipp.viewer.particlepicker.ParticleCanvasinline
paint(Graphics g)xmipp.viewer.particlepicker.ParticleCanvasinline
ParticleCanvas(PickerParticle pickerParticle, ParticlePickerJFrame frame)xmipp.viewer.particlepicker.ParticleCanvasinline
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xmipp.viewer.particlepicker.ParticleCanvas Class Reference
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-Public Member Functions

 ParticleCanvas (PickerParticle pickerParticle, ParticlePickerJFrame frame)
 
void paint (Graphics g)
 
void mouseDragged (MouseEvent e)
 
void mousePressed (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
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Detailed Description

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Definition at line 19 of file ParticleCanvas.java.

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Constructor & Destructor Documentation

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◆ ParticleCanvas()

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xmipp.viewer.particlepicker.ParticleCanvas.ParticleCanvas (PickerParticle pickerParticle,
ParticlePickerJFrame frame 
)
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Definition at line 31 of file ParticleCanvas.java.

-
32  {
33  super(pickerParticle.getMicrograph().getImagePlus());
34  this.particle = pickerParticle;
35  this.frame = frame;
36  this.canvas = (pickerParticle instanceof TiltedParticle) ? ((TiltPairPickerJFrame) frame).getTiltedCanvas() : frame.getCanvas();
37 
38  this.size = (int) (frame.getParticlePicker().getSize());
39  side = frame.getSide();
40  setMagnification((float) side / size);
41  setDrawingSize(side, side);
42  addMouseMotionListener(this);
43  addMouseListener(this);
44  }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
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◆ mouseDragged()

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void xmipp.viewer.particlepicker.ParticleCanvas.mouseDragged (MouseEvent e)
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Definition at line 64 of file ParticleCanvas.java.

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65  {
66  if (dragged)
67  {
68  int movex = lastx - e.getX();
69  int movey = lasty - e.getY();
70  int x = particle.getX() + movex;
71  int y = particle.getY() + movey;
72  try
73  {
74  particle.setPosition(x, y);
75  repaint();
76  canvas.repaint();
77  frame.setChanged(true);
78  }
79  catch (Exception ex)
80  {
81  canvas.repaint();
82  repaint();
83  XmippDialog.showInfo(frame, ex.getMessage());
84 
85  }
86  }
87  lastx = e.getX();
88  lasty = e.getY();
89  }
xmipp.jni.Particle.setPosition
void setPosition(int x, int y)
Definition: Particle.java:65
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void xmipp.viewer.particlepicker.ParticleCanvas.mousePressed (MouseEvent e)
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Definition at line 92 of file ParticleCanvas.java.

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93  {
94  if (frame.isPickingAvailable(e))
95  {
96  dragged = true;
97  lastx = e.getX();
98  lasty = e.getY();
99 
100  if (SwingUtilities.isLeftMouseButton(e) && e.isShiftDown()) {
101  if (frame instanceof SupervisedPickerJFrame)
102  ((SupervisedPickerMicrograph) frame.getMicrograph()).removeParticle(particle, ((SupervisedPickerJFrame) frame).getParticlePicker());
103  else if (frame instanceof TiltPairPickerJFrame) {
104  if (frame.getMicrograph() instanceof UntiltedMicrograph)
105  ((UntiltedMicrograph) frame.getMicrograph()).removeParticle((UntiltedParticle) particle);
106  else if (frame.getMicrograph() instanceof TiltedMicrograph)
107  ((TiltedMicrograph) frame.getMicrograph()).removeParticle((TiltedParticle) particle);
108  }
109  canvas.repaint();
110  frame.updateMicrographsModel();
111  frame.loadParticles(false);
112  }else
113  {
114  canvas.moveTo(particle);
115  canvas.refreshActive(particle);
116  }
117  }
118 
119  }
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Definition at line 122 of file ParticleCanvas.java.

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124  dragged = false;
125 
126  }
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Definition at line 46 of file ParticleCanvas.java.

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47  {
48  Rectangle source = new Rectangle(particle.getX0(size), particle.getY0(size), size, size);
49  setSourceRect(source);
50  super.paint(g);
51  g.setColor(Color.white);
52  g.drawRect(0, 0, side - 1, side - 1);
53 
54  if(particle instanceof UntiltedParticle){
55  String type = "U";
56  g.drawString(type, 5, side - 2);
57  } else if(particle instanceof TiltedParticle) {
58  String type = "T";
59  g.drawString(type, 5, side - 2);
60  }
61  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__coll__graph.dot deleted file mode 100644 index d0c1ba55..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__coll__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.particlepicker.ParticleCanvas" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node4 [label="xmipp.viewer.particlepicker.\lParticleCanvas",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node5 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="ImageCanvas",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="MouseMotionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="MouseListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__coll__graph.md5 deleted file mode 100644 index bce10926..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -e12aeacf083c9528df1872bd73b443ef \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__inherit__graph.dot deleted file mode 100644 index 3ae21eca..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__inherit__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.particlepicker.ParticleCanvas" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.\lParticleCanvas",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="ImageCanvas",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="MouseMotionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="MouseListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__inherit__graph.md5 deleted file mode 100644 index 29a249e9..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticleCanvas__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -5bfedd089e76fdbd768960ebba39c4ab \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePicker-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePicker-members.html deleted file mode 100644 index 35ba4e06..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePicker-members.html +++ /dev/null @@ -1,169 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.ParticlePicker Member List
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This is the complete list of members for xmipp.viewer.particlepicker.ParticlePicker, including all inherited members.

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addFilter(String command, String options)xmipp.viewer.particlepicker.ParticlePickerinline
blockxmipp.viewer.particlepicker.ParticlePickerprotected
changedxmipp.viewer.particlepicker.ParticlePickerprotected
colorxmipp.viewer.particlepicker.ParticlePickerprotected
colorsxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
configfilexmipp.viewer.particlepicker.ParticlePickerprotected
detectFileFormat(String path)xmipp.viewer.particlepicker.ParticlePickerinline
detectFormat(String path, String preffix, StringBuffer suffix)xmipp.viewer.particlepicker.ParticlePickerinline
emextensionsxmipp.viewer.particlepicker.ParticlePicker
fillParticlesMdFromEmanFile(String file, Micrograph m, MetaData md, float scale)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromRelionFile(String file, Micrograph m, MetaData md)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromXmipp301File(String file, Micrograph m, MetaData md)xmipp.viewer.particlepicker.ParticlePickerinline
filtersxmipp.viewer.particlepicker.ParticlePickerprotected
getColor()xmipp.viewer.particlepicker.ParticlePickerinline
getColor(String name)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getCoordsFiles(String folder)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getDefaultSize()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getExportFile(String path)xmipp.viewer.particlepicker.ParticlePickerinline
getFilters()xmipp.viewer.particlepicker.ParticlePickerinline
getLogger()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getMicrograph(String name)xmipp.viewer.particlepicker.ParticlePickerinline
getMicrograph()xmipp.viewer.particlepicker.ParticlePicker
getMicrographIndex()xmipp.viewer.particlepicker.ParticlePickerinline
getMicrographs()xmipp.viewer.particlepicker.ParticlePicker
getMicrographsSelFile()xmipp.viewer.particlepicker.ParticlePickerinline
getMode()xmipp.viewer.particlepicker.ParticlePickerinline
getNextColor()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getOutputDir()xmipp.viewer.particlepicker.ParticlePickerinline
getOutputPath(String file)xmipp.viewer.particlepicker.ParticlePickerinline
getParams()xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesAutoBlock(String file)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesAutoBlock(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesBlock(Format f, String file)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesBlock(String file)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesBlock(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesBlockName(Format f)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesCount()xmipp.viewer.particlepicker.ParticlePicker
getPicker()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getPort()xmipp.viewer.particlepicker.ParticlePickerinline
getPosFileFromXmipp24Project(String projectdir, String mname)xmipp.viewer.particlepicker.ParticlePickerinline
getRadius()xmipp.viewer.particlepicker.ParticlePickerinline
getSize()xmipp.viewer.particlepicker.ParticlePickerinline
getTemplatesFile(String name)xmipp.viewer.particlepicker.ParticlePickerinline
getZoom()xmipp.viewer.particlepicker.ParticlePickerinline
importSize(String path, Format f, double scale)xmipp.viewer.particlepicker.ParticlePickerinline
isChanged()xmipp.viewer.particlepicker.ParticlePickerinline
isFilterAdded(String filter)xmipp.viewer.particlepicker.ParticlePickerinline
isSaved()xmipp.viewer.particlepicker.ParticlePickerinline
isScipionSave()xmipp.viewer.particlepicker.ParticlePickerinline
isShowDeleted()xmipp.viewer.particlepicker.ParticlePickerinline
isValidSize(JFrame parent, int size)xmipp.viewer.particlepicker.ParticlePicker
loadConfig()xmipp.viewer.particlepicker.ParticlePickerinline
loadEmptyMicrographs()xmipp.viewer.particlepicker.ParticlePicker
loggerxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
macrosfilexmipp.viewer.particlepicker.ParticlePickerprotected
modexmipp.viewer.particlepicker.ParticlePickerprotected
nextcolorxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
outputdirxmipp.viewer.particlepicker.ParticlePickerprotected
paramsxmipp.viewer.particlepicker.ParticlePickerprotected
ParticlePicker(String selfile, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
ParticlePicker(String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
ParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
particlesAutoBlockxmipp.viewer.particlepicker.ParticlePickerstatic
pickerxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
runXmippProgram(String program, String args)xmipp.viewer.particlepicker.ParticlePickerinline
saveConfig()xmipp.viewer.particlepicker.ParticlePickerinline
saveConfig(MetaData md, long id)xmipp.viewer.particlepicker.ParticlePickerinlineprotected
savedxmipp.viewer.particlepicker.ParticlePickerprotected
saveData()xmipp.viewer.particlepicker.ParticlePickerinline
saveData(Micrograph m)xmipp.viewer.particlepicker.ParticlePicker
selfilexmipp.viewer.particlepicker.ParticlePickerprotected
setChanged(boolean changed)xmipp.viewer.particlepicker.ParticlePickerinline
setColor(Color color)xmipp.viewer.particlepicker.ParticlePickerinline
setFilterOptions(String command, String options)xmipp.viewer.particlepicker.ParticlePickerinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePicker
setSaved(boolean saved)xmipp.viewer.particlepicker.ParticlePickerinline
setShowDeleted(boolean showDeleted)xmipp.viewer.particlepicker.ParticlePickerinline
setSize(int size)xmipp.viewer.particlepicker.ParticlePickerinline
setZoom(double zoom)xmipp.viewer.particlepicker.ParticlePickerinline
sizexmipp.viewer.particlepicker.ParticlePickerprotected
sizemaxxmipp.viewer.particlepicker.ParticlePickerstatic
toggleShowDeleted()xmipp.viewer.particlepicker.ParticlePickerinline
updateFilters(String command)xmipp.viewer.particlepicker.ParticlePickerinline
validateState(Mode state)xmipp.viewer.particlepicker.ParticlePickerinline
xmippsmoothfilterxmipp.viewer.particlepicker.ParticlePickerstatic
zoomxmipp.viewer.particlepicker.ParticlePickerprotected
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xmipp.viewer.particlepicker.ParticlePicker Class Referenceabstract
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-Public Member Functions

boolean isShowDeleted ()
 
void setShowDeleted (boolean showDeleted)
 
void toggleShowDeleted ()
 
double getZoom ()
 
void setZoom (double zoom)
 
ParticlePickerParams getParams ()
 
String getParticlesAutoBlock (String file)
 
String getParticlesBlock (Micrograph m)
 
String getParticlesAutoBlock (Micrograph m)
 
 ParticlePicker (String selfile, ParticlePickerParams params)
 
 ParticlePicker (String selfile, String outputdir, ParticlePickerParams params)
 
 ParticlePicker (String block, String selfile, String outputdir, ParticlePickerParams params)
 
void loadConfig ()
 
synchronized void saveConfig ()
 
Format detectFileFormat (String path)
 
Format detectFormat (String path, String preffix, StringBuffer suffix)
 
String getExportFile (String path)
 
String getPosFileFromXmipp24Project (String projectdir, String mname)
 
abstract void loadEmptyMicrographs ()
 
void updateFilters (String command)
 
boolean isFilterAdded (String filter)
 
String getMicrographsSelFile ()
 
void setFilterOptions (String command, String options)
 
void addFilter (String command, String options)
 
List< IJCommand > getFilters ()
 
void setChanged (boolean changed)
 
boolean isChanged ()
 
boolean isSaved ()
 
void setSaved (boolean saved)
 
Mode getMode ()
 
String getOutputPath (String file)
 
String getOutputDir ()
 
abstract List<? extends Micrograph > getMicrographs ()
 
int getMicrographIndex ()
 
String getTemplatesFile (String name)
 
Mode validateState (Mode state)
 
void saveData ()
 
abstract void saveData (Micrograph m)
 
Micrograph getMicrograph (String name)
 
void fillParticlesMdFromFile (String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
 
void fillParticlesMdFromXmipp301File (String file, Micrograph m, MetaData md)
 
void fillParticlesMdFromRelionFile (String file, Micrograph m, MetaData md)
 
void fillParticlesMdFromEmanFile (String file, Micrograph m, MetaData md, float scale)
 
void runXmippProgram (String program, String args)
 
abstract Micrograph getMicrograph ()
 
abstract void setMicrograph (Micrograph m)
 
abstract boolean isValidSize (JFrame parent, int size)
 
int getSize ()
 
void setSize (int size)
 
Color getColor ()
 
void setColor (Color color)
 
int getRadius ()
 
void importSize (String path, Format f, double scale)
 
boolean isScipionSave ()
 
abstract int getParticlesCount ()
 
Integer getPort ()
 
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-Static Public Member Functions

static Color getNextColor ()
 
static String getParticlesBlock (Format f, String file)
 
static String getParticlesBlockName (Format f)
 
static String getParticlesBlock (String file)
 
static Logger getLogger ()
 
static Color getColor (String name)
 
static int getDefaultSize ()
 
static File [] getCoordsFiles (String folder)
 
static ParticlePicker getPicker ()
 
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-Public Attributes

final HashMap< Format, String > emextensions
 
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static final String xmippsmoothfilter = "Xmipp Smooth Filter"
 
static final String particlesAutoBlock = "particles_auto"
 
static final int sizemax = 2000
 
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void saveConfig (MetaData md, long id)
 
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String macrosfile
 
String outputdir = "."
 
boolean changed
 
boolean saved
 
Mode mode
 
List< IJCommand > filters
 
String selfile
 
String configfile
 
Color color
 
int size
 
String block
 
ParticlePickerParams params
 
double zoom = -1.f
 
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static Logger logger
 
static Color [] colors = new Color[]{Color.GREEN, Color.BLUE, Color.CYAN, Color.MAGENTA, Color.ORANGE, Color.PINK, Color.YELLOW}
 
static int nextcolor
 
static ParticlePicker picker
 
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Detailed Description

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Business object for ParticlePicker common GUI. SingleParticlePicker and TiltPairPicker inherit from this class.

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Definition at line 34 of file ParticlePicker.java.

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Constructor & Destructor Documentation

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◆ ParticlePicker() [1/3]

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xmipp.viewer.particlepicker.ParticlePicker.ParticlePicker (String selfile,
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Definition at line 140 of file ParticlePicker.java.

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140  {
141  this(null, selfile, ".", params);
142  }
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xmipp.viewer.particlepicker.ParticlePicker.ParticlePicker (String selfile,
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Definition at line 144 of file ParticlePicker.java.

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144  {
145  this(null, selfile, outputdir, params);
146  }
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xmipp.viewer.particlepicker.ParticlePicker.ParticlePicker (String block,
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Definition at line 148 of file ParticlePicker.java.

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148  {
149 
150  this.params = params;
151  this.block = block;
152  this.outputdir = outputdir;
153  if(!new File(outputdir).isDirectory())
154  throw new IllegalArgumentException(XmippMessage.getInvalidDirectoryMsg(outputdir));
155  this.selfile = selfile;
156  this.mode = params.mode;
157  this.configfile = getOutputPath("config.xmd");
158  picker = this;
159  filters = new ArrayList<IJCommand>();
160  loadEmptyMicrographs();
161  loadConfig();
162  emextensions = new HashMap<Format, String>();
163  emextensions.put(Format.Xmipp, ".pos");
164  emextensions.put(Format.Xmipp24, ".pos");
165  emextensions.put(Format.Xmipp30, ".pos");
166  emextensions.put(Format.Xmipp301, ".pos");
167  emextensions.put(Format.Relion, ".star");
168  emextensions.put(Format.Eman, ".box");
169 
170  }
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xmipp.viewer.particlepicker.ParticlePicker.emextensions
final HashMap< Format, String > emextensions
Definition: ParticlePicker.java:60
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◆ addFilter()

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void xmipp.viewer.particlepicker.ParticlePicker.addFilter (String command,
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Definition at line 398 of file ParticlePicker.java.

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398  {
399  IJCommand f = new IJCommand(command, options);
400  filters.add(f);
401  }
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Definition at line 271 of file ParticlePicker.java.

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271  {
272  if(!new File(path).exists())
273  return Format.None;
274  if (path.endsWith(emextensions.get(Format.Xmipp)))
275  {
276  if(MetaData.isPlainPos(path) )
277  return Format.Xmipp24;
278  if (MetaData.containsBlock(path, getParticlesBlockName(Format.Xmipp30))) {
279  return Format.Xmipp30;
280  }
281  return Format.Xmipp301;
282  }
283  else if (path.endsWith(emextensions.get(Format.Eman))) {
284  return Format.Eman;
285  }
286  else if (path.endsWith(emextensions.get(Format.Relion)))
287  return Format.Relion;
288 
289  return Format.None;
290  }
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final HashMap< Format, String > emextensions
Definition: ParticlePicker.java:60
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Definition at line 295 of file ParticlePicker.java.

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295  {
296  Format f;
297  if(suffix.length() == 0)
298  for(String ext: emextensions.values())
299  {
300  suffix.setLength(0);
301  suffix.append(ext);
302  f = detectFormat(path, preffix, suffix);
303  if(f != Format.None)
304  return f;
305  }
306  else
307  {
308  String file;
309  for (Micrograph m : getMicrographs())
310  {
311  file = Filename.join(path, preffix + m.getName() + suffix);
312  f = detectFileFormat(file);
313  if(f != Format.None)
314  return f;
315  }
316  }
317  return Format.None;
318  }
xmipp.viewer.particlepicker.ParticlePicker.detectFormat
Format detectFormat(String path, String preffix, StringBuffer suffix)
Definition: ParticlePicker.java:295
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xmipp.viewer.particlepicker.ParticlePicker.getMicrographs
abstract List<? extends Micrograph > getMicrographs()
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xmipp.viewer.particlepicker.ParticlePicker.emextensions
final HashMap< Format, String > emextensions
Definition: ParticlePicker.java:60
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◆ fillParticlesMdFromEmanFile()

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void xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromEmanFile (String file,
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Definition at line 577 of file ParticlePicker.java.

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577  {
578  // inverty = true;
579  md.readPlain(file, "xcoor ycoor particleSize");
580  //System.err.format("After readPlain: md.size: %d\n", md.size());
581 
582  long fid = md.firstObject();
583  int size = md.getValueInt(MDLabel.MDL_PICKING_PARTICLE_SIZE, fid);
584 
585  int half = size / 2;
586  //System.err.format("Operate string: %s\n", String.format("xcoor=xcoor+%d,ycoor=ycoor+%d", half, half));
587  md.operate(String.format("xcoor=xcoor+%d,ycoor=ycoor+%d", half, half));
588 
589  setSize(Math.round(size * scale));
590  }// function fillParticlesMdFromEmanFile
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◆ fillParticlesMdFromFile()

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void xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromFile (String path,
Format f,
Micrograph m,
MetaData md,
float scale,
boolean invertx,
boolean inverty 
)
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-
-

Return the number of particles imported from a file

- -

Definition at line 497 of file ParticlePicker.java.

-
497  {
498 
499  if (f == Format.Auto) {
500  f = detectFileFormat(path);
501  }
502  String blockname;
503  switch (f) {
504  case Xmipp24:
505  md.readPlain(path, "xcoor ycoor");
506  break;
507  case Xmipp30:
508  blockname = getParticlesBlockName(f); //only used with Xmipp
509  if (MetaData.containsBlock(path, blockname)) {
510  md.read(getParticlesBlock(f, path));
511  }
512  break;
513  case Xmipp301:
514  fillParticlesMdFromXmipp301File(path, m, md);
515  break;
516  case Eman:
517  fillParticlesMdFromEmanFile(path, m, md, scale);
518  break;
519  case Relion:
520  fillParticlesMdFromRelionFile(path, m, md);
521 
522  break;
523  default:
524  md.clear();
525  }
526  if (scale != 1.f) {
527  String command = String.format(Locale.ENGLISH, "xcoor=xcoor*%f,ycoor=ycoor*%f", scale, scale);
528  md.operate(command);
529  }
530  int width = (int) (m.getWidth() / scale);// original width
531  int height = (int) (m.getHeigth() / scale);// original height
532  if (invertx) {
533  md.operate(String.format("xcoor=%d-xcoor", width));
534  }
535  if (inverty) {
536  md.operate(String.format("ycoor=%d-ycoor", height));
537  }
538 
539 
540  }// function importParticlesFromFile
xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromEmanFile
void fillParticlesMdFromEmanFile(String file, Micrograph m, MetaData md, float scale)
Definition: ParticlePicker.java:577
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromXmipp301File
void fillParticlesMdFromXmipp301File(String file, Micrograph m, MetaData md)
Definition: ParticlePicker.java:542
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xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromRelionFile
void fillParticlesMdFromRelionFile(String file, Micrograph m, MetaData md)
Definition: ParticlePicker.java:558
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◆ fillParticlesMdFromRelionFile()

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void xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromRelionFile (String file,
Micrograph m,
MetaData md 
)
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Definition at line 558 of file ParticlePicker.java.

-
558  {
559  MetaData relionmd = new MetaData(file);
560  if(!relionmd.containsLabel(MDLabel.RLN_IMAGE_COORD_X))
561  throw new IllegalArgumentException(String.format("File %s format is not supported", file));
562  long[] ids = relionmd.findObjects();
563  int xcoor, ycoor;
564  long id;
565  for(int i = 0; i < ids.length; i++ )
566  {
567  xcoor = (int)relionmd.getValueDouble(MDLabel.RLN_IMAGE_COORD_X, ids[i]);
568  ycoor = (int)relionmd.getValueDouble(MDLabel.RLN_IMAGE_COORD_Y, ids[i]);
569  id = md.addObject();
570  md.setValueInt(MDLabel.MDL_XCOOR, xcoor, id);
571  md.setValueInt(MDLabel.MDL_YCOOR, ycoor, id);
572  }
573  relionmd.destroy();
574 
575  }
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◆ fillParticlesMdFromXmipp301File()

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void xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromXmipp301File (String file,
Micrograph m,
MetaData md 
)
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Definition at line 542 of file ParticlePicker.java.

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542  {
543 
544  String blockname = getParticlesBlockName(Format.Xmipp301); //only used with Xmipp
545  if (MetaData.containsBlock(file, blockname)) {
546  md.read(getParticlesBlock(Format.Xmipp301, file));
547  }
548  if (MetaData.containsBlock(file, particlesAutoBlock)) {
549  MetaData mdAuto = new MetaData();
550  mdAuto.read(getParticlesAutoBlock(file));
551  mdAuto.removeDisabled();
552  md.unionAll(mdAuto);
553  mdAuto.destroy();
554  }
555 
556  }
xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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◆ getColor() [1/2]

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Color xmipp.viewer.particlepicker.ParticlePicker.getColor ()
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Definition at line 616 of file ParticlePicker.java.

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616  {
617  return color;
618  }
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Definition at line 624 of file ParticlePicker.java.

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624  {
625  Color color;
626  try {
627  Field field = Class.forName("java.awt.Color").getField(name);
628  color = (Color) field.get(null);// static field, null for parameter
629  } catch (Exception e) {
630  color = null; // Not defined
631  }
632  return color;
633  }
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◆ getCoordsFiles()

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static File [] xmipp.viewer.particlepicker.ParticlePicker.getCoordsFiles (String folder)
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Definition at line 660 of file ParticlePicker.java.

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661  {
662  return new File(folder).listFiles(new FilenameFilter() {
663  public boolean accept(File dir, String name) {
664  String lowercasename = name.toLowerCase();
665  return lowercasename.endsWith(".pos") || lowercasename.endsWith(".box");
666  }
667  });
668  }
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◆ getDefaultSize()

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static int xmipp.viewer.particlepicker.ParticlePicker.getDefaultSize ()
- 		-inlinestatic
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Definition at line 635 of file ParticlePicker.java.

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635  {
636  return 100;
637  }
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◆ getExportFile()

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String xmipp.viewer.particlepicker.ParticlePicker.getExportFile (String path)
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Definition at line 320 of file ParticlePicker.java.

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320  {
321  String particlesfile;
322  File folderToScan = new File(path);
323  File[] listOfFiles = folderToScan.listFiles();
324 
325  //Checking file with exported particles
326  for (int i = 0; i < listOfFiles.length; i++) {
327  if (listOfFiles[i].isFile()) {
328  particlesfile = listOfFiles[i].getName();
329  if (particlesfile.endsWith("extract_list.xmd")) {
330  return Filename.join(path, particlesfile);
331  }
332  }
333  }
334  return null;
335  }
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◆ getFilters()

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List<IJCommand> xmipp.viewer.particlepicker.ParticlePicker.getFilters ()
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Definition at line 403 of file ParticlePicker.java.

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403  {
404  return filters;
405  }
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◆ getLogger()

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static Logger xmipp.viewer.particlepicker.ParticlePicker.getLogger ()
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Definition at line 427 of file ParticlePicker.java.

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427  {
428  try {
429  if (logger == null) {
430  // FileHandler fh = new FileHandler("PPicker.log", true);
431  // fh.setFormatter(new SimpleFormatter());
432  logger = Logger.getLogger("PPickerLogger");
433  // logger.addHandler(fh);
434  }
435  return logger;
436  } catch (Exception e) {
437  // TODO Auto-generated catch block
438  e.printStackTrace();
439  }
440  return null;
441  }
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Micrograph xmipp.viewer.particlepicker.ParticlePicker.getMicrograph (String name)
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Definition at line 485 of file ParticlePicker.java.

-
485  {
486  for (Micrograph m : getMicrographs()) {
487  if (m.getName().equalsIgnoreCase(name)) {
488  return m;
489  }
490  }
491  return null;
492  }
xmipp.viewer.particlepicker.ParticlePicker.getMicrographs
abstract List<? extends Micrograph > getMicrographs()
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◆ getMicrograph() [2/2]

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◆ getMicrographIndex()

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int xmipp.viewer.particlepicker.ParticlePicker.getMicrographIndex ()
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Definition at line 453 of file ParticlePicker.java.

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453  {
454  return getMicrographs().indexOf(getMicrograph());
455  }
xmipp.viewer.particlepicker.ParticlePicker.getMicrographs
abstract List<? extends Micrograph > getMicrographs()
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◆ getMicrographs()

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abstract List<? extends Micrograph> xmipp.viewer.particlepicker.ParticlePicker.getMicrographs ()
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◆ getMicrographsSelFile()

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String xmipp.viewer.particlepicker.ParticlePicker.getMicrographsSelFile ()
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Definition at line 385 of file ParticlePicker.java.

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385  {
386  return selfile;
387  }
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◆ getMode()

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Mode xmipp.viewer.particlepicker.ParticlePicker.getMode ()
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Definition at line 423 of file ParticlePicker.java.

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423  {
424  return mode;
425  }
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◆ getNextColor()

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Definition at line 88 of file ParticlePicker.java.

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88  {
89  Color next = colors[nextcolor];
90  nextcolor++;
91  if (nextcolor == colors.length) {
92  nextcolor = 0;
93  }
94  return next;
95  }
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◆ getOutputDir()

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Definition at line 447 of file ParticlePicker.java.

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447  {
448  return outputdir;
449  }
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◆ getOutputPath()

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String xmipp.viewer.particlepicker.ParticlePicker.getOutputPath (String file)
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Definition at line 443 of file ParticlePicker.java.

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443  {
444  return outputdir + File.separator + file;
445  }
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◆ getParams()

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ParticlePickerParams xmipp.viewer.particlepicker.ParticlePicker.getParams ()
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Definition at line 121 of file ParticlePicker.java.

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122  {
123  return params;
124  }
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Definition at line 127 of file ParticlePicker.java.

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127  {
128  return particlesAutoBlock + "@" + file;
129  }
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Definition at line 136 of file ParticlePicker.java.

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136  {
137  return getParticlesAutoBlock(getOutputPath(m.getPosFile()));
138  }
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static String xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock (Format f,
String file 
)
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Definition at line 97 of file ParticlePicker.java.

-
97  {
98  String blockname = getParticlesBlockName(f);
99  if (f == null) {
100  return null;
101  }
102  return blockname + "@" + file;
103 
104  }
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Definition at line 116 of file ParticlePicker.java.

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116  {
117  return getParticlesBlock(Format.Xmipp301, file);
118 
119  }
xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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Definition at line 131 of file ParticlePicker.java.

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131  {
132  return getParticlesBlock(getOutputPath(m.getPosFile()));
133 
134  }
xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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◆ getParticlesBlockName()

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static String xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlockName (Format f)
- 		-inlinestatic
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Definition at line 106 of file ParticlePicker.java.

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106  {
107  if (f == Format.Xmipp301) {
108  return "particles";
109  }
110  if (f == Format.Xmipp30) {
111  return "DefaultFamily";
112  }
113  return null;
114  }
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◆ getParticlesCount()

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◆ getPicker()

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Definition at line 682 of file ParticlePicker.java.

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683  {
684  return picker;
685  }
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◆ getPort()

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Definition at line 687 of file ParticlePicker.java.

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688  {
689  return params.port;
690  }
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◆ getPosFileFromXmipp24Project()

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String xmipp.viewer.particlepicker.ParticlePicker.getPosFileFromXmipp24Project (String projectdir,
String mname 
)
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Definition at line 338 of file ParticlePicker.java.

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338  {
339  String suffix = ".raw.Common.pos";
340  return String.format("%1$s%2$sPreprocessing%2$s%3$s%2$s%3$s%4$s", projectdir, File.separator, mname, suffix);
341  }
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◆ getRadius()

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Definition at line 639 of file ParticlePicker.java.

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639  {
640  return size / 2;
641  }
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◆ getSize()

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Definition at line 607 of file ParticlePicker.java.

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607  {
608  return size;
609  }
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◆ getTemplatesFile()

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Definition at line 457 of file ParticlePicker.java.

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457  {
458  return getOutputPath(name + "_templates.stk");
459  }
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◆ getZoom()

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Definition at line 77 of file ParticlePicker.java.

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78  {
79  return zoom;
80  }
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◆ importSize()

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void xmipp.viewer.particlepicker.ParticlePicker.importSize (String path,
Format f,
double scale 
)
- 		-inline
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Definition at line 643 of file ParticlePicker.java.

-
644  {
645  if(f == Format.Xmipp301)
646  {
647  String configfile = String.format("%s%s%s", path, File.separator, "config.xmd");
648  if(new File(configfile).exists())
649  {
650  MetaData configmd = new MetaData(configfile);
651  int size = configmd.getValueInt(MDLabel.MDL_PICKING_PARTICLE_SIZE, configmd.firstObject());
652  size = (int)(size * scale);
653  setSize(size);
654  saveConfig();
655  configmd.destroy();
656  }
657  }
658  }
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◆ isChanged()

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boolean xmipp.viewer.particlepicker.ParticlePicker.isChanged ()
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Definition at line 411 of file ParticlePicker.java.

-
411  {
412  return changed;
413  }
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◆ isFilterAdded()

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boolean xmipp.viewer.particlepicker.ParticlePicker.isFilterAdded (String filter)
- 		-inline
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Definition at line 375 of file ParticlePicker.java.

-
375  {
376  for (IJCommand f : filters) {
377  if (f.getCommand().equals(filter)) {
378  return true;
379  }
380  }
381  return false;
382  }// function isFilterSelected
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◆ isSaved()

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boolean xmipp.viewer.particlepicker.ParticlePicker.isSaved ()
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Definition at line 415 of file ParticlePicker.java.

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415  {
416  return saved;
417  }
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◆ isScipionSave()

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boolean xmipp.viewer.particlepicker.ParticlePicker.isScipionSave ()
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Definition at line 670 of file ParticlePicker.java.

-
671  {
672  if(params == null)
673  return false;
674  return params.port != null && mode != Mode.ReadOnly;
675  }
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◆ isShowDeleted()

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boolean xmipp.viewer.particlepicker.ParticlePicker.isShowDeleted ()
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Definition at line 66 of file ParticlePicker.java.

-
66  {
67  return showDeleted;
68  }
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◆ isValidSize()

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abstract boolean xmipp.viewer.particlepicker.ParticlePicker.isValidSize (JFrame parent,
int size 
)
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◆ loadConfig()

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void xmipp.viewer.particlepicker.ParticlePicker.loadConfig ()
- 		-inline
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Definition at line 172 of file ParticlePicker.java.

-
172  {
173 
174  try {
175  String file = configfile;
176  filters.clear();
177  Micrograph m = getMicrographs().get(0);
178  boolean existsConfig = new File(file).exists();
179  color = getNextColor();
180  if (!existsConfig) {
181  size = getDefaultSize();
182  setMicrograph(m);
183 
184  }
185  else
186  {
187  String mname;
188  int rgb;
189  MetaData md = new MetaData("properties@" + file);
190  long id = md.firstObject();
191  if(md.containsLabel(MDLabel.MDL_MICROGRAPH))
192  {
193  mname = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
194  m = getMicrograph(mname);
195  if(m == null)
196  m = getMicrographs().get(0);
197  }
198  setMicrograph(m);
199  if(md.containsLabel(MDLabel.MDL_COLOR))
200  {
201  rgb = md.getValueInt(MDLabel.MDL_COLOR, id);
202  color = new Color(rgb);
203  }
204  size = md.getValueInt(MDLabel.MDL_PICKING_PARTICLE_SIZE, id);
205  md.destroy();
206  String command, options;
207  if (MetaData.containsBlock(file, "filters")) {
208  md = new MetaData("filters@" + file);
209  long[] ids = md.findObjects();
210  for (long filterid : ids) {
211  command = IJCommand.getString(md.getValueString(MDLabel.MDL_MACRO_CMD, filterid));
212  options = IJCommand.getString(md.getValueString(MDLabel.MDL_MACRO_CMD_ARGS, filterid));
213  if (options.equals("NULL")) {
214  options = "";
215  }
216  filters.add(new IJCommand(command, options));
217  }
218  md.destroy();
219  }
220  }
221  if (!existsConfig || (existsConfig && !MetaData.containsBlock(file, "filters")))
222  {
223  filters.add(new IJCommand(XmippImageJ.gaussianBlurFilter, "sigma=2"));
224  filters.add(new IJCommand(XmippImageJ.enhanceContrastFilter, "saturated=0.4"));
225  saveConfig();
226  }
227 
228  } catch (Exception e) {
229  getLogger().log(Level.SEVERE, e.getMessage(), e);
230  throw new IllegalArgumentException(e.getMessage());
231  }
232 
233  }
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xmipp.viewer.particlepicker.ParticlePicker.setMicrograph
abstract void setMicrograph(Micrograph m)
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void xmipp.viewer.particlepicker.ParticlePicker.runXmippProgram (String program,
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Definition at line 592 of file ParticlePicker.java.

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592  {
593  try {
594  Program.runByName(program, args);
595  } catch (Exception e) {
596  getLogger().log(Level.SEVERE, e.getMessage(), e);
597  throw new IllegalArgumentException(e);
598  }
599  }
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Definition at line 235 of file ParticlePicker.java.

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235  {
236  try {
237  MetaData md;
238  String file = configfile;
239  md = new MetaData();
240  long id = md.addObject();
241  saveConfig(md, id);
242  md.write("properties@" + file);
243  md.destroy();
244  String cmd, options;
245  md = new MetaData();
246  for (IJCommand f : filters) {
247  id = md.addObject();
248  cmd = f.getMdCommand();
249  md.setValueString(MDLabel.MDL_MACRO_CMD, cmd, id);
250  options = f.getMdOptions();
251  md.setValueString(MDLabel.MDL_MACRO_CMD_ARGS, options, id);
252  }
253  md.writeBlock("filters@" + file);
254  md.destroy();
255 
256 
257  } catch (Exception e) {
258  getLogger().log(Level.SEVERE, e.getMessage(), e);
259  throw new IllegalArgumentException(e.getMessage());
260  }
261 
262  }
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void xmipp.viewer.particlepicker.ParticlePicker.saveConfig (MetaData md,
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Definition at line 264 of file ParticlePicker.java.

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264  {
265  Micrograph m = getMicrograph();
266  md.setValueString(MDLabel.MDL_MICROGRAPH, m.getName(), id);
267  md.setValueInt(MDLabel.MDL_COLOR, getColor().getRGB(), id);
268  md.setValueInt(MDLabel.MDL_PICKING_PARTICLE_SIZE, getSize(), id);
269  }
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Definition at line 477 of file ParticlePicker.java.

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477  {
478  saveConfig();
479  //saveData(getMicrograph());
480  //setChanged(false);
481  }// function saveData
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Definition at line 407 of file ParticlePicker.java.

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407  {
408  this.changed = changed;
409  }
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Definition at line 620 of file ParticlePicker.java.

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620  {
621  this.color = color;
622  }
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Definition at line 389 of file ParticlePicker.java.

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390  {
391  for (IJCommand f : filters) {
392  if (f.getCommand().equals(command)) {
393  f.setOptions(options);
394  }
395  }
396  }
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Definition at line 419 of file ParticlePicker.java.

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419  {
420  this.saved = saved;
421  }
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Definition at line 70 of file ParticlePicker.java.

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71  this.showDeleted = showDeleted;
72  }
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611  {
612 
613  this.size = size;
614  }
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Definition at line 82 of file ParticlePicker.java.

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83  {
84  this.zoom = zoom;
85  }
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Definition at line 73 of file ParticlePicker.java.

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74  this.showDeleted = ! this.showDeleted;
75  }
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Definition at line 348 of file ParticlePicker.java.

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348  {
349  if (command != null) {
350  String options = "";
351  if (Recorder.getCommandOptions() != null) {
352  options = Recorder.getCommandOptions();
353  }
354  //boolean isavailable = availableFilters.contains(command);
355  boolean isadded = isFilterAdded(command);
356  if (!isadded) {
357  addFilter(command, options);
358  } else if (!(options == null || options.equals(""))) {
359  setFilterOptions(command, options);
360  }
361  saveConfig();
362  }
363  }
xmipp.viewer.particlepicker.ParticlePicker.setFilterOptions
void setFilterOptions(String command, String options)
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Definition at line 461 of file ParticlePicker.java.

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461  {
462 
463  if (mode == Mode.Review && state != Mode.Review) {
464  setChanged(true);
465  return Mode.Review;
466  }
467  if (mode == Mode.Manual && !(state == Mode.Manual || state == Mode.Available)) {
468  throw new IllegalArgumentException(String.format("Can not use %s mode on this data", mode));
469  }
470  if (mode == Mode.Supervised && state == Mode.Review) {
471  throw new IllegalArgumentException(String.format("Can not use %s mode on this data", mode));
472  }
473  return state;
474 
475  }// function validateState
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String xmipp.viewer.particlepicker.ParticlePicker.block
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Definition at line 55 of file ParticlePicker.java.

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Definition at line 39 of file ParticlePicker.java.

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Definition at line 51 of file ParticlePicker.java.

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Color [] xmipp.viewer.particlepicker.ParticlePicker.colors = new Color[]{Color.GREEN, Color.BLUE, Color.CYAN, Color.MAGENTA, Color.ORANGE, Color.PINK, Color.YELLOW}
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Definition at line 57 of file ParticlePicker.java.

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Definition at line 45 of file ParticlePicker.java.

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Definition at line 60 of file ParticlePicker.java.

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List<IJCommand> xmipp.viewer.particlepicker.ParticlePicker.filters
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Definition at line 42 of file ParticlePicker.java.

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Definition at line 37 of file ParticlePicker.java.

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Definition at line 36 of file ParticlePicker.java.

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Definition at line 41 of file ParticlePicker.java.

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Definition at line 59 of file ParticlePicker.java.

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Definition at line 38 of file ParticlePicker.java.

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Definition at line 61 of file ParticlePicker.java.

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Definition at line 49 of file ParticlePicker.java.

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Definition at line 62 of file ParticlePicker.java.

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Definition at line 40 of file ParticlePicker.java.

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Definition at line 43 of file ParticlePicker.java.

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Definition at line 52 of file ParticlePicker.java.

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Definition at line 54 of file ParticlePicker.java.

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Definition at line 48 of file ParticlePicker.java.

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double xmipp.viewer.particlepicker.ParticlePicker.zoom = -1.f
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Definition at line 63 of file ParticlePicker.java.

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xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle > Member List
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This is the complete list of members for xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >, including all inherited members.

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activexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activemovedxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activestxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
adjustMagnification()xmipp.ij.commons.XmippImageCanvasinline
captureWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
continuousstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
customScrollSetup(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
dashedstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
doCustomPaint(Graphics2D g2)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
drawLine(double alpha, Graphics2D g2)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
erase(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
eraserCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
framexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
getActive()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
getFrame()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
getIw()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getLastParticle()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
getMicrograph()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
getParticlePicker()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
getPreferredMagnification()xmipp.ij.commons.XmippImageCanvasinline
getTool()xmipp.ij.commons.XmippImageCanvasinline
getXOnImage(int x)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getYOnImage(int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
hasActiveParticle()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
isDragImage(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinlineprotected
isKeyPressed(int keyCode)xmipp.ij.commons.XmippImageCanvasinlineprotected
iwxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
keyPressed(KeyEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
keyReleased(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyTyped(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
linearCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
loadData(XmippIJWindow xiw)xmipp.ij.commons.XmippImageCanvasinline
manageActive(int x, int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
micrographxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
mouseDragged(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseEntered(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseExited(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseMoved(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mousePressed(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseReleased(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseWheelMoved(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
moveActiveParticle(int x, int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
moveTo(PickerParticle p)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
offScreenX(int x)xmipp.ij.commons.XmippImageCanvasinline
offScreenY(int y)xmipp.ij.commons.XmippImageCanvasinline
paint(Graphics g)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
paintEraser(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
ParticlePickerCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
ParticlePickerCanvas(ParticlePickerJFrame frame, Micrograph micrograph)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
pickerxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
pickingCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
refresh()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
refreshActive(PickerParticle p)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
removeParticle(P particleToRemove)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
restoreWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setActiveMoved(boolean b)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setCustomCursor()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
setCustomCursor(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setInvertX(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setInvertY(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
thinContinuousStxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
updateMicrograph()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
updateMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
XmippImageCanvas(ImagePlus imp)xmipp.ij.commons.XmippImageCanvasinline
zoomIn(int sx, int sy)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
zoomOut(int sx, int sy)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerCanvas.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerCanvas.html deleted file mode 100644 index 52550d4c..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerCanvas.html +++ /dev/null @@ -1,2037 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle > Class Template Reference - - - - - - - - - -
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xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle > Class Template Referenceabstract
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-Public Member Functions

void setMicrograph (Micrograph m)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame, Micrograph micrograph)
 
void keyPressed (KeyEvent e)
 
void zoomIn (int sx, int sy)
 
void zoomOut (int sx, int sy)
 
boolean hasActiveParticle ()
 
ImageWindow getIw ()
 
void moveTo (PickerParticle p)
 
void mouseEntered (MouseEvent e)
 
void mouseExited (MouseEvent e)
 
void setCustomCursor ()
 
abstract void refreshActive (PickerParticle p)
 
abstract P getActive ()
 
abstract ParticlePickerJFrame getFrame ()
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void updateMicrograph ()
 
void updateMicrograph (Micrograph m)
 
abstract Micrograph getMicrograph ()
 
void paint (Graphics g)
 
void mouseMoved (MouseEvent e)
 
abstract ParticlePicker getParticlePicker ()
 
void mouseWheelMoved (MouseWheelEvent e)
 
- Public Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
Tool getTool ()
 
 XmippImageCanvas (ImagePlus imp)
 
void mousePressed (MouseEvent e)
 
void customScrollSetup (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void mouseWheelMoved (MouseWheelEvent e)
 
void mouseMoved (MouseEvent e)
 
int offScreenX (int x)
 
int offScreenY (int y)
 
void loadData (XmippIJWindow xiw)
 
double getPreferredMagnification ()
 
void adjustMagnification ()
 
void setInvertX (boolean value)
 
void setInvertY (boolean value)
 
void keyTyped (KeyEvent keyEvent)
 
void keyPressed (KeyEvent keyEvent)
 
void keyReleased (KeyEvent keyEvent)
 
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-Static Public Attributes

static final BasicStroke dashedst = new BasicStroke(2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 10.0f, new float[] { 10.0f }, 0.0f)
 
static final BasicStroke continuousst = new BasicStroke(2.0f)
 
static final BasicStroke thinContinuousSt = new BasicStroke(1.5f)
 
static final BasicStroke activest = new BasicStroke(1.5f)
 
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-Protected Member Functions

void captureWindowSize ()
 
void restoreWindowSize ()
 
abstract P getLastParticle ()
 
abstract void manageActive (int x, int y)
 
void setActiveMoved (boolean b)
 
void refresh ()
 
void setCustomCursor (MouseEvent e)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)
 
void drawLine (double alpha, Graphics2D g2)
 
void erase (MouseEvent e)
 
abstract void removeParticle (P particleToRemove)
 
void moveActiveParticle (int x, int y)
 
abstract void doCustomPaint (Graphics2D g2)
 
void paintEraser (MouseEvent e)
 
- Protected Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
boolean isDragImage (MouseEvent e)
 
boolean isKeyPressed (int keyCode)
 
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-Protected Attributes

ParticlePickerJFrame frame
 
Micrograph micrograph
 
ParticlePicker picker
 
XmippImageWindow iw
 
Cursor eraserCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("eraserC.png").getImage(), new Point(3, 31), "Eraser")
 
Cursor linearCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("linearPickingC.png").getImage(), new Point(0, 0), "Linear")
 
Cursor pickingCursor = getPickingCursor(pickingCursorIndex)
 
P active
 
boolean activemoved
 
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Detailed Description

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Definition at line 31 of file ParticlePickerCanvas.java.

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Constructor & Destructor Documentation

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◆ ParticlePickerCanvas() [1/2]

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xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.ParticlePickerCanvas (ParticlePickerJFrame frame)
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Definition at line 59 of file ParticlePickerCanvas.java.

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60  {
61  this(frame, frame.getMicrograph());
62  }
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◆ ParticlePickerCanvas() [2/2]

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xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.ParticlePickerCanvas (ParticlePickerJFrame frame,
Micrograph micrograph 
)
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Definition at line 64 of file ParticlePickerCanvas.java.

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65  {
66  super(micrograph.getImagePlus(frame.getParticlePicker().getFilters()));
67  this.frame = frame;
68  this.picker = frame.getParticlePicker();
69  this.micrograph = micrograph;
70  micrograph.runImageJFilters(picker.getFilters());
71 
72  addKeyListener(this);
73  addMouseMotionListener(this);
74 
75  this.iw = new XmippImageWindow(getImage(), this, null);
76  getFrame().displayZoom(getMagnification());
77  iw.setTitle(getMicrograph().getName());
78 
79  }
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xmipp.viewer.particlepicker.Micrograph.runImageJFilters
void runImageJFilters(List< IJCommand > filters)
Definition: Micrograph.java:234
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xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
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Member Function Documentation

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◆ captureWindowSize()

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.captureWindowSize ()
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Definition at line 176 of file ParticlePickerCanvas.java.

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176  {
177  size = this.imp.getWindow().getSize();
178  this.imp.getWindow().setIgnoreRepaint(true);
179 
180  }
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abstract void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.doCustomPaint (Graphics2D g2)
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◆ drawLine()

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.drawLine (double alpha,
Graphics2D g2 
)
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Definition at line 346 of file ParticlePickerCanvas.java.

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347  {
348  int width = imp.getWidth();
349  int height = imp.getHeight();
350  double m;
351  double x1, y1, x2, y2;
352  if (alpha != Math.PI / 2)
353  {
354  m = Math.tan(alpha - Math.PI / 2);
355 
356  double y = height / 2.f;
357  double x = y / m;
358 
359  if (Math.abs(x) > width / 2.f)// cuts in image sides
360  {
361  x1 = width;// on image
362  y1 = getYCutOnImage(m, width / 2.f);
363  x2 = 0;
364  y2 = getYCutOnImage(m, -width / 2.f);
365  }
366  else
367  // cuts in image top and bottom
368  {
369  y1 = 0;
370  x1 = getXCutOnImage(m, height / 2.f);
371  y2 = height;
372  x2 = getXCutOnImage(m, -height / 2.f);
373  }
374  }
375  else
376  {
377  x1 = 0;
378  y1 = y2 = height / 2.f;
379  x2 = width;
380 
381  }
382  Color ccolor = g2.getColor();
383  g2.setColor(Color.yellow);
384  g2.drawLine((int) (x1 * magnification), (int) (y1 * magnification), (int) (x2 * magnification), (int) (y2 * magnification));
385  g2.setColor(ccolor);
386  }
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◆ drawShape() [1/5]

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.drawShape (Graphics2D g2,
ManualParticle p,
boolean all,
Stroke stroke 
)
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Definition at line 303 of file ParticlePickerCanvas.java.

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304  {
305  drawShape(g2, p.getX(), p.getY(), picker.getSize(), all, stroke);
306  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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◆ drawShape() [2/5]

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.drawShape (Graphics2D g2,
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boolean all 
)
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Definition at line 308 of file ParticlePickerCanvas.java.

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309  {
310  drawShape(g2, p, all, continuousst);
311  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.drawShape (Graphics2D g2,
int x,
int y,
int size,
boolean all 
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Definition at line 313 of file ParticlePickerCanvas.java.

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314  {
315  drawShape(g2, x, y, size, all, continuousst);
316 
317  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.drawShape (Graphics2D g2,
int x,
int y,
int size,
boolean all,
Stroke stroke,
Color color 
)
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Definition at line 318 of file ParticlePickerCanvas.java.

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319  {
320  g2.setColor(color);
321  drawShape(g2, x, y, size, all, stroke);
322  }
xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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◆ drawShape() [5/5]

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.drawShape (Graphics2D g2,
int x,
int y,
int size,
boolean all,
Stroke stroke 
)
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Definition at line 323 of file ParticlePickerCanvas.java.

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324  {
325 
326  g2.setStroke(stroke);
327  int length = (int) (size * magnification);
328  int radius = (int) (size / 2. * magnification);
329  x = getXOnImage(x);
330  y = getYOnImage(y);
331  int distance = Math.min(10, (int) (radius/4. * magnification));
332 
333  if (getFrame().isShapeSelected(Shape.Rectangle) || all)
334  g2.drawRect(x - radius, y - radius, length, length);
335  if (getFrame().isShapeSelected(Shape.Circle) || all)
336  g2.drawOval(x - radius, y - radius, length, length);
337  if (getFrame().isShapeSelected(Shape.Center) || all)
338  {
339  g2.setStroke(activest);
340  g2.drawLine(x, y - distance, x, y + distance);
341  g2.drawLine(x + distance, y, x - distance, y);
342  }
343  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
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◆ erase()

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.erase (MouseEvent e)
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Definition at line 452 of file ParticlePickerCanvas.java.

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453  {
454  // Get the eraser size and coordinates and apply zoom
455  int size = getFrame().getEraserSize()/2;
456  double distance = (size);
457 
458  // Add the radio of the particles: we want to eras particle if eraser touches the circle of the particle
459  distance = distance + (getParticlePicker().getSize()/2);
460 
461 
462  int cursorX = offScreenX(e.getX());
463  int cursorY = offScreenY (e.getY());
464 
465  List<PickerParticle> particlesToDelete = new ArrayList<PickerParticle>();
466  // Go through the list of particles
467  for (PickerParticle particle : getMicrograph().getParticleList()) {
468 
469  // if particle is within the distance (inside eraser)
470  int length = length(particle.getX(),particle.getY(), cursorX, cursorY);
471 
472  if (length <= distance){
473  particlesToDelete.add(particle);
474  }
475  }
476 
477  // For each particle to delete
478  for (PickerParticle particle : particlesToDelete) {
479  removeParticle((P) particle);
480  }
481 
482  active = getLastParticle();
483  refresh();
484  paintEraser(e);
485  }
xmipp.viewer.particlepicker.Micrograph.getParticleList
List<? extends PickerParticle > getParticleList()
Definition: Micrograph.java:279
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xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
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xmipp.viewer.particlepicker.ParticlePickerCanvas.removeParticle
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◆ getActive()

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◆ getIw()

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Definition at line 230 of file ParticlePickerCanvas.java.

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231  {
232  return iw;
233  }
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◆ getLastParticle()

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◆ getMicrograph()

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Definition at line 389 of file ParticlePickerCanvas.java.

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390  {
391  int x0 = (int) getSrcRect().getX();
392  return (int) ((x - x0) * magnification);
393  }
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Definition at line 395 of file ParticlePickerCanvas.java.

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396  {
397  int y0 = (int) getSrcRect().getY();
398  return (int) ((y - y0) * magnification);
399  }
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Definition at line 213 of file ParticlePickerCanvas.java.

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214  {
215  return active != null;
216  }
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Definition at line 81 of file ParticlePickerCanvas.java.

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82  {
83  super.keyPressed(e);
84 
85  P active = getActive();
86  int step = 1;
87  int code = e.getKeyCode();
88 // int x = screenX(imp.getWidth()/2);
89 // int y = screenY(imp.getHeight()/2);
90  if(active != null)
91  {
92  if (code == KeyEvent.VK_UP)
93  {
94  setActiveMoved(true);
95  manageActive(active.getX(), active.getY() - step);
96  }
97  else if (code == KeyEvent.VK_DOWN)
98  {
99  setActiveMoved(true);
100  manageActive(active.getX(), active.getY() + step);
101  }
102  else if (code == KeyEvent.VK_LEFT)
103  {
104  setActiveMoved(true);
105  manageActive(active.getX() - step, active.getY());
106  }
107  else if (code == KeyEvent.VK_RIGHT)
108  {
109  setActiveMoved(true);
110  manageActive(active.getX() + step, active.getY());
111  }
112  else if (code == ParticlePickerJFrame.ERASE_ACTIVE)
113  {
114  removeParticle((P) active);
115  this.active = getLastParticle();
116  refresh();
117  }
118  }
119  if (code == ParticlePickerJFrame.TOGGLE_MARKER_KEY)
120  {
121  getFrame().circlechb.setSelected(tongleSetSelected);
122  getFrame().rectanglechb.setSelected(tongleSetSelected);
123  tongleSetSelected = !tongleSetSelected;
124  }else if (code == ParticlePickerJFrame.TOGGLE_ERASE_MODE_KEY){
125  // Toggle erase mode.
126  getFrame().activateEraseMode();
127  } else if (code == ParticlePickerJFrame.NEXT_MICROGRAPH_KEY)
128  {
129  getFrame().moveToNextMicrograph();
130  } else if (code == ParticlePickerJFrame.PREVIOUS_MICROGRAPH_KEY)
131  {
132  getFrame().moveToPreviousMicrograph();
133  }else if (code == ParticlePickerJFrame.TOGGLE_LINEAR_MODE_KEY){
134  // Toggle linear mode
135  getFrame().activateLinearMode();
136  }else if (code == ParticlePickerJFrame.TOGGLE_NORMAL_MODE_KEY){
137  // Toggle linear mode
138  getFrame().activateNormalMode();
139 
140  }else if (code == KeyEvent.VK_PLUS){
141  changePickingCursor((byte) (pickingCursorIndex+1));
142 
143  }else if (code == KeyEvent.VK_MINUS){
144  changePickingCursor((byte) (pickingCursorIndex-1));
145 
146  }else
147  return;// do not repaint if not needed
148  repaint();
149  }
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Definition at line 257 of file ParticlePickerCanvas.java.

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258  {
259  super.mouseEntered(e);
260  this.requestFocus();
261  setCustomCursor(e);
262  }
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Definition at line 264 of file ParticlePickerCanvas.java.

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265  {
266  super.mouseExited(e);
267  setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
268 
269  }
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Definition at line 528 of file ParticlePickerCanvas.java.

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528  {
529  super.mouseMoved(e);
530 
531  if (getFrame().isEraserMode(e)){
532  paintEraser(e);
533  }
534  }
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Definition at line 568 of file ParticlePickerCanvas.java.

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568  {
569  // Resize the eraser brush
570  if (!e.isShiftDown()){
571  // if erase mode
572  if (getFrame().isEraserMode(e)){
573  getFrame().setEraserSize(getFrame().getEraserSize()+(e.getWheelRotation()*50));
574  paintEraser(e);
575  } else {
576  getFrame().processSizeMouseWheelEvent(e);
577  }
578 
579  } else {
580  super.mouseWheelMoved(e);
581 
582  }
583  }
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Definition at line 497 of file ParticlePickerCanvas.java.

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498  {
499  if (active == null)
500  return;
501  try{
502  active.setPosition(x, y);
503 
504  }catch (Exception e){
505  XmippDialog.showError(getFrame(), e.getMessage());
506  }
507  if (getFrame().getParticlesJDialog() != null)
508  active.getParticleCanvas(getFrame()).repaint();
509  }
- -
xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
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◆ moveTo()

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.moveTo (PickerParticle p)
- 		-inline
-
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Definition at line 235 of file ParticlePickerCanvas.java.

-
236  {
237  int width = (int) getSrcRect().getWidth();
238  int height = (int) getSrcRect().getHeight();
239  int x0 = p.getX() - width / 2;
240  if (x0 < 0)
241  x0 = 0;
242  if (x0 + width > imp.getWidth())
243  x0 = imp.getWidth() - width;
244  int y0 = p.getY() - height / 2;
245  if (y0 < 0)
246  y0 = 0;
247  if (y0 + height > imp.getHeight())
248  y0 = imp.getHeight() - height;
249  Rectangle r = new Rectangle(x0, y0, width, height);
250  if (!getSrcRect().contains(r))
251  {
252  setSourceRect(r);
253  repaint();
254  }
255  }
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◆ paint()

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.paint (Graphics g)
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Definition at line 511 of file ParticlePickerCanvas.java.

-
511  {
512  Graphics offgc;//Off screen graphic
513  Image offscreen = null;//Off screen image
514  Dimension d = getSize();
515 
516  // create the offscreen buffer and associated Graphics
517  offscreen = createImage(d.width, d.height);
518  offgc = offscreen.getGraphics();
519 
520  super.paint(offgc);//super paint in off screen
521  //my paint in offscreen
522  Graphics2D g2 = (Graphics2D) offgc;
523  doCustomPaint(g2);
524  //drawing offscreen image
525  g.drawImage(offscreen, 0, 0, this);
526  }
xmipp.viewer.particlepicker.ParticlePickerCanvas.doCustomPaint
abstract void doCustomPaint(Graphics2D g2)
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◆ paintEraser()

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.paintEraser (MouseEvent e)
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Definition at line 540 of file ParticlePickerCanvas.java.

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540  {
541 
542  paintEraser(e.getX(),e.getY());
543 
544  }
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.refresh ()
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Definition at line 223 of file ParticlePickerCanvas.java.

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224  {
225  getFrame().updateMicrographsModel();
226  getFrame().setChanged(true);
227  repaint();
228  }
xmipp.viewer.particlepicker.ParticlePickerJFrame.setChanged
abstract void setChanged(boolean changed)
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xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
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abstract void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.refreshActive (PickerParticle p)
- 		-abstract
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abstract void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.removeParticle (P particleToRemove)
- 		-abstractprotected
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.restoreWindowSize ()
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Definition at line 181 of file ParticlePickerCanvas.java.

-
181  {
182  if (size != null) {
183  this.imp.getWindow().setSize(size);
184  this.imp.getWindow().setIgnoreRepaint(false);
185  }
186  }
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.setActiveMoved (boolean b)
- 		-inlineprotected
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Definition at line 218 of file ParticlePickerCanvas.java.

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219  {
220  activemoved = b;
221  }
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.setCustomCursor ()
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Definition at line 271 of file ParticlePickerCanvas.java.

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271  {
272  setCustomCursor(null);
273  }
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.setCustomCursor (MouseEvent e)
- 		-inlineprotected
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Definition at line 274 of file ParticlePickerCanvas.java.

-
275  {
276  boolean proceed = true;
277 
278  if (e != null) {
279  proceed = getFrame().isPickingAvailable(e);
280  }
281 
282  if (proceed) {
283  if (getFrame().isEraserMode(null))
284  setCursor(eraserCursor);
285 
286  else if (getFrame().isLinearMode())
287  setCursor(linearCursor);
288 
289  else
290  setCursor(pickingCursor);
291  }
292  }
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abstract ParticlePickerJFrame getFrame()
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◆ setMicrograph()

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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.setMicrograph (Micrograph m)
- 		-inline
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Definition at line 49 of file ParticlePickerCanvas.java.

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50  {
51  micrograph = m;
52 
53  }
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.updateMicrograph ()
- 		-inline
-
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Definition at line 414 of file ParticlePickerCanvas.java.

-
415  {
416  Micrograph m = getFrame().getMicrograph();
417  updateMicrograph(m);
418  }
- -
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abstract ParticlePickerJFrame getFrame()
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.updateMicrograph (Micrograph m)
- 		-inline
-
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Definition at line 420 of file ParticlePickerCanvas.java.

-
421  {
422  getMicrograph().releaseImage();
423  setMicrograph(m);
424  imp = m.getImagePlus(picker.getFilters());
425  m.runImageJFilters(picker.getFilters());
426  refreshActive(null);
427  Rectangle previousRect = (Rectangle)srcRect.clone();
428  int previousDstWidth = dstWidth;
429  int previousDstHeight = dstHeight;
430  if(iw.isClosing())
431  iw = new XmippImageWindow(getImage(), this, null);
432  iw.setImage(imp);
433  double zoom = getParticlePicker().getZoom();
434  int imageWidth = imp.getWidth();
435  int imageHeight = imp.getHeight();
436  if(zoom != -1)
437  {
438 
439  setDrawingSize(previousDstWidth, previousDstHeight);
440  if (previousRect.width < imageWidth && previousRect.height < imageHeight)
441  setSourceRect(previousRect);
442  setMagnification(zoom);
443  iw.pack();
444  }
445  else
446  iw.maximize();
447  getFrame().displayZoom(getMagnification());
448  iw.setTitle(getMicrograph().getName());
449 
450  }
- - - - - -
xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
- - - -
xmipp.viewer.particlepicker.ParticlePickerCanvas.refreshActive
abstract void refreshActive(PickerParticle p)
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.zoomIn (int sx,
int sy 
)
- 		-inline
-
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Definition at line 188 of file ParticlePickerCanvas.java.

-
189  {
190 
191  captureWindowSize();
192 
193  super.zoomIn(sx, sy);
194  getFrame().displayZoom(getMagnification());
195 
196  restoreWindowSize();
197  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
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void xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.zoomOut (int sx,
int sy 
)
- 		-inline
-
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Definition at line 199 of file ParticlePickerCanvas.java.

-
200  {
201  captureWindowSize();
202 
203  super.zoomOut(sx, sy);
204  getFrame().displayZoom(getMagnification());
205 
206  restoreWindowSize();
207  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.getFrame
abstract ParticlePickerJFrame getFrame()
- - -
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Member Data Documentation

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◆ active

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P xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.active
- 		-protected
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Definition at line 46 of file ParticlePickerCanvas.java.

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◆ activemoved

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boolean xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.activemoved
- 		-protected
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Definition at line 55 of file ParticlePickerCanvas.java.

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◆ activest

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final BasicStroke xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.activest = new BasicStroke(1.5f)
- 		-static
-
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Definition at line 36 of file ParticlePickerCanvas.java.

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◆ continuousst

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final BasicStroke xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.continuousst = new BasicStroke(2.0f)
- 		-static
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Definition at line 34 of file ParticlePickerCanvas.java.

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◆ dashedst

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final BasicStroke xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.dashedst = new BasicStroke(2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 10.0f, new float[] { 10.0f }, 0.0f)
- 		-static
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Definition at line 33 of file ParticlePickerCanvas.java.

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◆ eraserCursor

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Cursor xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.eraserCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("eraserC.png").getImage(), new Point(3, 31), "Eraser")
- 		-protected
-
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Definition at line 42 of file ParticlePickerCanvas.java.

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◆ frame

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ParticlePickerJFrame xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.frame
- 		-protected
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Definition at line 38 of file ParticlePickerCanvas.java.

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◆ iw

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XmippImageWindow xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.iw
- 		-protected
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Definition at line 41 of file ParticlePickerCanvas.java.

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◆ linearCursor

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Cursor xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.linearCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("linearPickingC.png").getImage(), new Point(0, 0), "Linear")
- 		-protected
-
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Definition at line 43 of file ParticlePickerCanvas.java.

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◆ micrograph

- -
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Micrograph xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.micrograph
- 		-protected
-
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Definition at line 39 of file ParticlePickerCanvas.java.

- -
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◆ picker

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ParticlePicker xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.picker
- 		-protected
-
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Definition at line 40 of file ParticlePickerCanvas.java.

- -
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◆ pickingCursor

- -
-
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Cursor xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.pickingCursor = getPickingCursor(pickingCursorIndex)
- 		-protected
-
- -

Definition at line 45 of file ParticlePickerCanvas.java.

- -
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◆ thinContinuousSt

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-
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final BasicStroke xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >.thinContinuousSt = new BasicStroke(1.5f)
- 		-static
-
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Definition at line 35 of file ParticlePickerCanvas.java.

- -
-
-
The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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xmipp.viewer.particlepicker.ParticlePickerJFrame Member List
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This is the complete list of members for xmipp.viewer.particlepicker.ParticlePickerJFrame, including all inherited members.

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actionPerformed(ActionEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateEraseMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateLinearMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateNormalMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activefilterxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
addFilterAppliedListener()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
applyFilter(String filter)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
bundlexmipp.viewer.particlepicker.ParticlePickerJFrameprotected
canExit()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
centerchbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
changeShapes()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
circlechbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
close()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
closebtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorpnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
commandxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
displayZoom(double zoom)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
enableEdition(boolean enable)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
ERASE_ACTIVExmipp.viewer.particlepicker.ParticlePickerJFramestatic
eraseAvailable()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
eSizexmipp.viewer.particlepicker.ParticlePickerJFrameprotected
eSizelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
eSizepnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
executeScipionSaveAndExit()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
exitmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
exportmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
filemnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
filtersmnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
getAvailableParticles()xmipp.viewer.particlepicker.ParticlePickerJFrame
getCanvas()xmipp.viewer.particlepicker.ParticlePickerJFrame
getEraserSize()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getKeyAssist()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrame
getParticlePicker()xmipp.viewer.particlepicker.ParticlePickerJFrame
getParticlesJDialog()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getResetMsg()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getSide()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getStep()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getTextField(JSpinner spinner)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
hcontentsmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
helpmnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
ijmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
importmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.ParticlePickerJFrame
importpjdxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
initColorPane(Color color)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initEraserSizePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initParticlesJDialog()xmipp.viewer.particlepicker.ParticlePickerJFrame
initShapePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initSizePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initStepPane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initToolBar()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isEraserMode(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isLinearMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isNormalMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isPickingAvailable(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isShapeSelected(Shape shape)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
linearModeAvailable()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
loadMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameprotected
loadParticles(boolean reset)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
micrographstbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
modesgrpxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
moveToNextMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
moveToPreviousMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
NEXT_MICROGRAPH_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
openHelpURl()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
ParticlePickerJFrame(ParticlePicker picker)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
particlesdialogxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
pmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
positionlbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
PREVIOUS_MICROGRAPH_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
processSizeMouseWheelEvent(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
readSizeFromTextField()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
rectanglechbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
reloadImage()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
resetbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
resetMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameprotected
saveandexitbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
savebtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
saveData(boolean notify)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
savemixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
setCanvasCursor()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
setChanged(boolean changed)xmipp.viewer.particlepicker.ParticlePickerJFrame
setEraserSize(int newSize)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
setSaved(boolean saved)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
setTitle()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
shapelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
showException(Exception e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
showHideModeParameters()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
showMessage(String message)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
sizelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sizepnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sizetfxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
tbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
TOGGLE_ERASE_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_LINEAR_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_MARKER_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_NORMAL_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
updateColor(Color color)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
updateMicrographsModel()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
updateMicrographsModel(boolean all)xmipp.viewer.particlepicker.ParticlePickerJFrame
updateSize(int size)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
usezoombtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
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-Generated by   -doxygen - 1.8.13 -
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-Classes | -Public Member Functions | -Static Public Attributes | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.viewer.particlepicker.ParticlePickerJFrame Class Referenceabstract
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-Inheritance diagram for xmipp.viewer.particlepicker.ParticlePickerJFrame:
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-Classes

class  ColorActionListener
 
class  MicrographsSelectionListener
 
class  ShapeItemListener
 
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-Public Member Functions

 ParticlePickerJFrame (ParticlePicker picker)
 
void moveToNextMicrograph ()
 
void moveToPreviousMicrograph ()
 
void processSizeMouseWheelEvent (MouseWheelEvent e)
 
String getResetMsg ()
 
void actionPerformed (ActionEvent e)
 
void applyFilter (String filter)
 
int getSide ()
 
abstract ParticlePickerCanvas getCanvas ()
 
abstract ParticlesDialog initParticlesJDialog ()
 
void loadParticles (boolean reset)
 
void updateMicrographsModel ()
 
abstract void updateMicrographsModel (boolean all)
 
ParticlesDialog getParticlesJDialog ()
 
abstract Micrograph getMicrograph ()
 
abstract List<? extends PickerParticle > getAvailableParticles ()
 
boolean isPickingAvailable (MouseEvent e)
 
void updateColor (Color color)
 
void initToolBar ()
 
boolean isEraserMode (MouseEvent e)
 
void activateEraseMode ()
 
boolean isLinearMode ()
 
boolean isNormalMode ()
 
void activateLinearMode ()
 
void activateNormalMode ()
 
int getEraserSize ()
 
void setEraserSize (int newSize)
 
int getStep ()
 
void changeShapes ()
 
boolean isShapeSelected (Shape shape)
 
abstract ParticlePicker getParticlePicker ()
 
abstract void setChanged (boolean changed)
 
void setSaved (boolean saved)
 
JFormattedTextField getTextField (JSpinner spinner)
 
void updateSize (int size)
 
boolean showMessage (String message)
 
boolean showException (Exception e)
 
void close ()
 
abstract String importParticles (Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
Map< Object, Object > getKeyAssist ()
 
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-Static Public Attributes

static final int TOGGLE_LINEAR_MODE_KEY = KeyEvent.VK_L
 
static final int TOGGLE_ERASE_MODE_KEY = KeyEvent.VK_E
 
static final int NEXT_MICROGRAPH_KEY = KeyEvent.VK_R
 
static final int PREVIOUS_MICROGRAPH_KEY = KeyEvent.VK_W
 
static final int TOGGLE_MARKER_KEY = KeyEvent.VK_SPACE
 
static final int TOGGLE_NORMAL_MODE_KEY = KeyEvent.VK_P
 
static final int ERASE_ACTIVE = KeyEvent.VK_DELETE
 
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-Protected Member Functions

boolean canExit ()
 
abstract void loadMicrograph ()
 
boolean saveData (boolean notify)
 
void addFilterAppliedListener ()
 
void openHelpURl ()
 
abstract void resetMicrograph ()
 
void enableEdition (boolean enable)
 
void reloadImage ()
 
void initShapePane ()
 
boolean eraseAvailable ()
 
void setCanvasCursor ()
 
boolean linearModeAvailable ()
 
void showHideModeParameters ()
 
void displayZoom (double zoom)
 
void setTitle ()
 
void initColorPane (Color color)
 
void initStepPane ()
 
void initEraserSizePane ()
 
void initSizePane ()
 
void readSizeFromTextField ()
 
void executeScipionSaveAndExit ()
 
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-Protected Attributes

ParticlesDialog particlesdialog
 
JMenuItem ijmi
 
JToggleButton circlechb
 
JToggleButton rectanglechb
 
JToggleButton centerchb
 
JLabel shapelb
 
JMenuItem savemi
 
JMenuItem hcontentsmi
 
JMenuItem pmi
 
JMenuItem exportmi
 
JMenu filtersmn
 
String activefilter
 
JPanel sizepn
 
JLabel sizelb
 
JFormattedTextField sizetf
 
JPanel eSizepn
 
JLabel eSizelb
 
JSpinner eSize
 
JMenu filemn
 
JMenuItem importmi
 
JButton colorbt
 
Color color
 
JPanel colorpn
 
JButton resetbt
 
JTable micrographstb
 
ImportParticlesJDialog importpjd = null
 
JMenuItem exitmi
 
JLabel positionlb
 
JToggleButton usezoombt
 
ButtonGroup modesgrp
 
JMenu helpmn
 
JButton savebt
 
JButton saveandexitbt
 
JToolBar tb
 
ResourceBundle bundle
 
String command
 
JButton closebt
 
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Detailed Description

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-

Definition at line 50 of file ParticlePickerJFrame.java.

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Constructor & Destructor Documentation

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◆ ParticlePickerJFrame()

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xmipp.viewer.particlepicker.ParticlePickerJFrame.ParticlePickerJFrame (ParticlePicker picker)
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-
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Definition at line 118 of file ParticlePickerJFrame.java.

-
119  {
120  try {
121  File file = new File(Filename.getXmippPath("resources"));
122  URL[] urls = new URL[]{file.toURI().toURL()};
123  ClassLoader loader = new URLClassLoader(urls);
124  bundle = ResourceBundle.getBundle("Bundle", Locale.getDefault(), loader);
125  XmippApplication.addInstance(false);
126  setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
127  addWindowListener(new WindowAdapter()
128  {
129  public void windowClosing(WindowEvent winEvt)
130  {
131 
132  if (canExit()) close();
133 
134  }
135  });
136 
137  initMenuBar(picker);
138 
139  resetbt = XmippWindowUtil.getTextButton(bundle.getString("resetmic"), new ActionListener()
140  {
141 
142  @Override
143  public void actionPerformed(ActionEvent e)
144  {
145  String resetmsg = getResetMsg();
146  XmippQuestionDialog qd = new XmippQuestionDialog(ParticlePickerJFrame.this, resetmsg, false);
147  if (qd.showDialog())
148  resetMicrograph();
149  }
150  });
151 
152  // Create the text button
153  createZoomButton();
154 
155  savebt = XmippWindowUtil.getTextIconButton(bundle.getString("save"), "save.gif", new ActionListener()
156  {
157 
158  @Override
159  public void actionPerformed(ActionEvent arg0)
160  {
161  saveData(false);
162 
163  }
164  });
165 
166  saveandexitbt = XmippWindowUtil.getTextButton(bundle.getString("saveandexit"), new ActionListener()
167  {
168 
169  @Override
170  public void actionPerformed(ActionEvent e)
171  {
172  ParticlePicker picker = getParticlePicker();
173  if (picker.getMode() != Mode.ReadOnly)
174  picker.saveData();
175  if(picker instanceof SupervisedParticlePicker)
176  ((SupervisedParticlePicker)picker).getClassifier().setApplyChanges(true);
177 
178  if(picker.isScipionSave())
179  {
180  int count = picker.getParticlesCount();
181  if(count == 0)
182  {
183  XmippDialog.showInfo(ParticlePickerJFrame.this, XmippMessage.getEmptyFieldMsg("coordinates"));
184  return;
185  }
186  HashMap<String, String> msgfields = new HashMap<String, String>();
187  boolean createprot = picker.getPort() == null;
188  if(createprot)
189  msgfields.put("Run name:", "ProtUserCoordinates");
190 
191  String msg = String.format("<html>Are you sure you want to register a new set of Coordinates with <font color=red>%s</font> %s?", count, (count != 1)?"elements":"element");
192  InputFieldsMessageDialog dlg = new InputFieldsMessageDialog(ParticlePickerJFrame.this, "Question", msg);
193 
194  if (dlg.action == InputFieldsMessageDialog.OK_OPTION)
195  executeScipionSaveAndExit();
196 
197  }
198  else
199  close();
200 
201  }
202  });
203  closebt = XmippWindowUtil.getTextIconButton("Close", "fa-times.png", new ActionListener()
204  {
205 
206  @Override
207  public void actionPerformed(ActionEvent e)
208  {
209  if (canExit()) close();
210  }
211  });
212  if(picker.isScipionSave())
213  {
214  saveandexitbt.setText("Coordinates");
215  Image img = Toolkit.getDefaultToolkit().getImage(Filename.getXmippPath("resources" + File.separator + "fa-plus-circle.png"));
216  saveandexitbt.setIcon(new ImageIcon(img));
217  saveandexitbt.setToolTipText("Create Coordinates");
218  Color color = XmippWindowUtil.firebrick;
219  saveandexitbt.setBackground(color);
220  saveandexitbt.setForeground(Color.WHITE);
221 
222  }
223  micrographstb = new JTable();
224  micrographstb.getSelectionModel().addListSelectionListener(new MicrographsSelectionListener());
225  micrographstb.addMouseListener(new MouseListener()
226  {
227 
228  @Override
229  public void mouseReleased(MouseEvent arg0)
230  {
231  // TODO Auto-generated method stub
232 
233  }
234 
235  @Override
236  public void mousePressed(MouseEvent arg0)
237  {
238  // TODO Auto-generated method stub
239 
240  }
241 
242  @Override
243  public void mouseExited(MouseEvent arg0)
244  {
245  // TODO Auto-generated method stub
246 
247  }
248 
249  @Override
250  public void mouseEntered(MouseEvent arg0)
251  {
252  // TODO Auto-generated method stub
253 
254  }
255 
256  @Override
257  public void mouseClicked(MouseEvent arg0)
258  {
259  if (micrographstb.getSelectedRow() == -1)
260  return;
261  loadMicrograph();
262  }
263  });
264 
265  XmippWindowUtil.setScipionImageIcon(this);
266 
267  } catch (Exception ex) {
268  Logger.getLogger(ParticlePickerJFrame.class.getName()).log(Level.SEVERE, null, ex);
269  throw new IllegalArgumentException(ex);
270  }
271  }
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-

Member Function Documentation

- -

◆ actionPerformed()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.actionPerformed (ActionEvent e)
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-
- -

Definition at line 566 of file ParticlePickerJFrame.java.

-
567  {
568  try
569  {
570  JCheckBoxMenuItem item = (JCheckBoxMenuItem) e.getSource();
571  activefilter = item.getText();
572  if (item.isSelected())// filter added, will be registered by picker
573  // with options if needed
574  if (activefilter.equals(ParticlePicker.xmippsmoothfilter))
575  {
576  getParticlePicker().addFilter(ParticlePicker.xmippsmoothfilter, "xmipp");
577  reloadImage();
578  }
579  else
580  {
581  command = activefilter;
582  applyFilter(activefilter);
583 
584  }
585  else
586  {
587  // filter removed
588  getParticlePicker().removeFilter(activefilter);
589  reloadImage();
590  if(particlesdialog != null)
591  loadParticles(true);
592 
593  }
594  if(getParticlePicker().getMode() != Mode.ReadOnly)
595  getParticlePicker().saveConfig();
596  }
597  catch (Exception ex)
598  {
599 
600  ex.printStackTrace();
601  showException(ex);
602  }
603 
604  }
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xmipp.viewer.particlepicker.ParticlePicker.addFilter
void addFilter(String command, String options)
Definition: ParticlePicker.java:398
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◆ activateEraseMode()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.activateEraseMode ()
- 		-inline
-
- -

Definition at line 855 of file ParticlePickerJFrame.java.

-
855  {
856  if (eraseAvailable()) {
857 
858  if (isEraserMode(null)) {
859  activateNormalMode();
860  } else {
861  eraserbt.setSelected(true);
862  setCanvasCursor();
863  showHideModeParameters();
864  }
865  }
866  }
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◆ activateLinearMode()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.activateLinearMode ()
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- -

Definition at line 885 of file ParticlePickerJFrame.java.

-
885  {
886  if (linearModeAvailable()) {
887 
888  if (isLinearMode()) {
889  activateNormalMode();
890  } else {
891  linearPickingbt.setSelected(true);
892  showHideModeParameters();
893  ((SupervisedPickerCanvas) getCanvas()).resetLinearPicking();
894  setCanvasCursor();
895  }
896  }
897  }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
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◆ activateNormalMode()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.activateNormalMode ()
- 		-inline
-
- -

Definition at line 899 of file ParticlePickerJFrame.java.

-
899  {
900 
901  normalPickingbt.setSelected(true);
902  showHideModeParameters();
903  setCanvasCursor();
904 
905  }
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◆ addFilterAppliedListener()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.addFilterAppliedListener ()
- 		-inlineprotected
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- -

Definition at line 501 of file ParticlePickerJFrame.java.

-
501  {
502 
503  Recorder.record = true;
504 
505  // detecting if a command is thrown by ImageJ
506 
507  ImagePlus.addImageListener(new ImageListener() {
508 
509  @Override
510  public void imageUpdated(ImagePlus imp) {
511  if(command != null)
512  {
513  getParticlePicker().updateFilters(command);
514  if(particlesdialog != null)
515  loadParticles(true);
516 
517  }
518  command = null;
519  }
520 
521  @Override
522  public void imageOpened(ImagePlus arg0) {
523 
524  }
525 
526  @Override
527  public void imageClosed(ImagePlus arg0) {
528  // TODO Auto-generated method stub
529 
530  }
531  });
532  }
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-
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◆ applyFilter()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.applyFilter (String filter)
- 		-inline
-
- -

Definition at line 606 of file ParticlePickerJFrame.java.

-
607  {
608  IJ.run(getMicrograph().getImagePlus(), filter, "");
609  }
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◆ canExit()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.canExit ()
- 		-inlineprotected
-
- -

Definition at line 289 of file ParticlePickerJFrame.java.

-
289  {
290 
291  if (getParticlePicker().getParams().tmp && (getParticlePicker().isSaved() || getParticlePicker().isChanged()))
292  {
293  XmippQuestionDialog qd = new XmippQuestionDialog(ParticlePickerJFrame.this, "You are picking in a temporary folder. None of the saved or changed data will remain unless you export \"Coordinates\". Do you really want to exit?", false );
294  boolean exit = qd.showDialog();
295  if (!exit)
296  return false;
297 
298  }else if (getParticlePicker().isChanged())
299  {
300  XmippQuestionDialog qd = new XmippQuestionDialog(ParticlePickerJFrame.this, "Save changes before closing?");
301  boolean save = qd.showDialog();
302  if (save)
303  return saveData(true);
304  else if (qd.isCanceled())
305  return false;
306  }
307  return true;
308  }
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◆ changeShapes()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.changeShapes ()
- 		-inline
-
- -

Definition at line 967 of file ParticlePickerJFrame.java.

-
968  {
969  getCanvas().repaint();
970 
971  }
xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
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-
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◆ close()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.close ()
- 		-inline
-
- -

Definition at line 1226 of file ParticlePickerJFrame.java.

-
1227  {
1228  setVisible(false);
1229  dispose();
1230  if (getCanvas() != null)
1231  getCanvas().getIw().close();
1232  XmippApplication.removeInstance(false);
1233  }
-
xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
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-
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◆ displayZoom()

- -
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void xmipp.viewer.particlepicker.ParticlePickerJFrame.displayZoom (double zoom)
- 		-inlineprotected
-
- -

Definition at line 949 of file ParticlePickerJFrame.java.

-
950  {
951 
952  usezoombt.setText(String.format(Locale.US, "%.2f", zoom));
953  if(usezoombt.isSelected())
954  getParticlePicker().setZoom(zoom);
955  pack();
956  }
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◆ enableEdition()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.enableEdition (boolean enable)
- 		-inlineprotected
-
- -

Definition at line 541 of file ParticlePickerJFrame.java.

-
542  {
543  importmi.setEnabled(enable);
544  savemi.setEnabled(enable);
545  sizetf.setEnabled(enable);
546  colorbt.setEnabled(enable);
547  resetbt.setEnabled(enable);
548  savebt.setEnabled(enable);
549  eraserbt.setEnabled(enable);
550 
551  }
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◆ eraseAvailable()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.eraseAvailable ()
- 		-inlineprotected
-
- -

Definition at line 851 of file ParticlePickerJFrame.java.

-
851  {
852  return eraserbt != null;
853  }
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◆ executeScipionSaveAndExit()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.executeScipionSaveAndExit ()
- 		-inlineprotected
-
- -

Definition at line 1265 of file ParticlePickerJFrame.java.

-
1266  {
1267  getCanvas().setEnabled(false);
1268  XmippWindowUtil.blockGUI(ParticlePickerJFrame.this, "Creating set ...");
1269  new Thread(new Runnable() {
1270 
1271  @Override
1272  public void run() {
1273 
1274  try {
1275  String cmd = String.format("run function registerCoords '%s'", getParticlePicker().getOutputDir());
1276  XmippWindowUtil.runCommand(cmd, getParticlePicker().getParams().port);
1277  XmippWindowUtil.releaseGUI(ParticlePickerJFrame.this.getRootPane());
1278  getCanvas().setEnabled(true);
1279 
1280  close();
1281 
1282  } catch (Exception ex) {
1283  ex.printStackTrace();
1284  throw new IllegalArgumentException(ex.getMessage());
1285  }
1286 
1287  }
1288  }).start();
1289  }
- -
xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
- -
-
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◆ getAvailableParticles()

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-
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abstract List<? extends PickerParticle> xmipp.viewer.particlepicker.ParticlePickerJFrame.getAvailableParticles ()
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◆ getCanvas()

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abstract ParticlePickerCanvas xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas ()
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◆ getEraserSize()

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int xmipp.viewer.particlepicker.ParticlePickerJFrame.getEraserSize ()
- 		-inline
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- -

Definition at line 911 of file ParticlePickerJFrame.java.

-
911  {
912  if (isEraserMode(null)){
913  return (Integer) eSize.getValue();
914  } else {
915  return 1;
916  }
917  }
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◆ getKeyAssist()

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Map<Object, Object> xmipp.viewer.particlepicker.ParticlePickerJFrame.getKeyAssist ()
- 		-inline
-
- -

Definition at line 1237 of file ParticlePickerJFrame.java.

-
1238  {
1239  Map<Object, Object> map = Collections.synchronizedMap(new LinkedHashMap<Object, Object>());
1240  map.put("Shift + scroll up / ctrl + left click", "Zoom in");
1241  map.put("Shift + scroll down / ctrl + right click", "Zoom out");
1242  map.put("Right click + mouse move", "Moves image previously expanded");
1243  map.put("Left click", "Adds or selects a particle. In erase mode, deletes or disables selected particles");
1244  map.put("Shift + left click", "Deletes or disables selected particle");
1245  map.put("Left click + mouse move", "Moves selected particle. In erase mode, deletes or disables particles");
1246  map.put("Left", "Moves selected particle to the left");
1247  map.put("Right", "Moves selected particle to the right");
1248  map.put("Up", "Moves selected particle up");
1249  map.put("Down", "Moves selected particle down");
1250  map.put((char)TOGGLE_ERASE_MODE_KEY, "Toggle between erase and picking");
1251  map.put((char)NEXT_MICROGRAPH_KEY, "Select Next Micrograph");
1252  map.put((char)PREVIOUS_MICROGRAPH_KEY, "Select Previous Micrograph");
1253  map.put("Space bar", "hide/show particle markers.");
1254 
1255  if (linearModeAvailable()) {
1256 
1257  map.put((char)TOGGLE_LINEAR_MODE_KEY, "Toggle between normal picking and linear picking mode");
1258  map.put((char)SupervisedPickerCanvas.POLIGONAL_MODE_KEY + " (continuous)", "While in linear picking mode, linear picking will be continuous (polygonal mode).");
1259  map.put("ESCAPE", "Will reset the linear picking canceling the pending line");
1260  }
1261 
1262  return map;
1263  }
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◆ getMicrograph()

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abstract Micrograph xmipp.viewer.particlepicker.ParticlePickerJFrame.getMicrograph ()
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◆ getParticlePicker()

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abstract ParticlePicker xmipp.viewer.particlepicker.ParticlePickerJFrame.getParticlePicker ()
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◆ getParticlesJDialog()

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ParticlesDialog xmipp.viewer.particlepicker.ParticlePickerJFrame.getParticlesJDialog ()
- 		-inline
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- -

Definition at line 660 of file ParticlePickerJFrame.java.

-
661  {
662  return particlesdialog;
663  }
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◆ getResetMsg()

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String xmipp.viewer.particlepicker.ParticlePickerJFrame.getResetMsg ()
- 		-inline
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Definition at line 333 of file ParticlePickerJFrame.java.

-
334  {
335  return "Are you sure you want to remove all particles from micrograph?";
336  }
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◆ getSide()

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int xmipp.viewer.particlepicker.ParticlePickerJFrame.getSide ()
- 		-inline
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Definition at line 617 of file ParticlePickerJFrame.java.

-
618  {
619  return 100;
620  }
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◆ getStep()

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int xmipp.viewer.particlepicker.ParticlePickerJFrame.getStep ()
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Definition at line 924 of file ParticlePickerJFrame.java.

-
924  {
925  if (linearModeAvailable()){
926  return Integer.parseInt(steptf.getText());
927  } else {
928  return 1000;
929  }
930  }
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-
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◆ getTextField()

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JFormattedTextField xmipp.viewer.particlepicker.ParticlePickerJFrame.getTextField (JSpinner spinner)
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Return the formatted text field used the spinner null if the editor doesn't descend from JSpinner.DefaultEditor.

- -

Definition at line 1057 of file ParticlePickerJFrame.java.

-
1057  {
1058  JComponent editor = spinner.getEditor();
1059  if (editor instanceof JSpinner.DefaultEditor) {
1060  return ((JSpinner.DefaultEditor)editor).getTextField();
1061  } else {
1062  System.err.println("Unexpected editor type: "
1063  + spinner.getEditor().getClass()
1064  + " isn't a descendant of DefaultEditor");
1065  return null;
1066  }
1067  }
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◆ importParticles()

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abstract String xmipp.viewer.particlepicker.ParticlePickerJFrame.importParticles (Format format,
String dir,
String preffix,
String suffix,
float scale,
boolean invertx,
boolean inverty 
)
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◆ initColorPane()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.initColorPane (Color color)
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Definition at line 1005 of file ParticlePickerJFrame.java.

-
1006  {
1007  colorpn = new JPanel();
1008  colorpn.setOpaque(false);
1009  this.color = color;
1010  colorpn.add(new JLabel("Color:"));
1011  colorbt = new JButton();
1012  colorbt.setContentAreaFilled(false);
1013  colorbt.setFocusPainted(false);
1014  colorbt.setIcon(new ColorIcon(color));
1015  colorbt.setBorderPainted(false);
1016  colorbt.setMargin(new Insets(0, 0, 0, 0));
1017  colorbt.addActionListener(new ColorActionListener());
1018  colorpn.add(colorbt);
1019  }
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◆ initEraserSizePane()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.initEraserSizePane ()
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- -

Definition at line 1035 of file ParticlePickerJFrame.java.

-
1036  {
1037  eSizepn = new JPanel();
1038  eSizepn.setOpaque(false);
1039  int size = 100;
1040  eSizelb = new JLabel("Eraser size:");
1041  eSizepn.add(eSizelb);
1042  eSize = new JSpinner();
1043  JFormattedTextField text = getTextField(eSize);
1044  text.setColumns(5);
1045  eSize.setValue(size);
1046  eSizepn.add(eSize);
1047  // Default : hidden.
1048  eSizepn.setVisible(false);
1049  tb.add(eSizepn);
1050 
1051  }
- -
xmipp.viewer.particlepicker.ParticlePickerJFrame.getTextField
JFormattedTextField getTextField(JSpinner spinner)
Definition: ParticlePickerJFrame.java:1057
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◆ initParticlesJDialog()

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abstract ParticlesDialog xmipp.viewer.particlepicker.ParticlePickerJFrame.initParticlesJDialog ()
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◆ initShapePane()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.initShapePane ()
- 		-inlineprotected
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Definition at line 720 of file ParticlePickerJFrame.java.

-
721  {
722 
723  ShapeItemListener shapeListener = new ShapeItemListener();
724  shapelb = new JLabel("Shape:");
725  tb.add(shapelb);
726 
727  // Add shapes buttons
728  circlechb = addShapeButton("circle.png", shapeListener);
729  rectanglechb = addShapeButton("square.png", shapeListener);
730  centerchb = addShapeButton("plus.png", shapeListener);
731 
732  }
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◆ initSizePane()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.initSizePane ()
- 		-inlineprotected
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- -

Definition at line 1069 of file ParticlePickerJFrame.java.

-
1070  {
1071  sizepn = new JPanel();
1072  sizepn.setOpaque(false);
1073  int size = getParticlePicker().getSize();
1074  sizelb = new JLabel("Size (px):");
1075  sizepn.add(sizelb);
1076  sizetf = new JFormattedTextField(NumberFormat.getIntegerInstance());
1077  sizetf.setColumns(4);
1078  sizetf.setValue(size);
1079  sizepn.add(sizetf);
1080  listenToFocusEventsOnSize();
1081  listenToChangeOnSize();
1082  // This is commented due to coredumps when rapid changes happen when pressing + or -
1083  //listenToKeysOnSize();
1084  listenToMouseOnSize();
1085  sizetf.setToolTipText("Use +, - or the mousewheel to quickly change the box size. Return will apply the size.");
1086 
1087  }
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◆ initStepPane()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.initStepPane ()
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- -

Definition at line 1021 of file ParticlePickerJFrame.java.

-
1021  {
1022  steppn = new JPanel();
1023  steppn.setOpaque(false);
1024 
1025  steplb = new JLabel("Step:");
1026  steppn.add(steplb);
1027 
1028 
1029  steptf = new JFormattedTextField(NumberFormat.getIntegerInstance());
1030  steptf.setColumns(3);
1031  steptf.setValue(100);
1032  steppn.add(steptf);
1033  }
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◆ initToolBar()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.initToolBar ()
- 		-inline
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Definition at line 773 of file ParticlePickerJFrame.java.

-
774  {
775  tb = new JToolBar();
776  tb.setFloatable(false);
777  tb.setBackground(this.color);
778 
779 
780  // To group modes buttons
781  modesgrp = new ButtonGroup();
782 
783  // Create an ItemListener to listen to mode changes
784  ItemListener changeListener = new ItemListener() {
785  @Override
786  public void itemStateChanged(ItemEvent itemEvent) {
787  showHideModeParameters();
788  }
789  };
790 
791  // Add the normal picking mode
792  normalPickingbt = createModeButton("picking.png",TOGGLE_NORMAL_MODE_KEY, changeListener, true);
793 
794  // If it's supervised picking.
795  if ((this instanceof SupervisedPickerJFrame))
796  {
797  // Linear picking mode
798  linearPickingbt = createModeButton("linearPicking.png",TOGGLE_LINEAR_MODE_KEY, changeListener, false);
799 
800  // Step pane
801  initStepPane();
802  }
803 
804  // Eraser modes
805  if (!(this instanceof ExtractPickerJFrame))
806  {
807  // Add eraser
808  eraserbt = createModeButton("eraser.png",TOGGLE_ERASE_MODE_KEY, changeListener, false);
809 
810  // Color pane
811  initColorPane(getParticlePicker().getColor());
812 
813  // Eraser size pane
814  initEraserSizePane();
815 
816  }
817 
818  tb.addSeparator();
819 
820  // Size pane
821  initSizePane();
822  tb.add(sizepn);
823 
824  // Shape pane
825  initShapePane();
826 
827  // Add color
828  if (colorbt != null) tb.add(colorpn);
829 
830  // Add step
831  if (steppn != null) tb.add(steppn);
832 
833  this.showHideModeParameters();
834 
835  }
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◆ isEraserMode()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.isEraserMode (MouseEvent e)
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Definition at line 837 of file ParticlePickerJFrame.java.

-
838  {
839  if (!eraseAvailable())
840  return false;
841 
842  boolean eraseHotKeyPressed = false;
843 
844  if (e != null) {
845  eraseHotKeyPressed = e.isShiftDown();
846  }
847 
848  return eraserbt.isSelected() || eraseHotKeyPressed;
849  }
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◆ isLinearMode()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.isLinearMode ()
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Definition at line 872 of file ParticlePickerJFrame.java.

-
872  {
873  if (linearModeAvailable()){
874  return linearPickingbt.isSelected();
875  } else {
876  return false;
877  }
878  }
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◆ isNormalMode()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.isNormalMode ()
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Definition at line 880 of file ParticlePickerJFrame.java.

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880  {
881 
882  return normalPickingbt.isSelected();
883  }
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◆ isPickingAvailable()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.isPickingAvailable (MouseEvent e)
- 		-inline
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Definition at line 669 of file ParticlePickerJFrame.java.

-
670  {
671  if (getCanvas().getTool() != Tool.PICKER)
672  return false;
673  if (SwingUtilities.isRightMouseButton(e))
674  return false;
675  if (getParticlePicker().getMode() == Mode.ReadOnly ||
676  getParticlePicker().getMode() == Mode.Automatic)
677  return false;
678  if (e.isControlDown())
679  return false;
680  return true;
681  }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
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◆ isShapeSelected()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.isShapeSelected (Shape shape)
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-
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Definition at line 973 of file ParticlePickerJFrame.java.

-
974  {
975  switch (shape)
976  {
977  case Rectangle:
978  return rectanglechb.isSelected();
979  case Circle:
980  return circlechb.isSelected();
981  case Center:
982  return centerchb.isSelected();
983  // case OnlyLast:
984  // return onlylastchb.isSelected();
985  }
986  return false;
987  }
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◆ linearModeAvailable()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.linearModeAvailable ()
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Definition at line 907 of file ParticlePickerJFrame.java.

-
907  {
908  return linearPickingbt != null;
909  }
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◆ loadMicrograph()

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abstract void xmipp.viewer.particlepicker.ParticlePickerJFrame.loadMicrograph ()
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◆ loadParticles()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.loadParticles (boolean reset)
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- -

Definition at line 626 of file ParticlePickerJFrame.java.

-
627  {
628  try
629  {
630  if(reset)
631  for (PickerParticle p : getAvailableParticles())
632  p.resetParticleCanvas();
633  if (particlesdialog == null)
634  particlesdialog = initParticlesJDialog();
635  else
636  {
637 
638  particlesdialog.loadParticles(false);
639  particlesdialog.setVisible(true);
640  }
641  }
642  catch (Exception ex)
643  {
644  showException(ex);
645  if (particlesdialog != null)
646  particlesdialog.close();
647  particlesdialog = null;
648  }
649 
650  }
xmipp.viewer.particlepicker.ParticlePickerJFrame.getAvailableParticles
abstract List<? extends PickerParticle > getAvailableParticles()
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xmipp.viewer.particlepicker.ParticlePickerJFrame.initParticlesJDialog
abstract ParticlesDialog initParticlesJDialog()
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◆ moveToNextMicrograph()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.moveToNextMicrograph ()
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Definition at line 273 of file ParticlePickerJFrame.java.

-
273  {
274  int selectedRow = micrographstb.getSelectedRow();
275  selectedRow = selectedRow +1;
276  if (selectedRow < micrographstb.getRowCount()){
277  micrographstb.setRowSelectionInterval(selectedRow,selectedRow);
278  }
279  }
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◆ moveToPreviousMicrograph()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.moveToPreviousMicrograph ()
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Definition at line 281 of file ParticlePickerJFrame.java.

-
281  {
282  int selectedRow = micrographstb.getSelectedRow();
283  selectedRow = selectedRow -1;
284  if (selectedRow > -1){
285  micrographstb.setRowSelectionInterval(selectedRow,selectedRow);
286  }
287  }
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◆ openHelpURl()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.openHelpURl ()
- 		-inlineprotected
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Definition at line 534 of file ParticlePickerJFrame.java.

-
535  {
536  XmippWindowUtil.openURI("https://github.com/I2PC/scipion/wiki/Picker");
537  }
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◆ processSizeMouseWheelEvent()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.processSizeMouseWheelEvent (MouseWheelEvent e)
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Definition at line 310 of file ParticlePickerJFrame.java.

-
310  {
311 
312  int notches = e.getWheelRotation();
313  increaseBoxSize(notches);
314  }
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◆ readSizeFromTextField()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.readSizeFromTextField ()
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Definition at line 1183 of file ParticlePickerJFrame.java.

-
1184  {
1185 
1186  int size = ((Number) sizetf.getValue()).intValue();
1187  if (size == getParticlePicker().getSize())
1188  return;
1189 
1190  if (!getParticlePicker().isValidSize(ParticlePickerJFrame.this, size))
1191  {
1192 
1193  int prevsize = getParticlePicker().getSize();
1194  sizetf.setText(Integer.toString(prevsize));
1195  return;
1196  }
1197  updateSize(size);
1198 
1199  }
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xmipp.viewer.particlepicker.ParticlePicker.isValidSize
abstract boolean isValidSize(JFrame parent, int size)
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◆ reloadImage()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.reloadImage ()
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Definition at line 611 of file ParticlePickerJFrame.java.

-
612  {
613  getCanvas().updateMicrograph();
614 
615  }
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◆ resetMicrograph()

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◆ saveData()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.saveData (boolean notify)
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Definition at line 489 of file ParticlePickerJFrame.java.

-
489  {
490  try {
491  getParticlePicker().saveData();
492  if (notify) showMessage("Data saved successfully");
493  setChanged(false);
494  return true;
495  } catch (Exception e1) {
496  XmippDialog.showException(getMyself(), e1);
497  return false;
498  }
499  }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.setChanged
abstract void setChanged(boolean changed)
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◆ setCanvasCursor()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.setCanvasCursor ()
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Definition at line 868 of file ParticlePickerJFrame.java.

-
868  {
869  getCanvas().setCustomCursor();
870  }
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◆ setChanged()

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abstract void xmipp.viewer.particlepicker.ParticlePickerJFrame.setChanged (boolean changed)
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◆ setEraserSize()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.setEraserSize (int newSize)
- 		-inline
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Definition at line 919 of file ParticlePickerJFrame.java.

-
919  {
920  if (newSize<1) newSize=1;
921  eSize.setValue(newSize);
922  }
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◆ setSaved()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.setSaved (boolean saved)
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Definition at line 1002 of file ParticlePickerJFrame.java.

-
1002  {
1003  };
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◆ setTitle()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.setTitle ()
- 		-inlineprotected
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Definition at line 993 of file ParticlePickerJFrame.java.

-
993  {
994 
995  String title = "Xmipp Particle Picker - " + getParticlePicker().getMode();
996 
997  if (this.getParticlePicker().getParams().tmp){
998  title = title + " - in Temporal folder.";
999  }
1000  setTitle(title);
1001  }
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◆ showException()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.showException (Exception e)
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Definition at line 1221 of file ParticlePickerJFrame.java.

-
1222  {
1223  return XmippDialog.showException(this, e);
1224  }
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◆ showHideModeParameters()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.showHideModeParameters ()
- 		-inlineprotected
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Definition at line 932 of file ParticlePickerJFrame.java.

-
932  {
933 
934  boolean isEraseMode = isEraserMode(null);
935  boolean isLinearMode = isLinearMode();
936 
937  sizepn.setVisible(!isEraseMode);
938  eSizepn.setVisible(isEraseMode);
939  colorpn.setVisible(!isEraseMode);
940  if (linearModeAvailable()) steppn.setVisible(isLinearMode);
941 
942  // Shapes
943  shapelb.setVisible(!isEraseMode);
944  circlechb.setVisible(!isEraseMode);
945  centerchb.setVisible(!isEraseMode);
946  rectanglechb.setVisible(!isEraseMode);
947  }
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◆ showMessage()

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boolean xmipp.viewer.particlepicker.ParticlePickerJFrame.showMessage (String message)
- 		-inline
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-

Shortcut function to show messages

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Definition at line 1216 of file ParticlePickerJFrame.java.

-
1217  {
1218  return XmippDialog.showInfo(this, message);
1219  }
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◆ updateColor()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.updateColor (Color color)
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Definition at line 711 of file ParticlePickerJFrame.java.

-
712  {
713  if (colorbt != null)
714  colorbt.setIcon(new ColorIcon(color));
715  getParticlePicker().setColor(color);
716  getCanvas().repaint();
717  getParticlePicker().saveConfig();
718  }
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◆ updateMicrographsModel() [1/2]

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.updateMicrographsModel ()
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Definition at line 652 of file ParticlePickerJFrame.java.

-
653  {
654  updateMicrographsModel(false);
655 
656  }
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◆ updateMicrographsModel() [2/2]

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abstract void xmipp.viewer.particlepicker.ParticlePickerJFrame.updateMicrographsModel (boolean all)
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◆ updateSize()

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.updateSize (int size)
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Definition at line 1201 of file ParticlePickerJFrame.java.

-
1202  {
1203 
1204  sizetf.setValue(size);
1205  sizetf.selectAll();
1206  if(getCanvas() != null)
1207  getCanvas().repaint();
1208  getParticlePicker().setSize(size);
1209  //updateMicrographsModel();
1210  if(particlesdialog != null)
1211  loadParticles(true);
1212  getParticlePicker().saveConfig();
1213  }
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Member Data Documentation

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◆ activefilter

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String xmipp.viewer.particlepicker.ParticlePickerJFrame.activefilter
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Definition at line 73 of file ParticlePickerJFrame.java.

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◆ bundle

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ResourceBundle xmipp.viewer.particlepicker.ParticlePickerJFrame.bundle
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Definition at line 114 of file ParticlePickerJFrame.java.

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◆ centerchb

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JToggleButton xmipp.viewer.particlepicker.ParticlePickerJFrame.centerchb
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Definition at line 65 of file ParticlePickerJFrame.java.

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◆ circlechb

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JToggleButton xmipp.viewer.particlepicker.ParticlePickerJFrame.circlechb
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Definition at line 63 of file ParticlePickerJFrame.java.

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◆ closebt

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JButton xmipp.viewer.particlepicker.ParticlePickerJFrame.closebt
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Definition at line 116 of file ParticlePickerJFrame.java.

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◆ color

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Definition at line 89 of file ParticlePickerJFrame.java.

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◆ colorbt

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JButton xmipp.viewer.particlepicker.ParticlePickerJFrame.colorbt
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Definition at line 88 of file ParticlePickerJFrame.java.

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◆ colorpn

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JPanel xmipp.viewer.particlepicker.ParticlePickerJFrame.colorpn
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Definition at line 90 of file ParticlePickerJFrame.java.

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◆ command

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String xmipp.viewer.particlepicker.ParticlePickerJFrame.command
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Definition at line 115 of file ParticlePickerJFrame.java.

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◆ ERASE_ACTIVE

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Definition at line 59 of file ParticlePickerJFrame.java.

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Definition at line 83 of file ParticlePickerJFrame.java.

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Definition at line 81 of file ParticlePickerJFrame.java.

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Definition at line 68 of file ParticlePickerJFrame.java.

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Definition at line 110 of file ParticlePickerJFrame.java.

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Definition at line 87 of file ParticlePickerJFrame.java.

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Definition at line 93 of file ParticlePickerJFrame.java.

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Definition at line 99 of file ParticlePickerJFrame.java.

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Definition at line 69 of file ParticlePickerJFrame.java.

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Definition at line 95 of file ParticlePickerJFrame.java.

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Definition at line 56 of file ParticlePickerJFrame.java.

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Definition at line 64 of file ParticlePickerJFrame.java.

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Definition at line 112 of file ParticlePickerJFrame.java.

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Definition at line 111 of file ParticlePickerJFrame.java.

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Definition at line 67 of file ParticlePickerJFrame.java.

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Definition at line 113 of file ParticlePickerJFrame.java.

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Definition at line 96 of file ParticlePickerJFrame.java.

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actionPerformed(ActionEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrame.ColorActionListenerinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener.html deleted file mode 100644 index bcb8f7d3..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener.html +++ /dev/null @@ -1,142 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.ParticlePickerJFrame.ColorActionListener Class Reference - - - - - - - - - -
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void actionPerformed (ActionEvent e)
 
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Definition at line 685 of file ParticlePickerJFrame.java.

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.ColorActionListener.actionPerformed (ActionEvent e)
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Definition at line 690 of file ParticlePickerJFrame.java.

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691  {
692  // Set up the dialog that the button brings up.
693  colorChooser = new JColorChooser();
694  colorChooser.setColor(getParticlePicker().getColor());
695  JDialog dialog = JColorChooser.createDialog(colorbt, "Pick a Color", true, // modal
696  colorChooser, new ActionListener()
697  {
698  @Override
699  public void actionPerformed(ActionEvent e)
700  {
701  updateColor(colorChooser.getColor());
702  getParticlePicker().setColor(colorChooser.getColor());
703  }
704  }, // OK button handler
705  null); // no CANCEL button handler
706  XmippWindowUtil.setLocation(0.5f, 0.5f, dialog);
707  dialog.setVisible(true);
708  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__coll__graph.dot deleted file mode 100644 index 4a0dd70d..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__coll__graph.dot +++ /dev/null @@ -1,10 +0,0 @@ -digraph "xmipp.viewer.particlepicker.ParticlePickerJFrame.ColorActionListener" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.\lParticlePickerJFrame.ColorAction\lListener",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node4 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" colorChooser" ,fontname="Helvetica"]; - Node4 [label="JColorChooser",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__coll__graph.md5 deleted file mode 100644 index fc3c8b40..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -5505c2bf16167b5a5d66bc3dc9a7c007 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__inherit__graph.dot deleted file mode 100644 index dc2012d5..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.ParticlePickerJFrame.ColorActionListener" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.\lParticlePickerJFrame.ColorAction\lListener",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__inherit__graph.md5 deleted file mode 100644 index d3d61362..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1ColorActionListener__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -2be61a489a9f6f3c5cca294ff6d37b3f \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1MicrographsSelectionListener-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1MicrographsSelectionListener-members.html deleted file mode 100644 index 61562a7d..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1MicrographsSelectionListener-members.html +++ /dev/null @@ -1,83 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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valueChanged(ListSelectionEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrame.MicrographsSelectionListenerinline
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void valueChanged (ListSelectionEvent e)
 
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Definition at line 316 of file ParticlePickerJFrame.java.

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void xmipp.viewer.particlepicker.ParticlePickerJFrame.MicrographsSelectionListener.valueChanged (ListSelectionEvent e)
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Definition at line 320 of file ParticlePickerJFrame.java.

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321  {
322  if (e.getValueIsAdjusting())
323  return;
324 
325  if (micrographstb.getSelectedRow() == -1)
326  return;// Probably from fireTableDataChanged raised
327  loadMicrograph();
328  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1MicrographsSelectionListener__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1MicrographsSelectionListener__coll__graph.dot deleted file mode 100644 index cb66a2e4..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame_1_1MicrographsSelectionListener__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.ParticlePickerJFrame.MicrographsSelectionListener" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.\lParticlePickerJFrame.Micrographs\lSelectionListener",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ListSelectionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; 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- node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node0 [label="xmipp.viewer.particlepicker.\lParticlePickerJFrame",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node0 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.particlepicker.extract.\lExtractPickerJFrame",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractPickerJFrame.html"]; - Node0 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; 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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.ParticlePickerParams Member List
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This is the complete list of members for xmipp.viewer.particlepicker.ParticlePickerParams, including all inherited members.

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CLASSIFIERxmipp.viewer.particlepicker.ParticlePickerParamsstatic
classifierPropertiesxmipp.viewer.particlepicker.ParticlePickerParams
defineArgs()xmipp.viewer.particlepicker.ParticlePickerParamsinline
fastxmipp.viewer.particlepicker.ParticlePickerParams
FASTOPTxmipp.viewer.particlepicker.ParticlePickerParamsstatic
incorexmipp.viewer.particlepicker.ParticlePickerParams
INCOREOPTxmipp.viewer.particlepicker.ParticlePickerParamsstatic
inputfilexmipp.viewer.particlepicker.ParticlePickerParams
INPUTOPTxmipp.viewer.particlepicker.ParticlePickerParamsstatic
isScipion()xmipp.viewer.particlepicker.ParticlePickerParamsinline
modexmipp.viewer.particlepicker.ParticlePickerParams
MODEOPTxmipp.viewer.particlepicker.ParticlePickerParamsstatic
outputdirxmipp.viewer.particlepicker.ParticlePickerParams
OUTPUTOPTxmipp.viewer.particlepicker.ParticlePickerParamsstatic
ParticlePickerParams(Mode mode)xmipp.viewer.particlepicker.ParticlePickerParamsinline
ParticlePickerParams(String[] args)xmipp.viewer.particlepicker.ParticlePickerParamsinline
portxmipp.viewer.particlepicker.ParticlePickerParams
processArgs(String args[])xmipp.viewer.particlepicker.ParticlePickerParamsinline
SCIPIONOPTxmipp.viewer.particlepicker.ParticlePickerParamsstatic
threadsxmipp.viewer.particlepicker.ParticlePickerParams
THREADSOPTxmipp.viewer.particlepicker.ParticlePickerParamsstatic
TMPxmipp.viewer.particlepicker.ParticlePickerParamsstatic
tmpxmipp.viewer.particlepicker.ParticlePickerParams
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-Generated by   -doxygen - 1.8.13 -
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Xmipp -  v20.07 -
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-Public Member Functions | -Public Attributes | -Static Public Attributes | -List of all members
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xmipp.viewer.particlepicker.ParticlePickerParams Class Reference
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-Collaboration diagram for xmipp.viewer.particlepicker.ParticlePickerParams:
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-Public Member Functions

 ParticlePickerParams (Mode mode)
 
 ParticlePickerParams (String[] args)
 
void defineArgs ()
 
void processArgs (String args[]) throws ParseException
 
boolean isScipion ()
 
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-Public Attributes

String inputfile
 
String outputdir
 
Integer port
 
Mode mode
 
Integer threads = 1
 
boolean fast
 
boolean incore
 
String classifierProperties
 
boolean tmp
 
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-Static Public Attributes

static final String SCIPIONOPT = "scipion"
 
static final String INPUTOPT = "input"
 
static final String OUTPUTOPT = "output"
 
static final String MODEOPT = "mode"
 
static final String THREADSOPT = "threads"
 
static final String FASTOPT = "fast"
 
static final String INCOREOPT = "incore"
 
static final String CLASSIFIER = "classifier"
 
static final String TMP = "tmp"
 
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Detailed Description

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Author
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Definition at line 21 of file ParticlePickerParams.java.

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Constructor & Destructor Documentation

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◆ ParticlePickerParams() [1/2]

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xmipp.viewer.particlepicker.ParticlePickerParams.ParticlePickerParams (Mode mode)
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Definition at line 47 of file ParticlePickerParams.java.

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48  {
49  this.mode = mode;
50  }
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◆ ParticlePickerParams() [2/2]

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xmipp.viewer.particlepicker.ParticlePickerParams.ParticlePickerParams (String [] args)
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Definition at line 52 of file ParticlePickerParams.java.

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53  {
54  try {
55  defineArgs();
56  processArgs(args);
57  } catch (ParseException ex) {
58  Logger.getLogger(ParticlePickerParams.class.getName()).log(Level.SEVERE, null, ex);
59  }
60  }
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Member Function Documentation

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◆ defineArgs()

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void xmipp.viewer.particlepicker.ParticlePickerParams.defineArgs ()
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Definition at line 62 of file ParticlePickerParams.java.

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62  {
63  options = new Options();
64  options.addOption(INPUTOPT, true, "");
65  options.addOption(OUTPUTOPT, true, "");
66  options.addOption(MODEOPT, true, "");
67  options.addOption(THREADSOPT, true, "");
68  options.addOption(FASTOPT, true, "");
69  options.addOption(INCOREOPT, true, "");
70  options.addOption(SCIPIONOPT, true, "");
71  options.addOption(CLASSIFIER, true, "");
72  options.addOption(TMP,true, "Warns about loosing data. Coordinates mus be generated.");
73  }
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◆ isScipion()

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boolean xmipp.viewer.particlepicker.ParticlePickerParams.isScipion ()
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Definition at line 116 of file ParticlePickerParams.java.

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117  {
118  return cmdLine.hasOption(SCIPIONOPT);
119  }
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◆ processArgs()

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void xmipp.viewer.particlepicker.ParticlePickerParams.processArgs (String args[]) throws ParseException
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Definition at line 75 of file ParticlePickerParams.java.

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75  {
76 
77  String[] cmdargs;
78  BasicParser parser = new BasicParser();
79  cmdLine = parser.parse(options, args);
80  inputfile = cmdLine.getOptionValue(INPUTOPT);
81  outputdir = cmdLine.getOptionValue(OUTPUTOPT);
82  mode = Mode.Manual;
83  if(cmdLine.hasOption(MODEOPT))
84  {
85  String str = cmdLine.getOptionValue(MODEOPT);
86  mode = Mode.getMode(str);
87  if(mode != Mode.Review && mode != Mode.ReadOnly && mode != Mode.Automatic)
88  throw new IllegalArgumentException("Only modes Automatic, Review, ReadOnly can be specified from the command line");
89  }
90  if (cmdLine.hasOption(THREADSOPT))
91  threads = Integer.parseInt(cmdLine.getOptionValue(THREADSOPT));
92  if (cmdLine.hasOption(FASTOPT))
93  fast = Boolean.parseBoolean(cmdLine.getOptionValue(FASTOPT));
94  if (cmdLine.hasOption(INCOREOPT))
95  incore = Boolean.parseBoolean(cmdLine.getOptionValue(INCOREOPT));
96 
97 
98  if (cmdLine.hasOption(SCIPIONOPT)) {
99  cmdargs = cmdLine.getOptionValues(SCIPIONOPT);
100  if(cmdargs != null)
101  port = Integer.parseInt(cmdargs[0]);
102  }
103  if (cmdLine.hasOption(CLASSIFIER)) {
104  classifierProperties = cmdLine.getOptionValue(CLASSIFIER);
105 
106  }
107  if (cmdLine.hasOption(TMP)) {
108  tmp = Boolean.parseBoolean(cmdLine.getOptionValue(TMP));
109 
110  }
111 
112 
113  }
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Member Data Documentation

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◆ CLASSIFIER

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final String xmipp.viewer.particlepicker.ParticlePickerParams.CLASSIFIER = "classifier"
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Definition at line 32 of file ParticlePickerParams.java.

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◆ classifierProperties

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String xmipp.viewer.particlepicker.ParticlePickerParams.classifierProperties
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Definition at line 44 of file ParticlePickerParams.java.

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◆ fast

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boolean xmipp.viewer.particlepicker.ParticlePickerParams.fast
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Definition at line 42 of file ParticlePickerParams.java.

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◆ FASTOPT

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final String xmipp.viewer.particlepicker.ParticlePickerParams.FASTOPT = "fast"
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Definition at line 30 of file ParticlePickerParams.java.

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◆ incore

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boolean xmipp.viewer.particlepicker.ParticlePickerParams.incore
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Definition at line 43 of file ParticlePickerParams.java.

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◆ INCOREOPT

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final String xmipp.viewer.particlepicker.ParticlePickerParams.INCOREOPT = "incore"
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Definition at line 31 of file ParticlePickerParams.java.

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◆ inputfile

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String xmipp.viewer.particlepicker.ParticlePickerParams.inputfile
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Definition at line 37 of file ParticlePickerParams.java.

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◆ INPUTOPT

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final String xmipp.viewer.particlepicker.ParticlePickerParams.INPUTOPT = "input"
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Definition at line 26 of file ParticlePickerParams.java.

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◆ mode

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Mode xmipp.viewer.particlepicker.ParticlePickerParams.mode
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Definition at line 40 of file ParticlePickerParams.java.

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◆ MODEOPT

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final String xmipp.viewer.particlepicker.ParticlePickerParams.MODEOPT = "mode"
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Definition at line 28 of file ParticlePickerParams.java.

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◆ outputdir

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String xmipp.viewer.particlepicker.ParticlePickerParams.outputdir
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Definition at line 38 of file ParticlePickerParams.java.

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◆ OUTPUTOPT

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final String xmipp.viewer.particlepicker.ParticlePickerParams.OUTPUTOPT = "output"
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Definition at line 27 of file ParticlePickerParams.java.

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◆ port

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Integer xmipp.viewer.particlepicker.ParticlePickerParams.port
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Definition at line 39 of file ParticlePickerParams.java.

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◆ SCIPIONOPT

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final String xmipp.viewer.particlepicker.ParticlePickerParams.SCIPIONOPT = "scipion"
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Definition at line 25 of file ParticlePickerParams.java.

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◆ threads

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Integer xmipp.viewer.particlepicker.ParticlePickerParams.threads = 1
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Definition at line 41 of file ParticlePickerParams.java.

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◆ THREADSOPT

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final String xmipp.viewer.particlepicker.ParticlePickerParams.THREADSOPT = "threads"
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Definition at line 29 of file ParticlePickerParams.java.

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◆ TMP

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final String xmipp.viewer.particlepicker.ParticlePickerParams.TMP = "tmp"
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Definition at line 33 of file ParticlePickerParams.java.

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◆ tmp

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boolean xmipp.viewer.particlepicker.ParticlePickerParams.tmp
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Definition at line 45 of file ParticlePickerParams.java.

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The documentation for this class was generated from the following file: -
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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.ParticlesDialog Member List
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This is the complete list of members for xmipp.viewer.particlepicker.ParticlesDialog, including all inherited members.

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close()xmipp.viewer.particlepicker.ParticlesDialoginline
constraintsxmipp.viewer.particlepicker.ParticlesDialogprotected
framexmipp.viewer.particlepicker.ParticlesDialogprotected
loadParticles(boolean resize)xmipp.viewer.particlepicker.ParticlesDialoginline
maxHeightxmipp.viewer.particlepicker.ParticlesDialogstatic
minWidthxmipp.viewer.particlepicker.ParticlesDialogstatic
ParticlesDialog(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.ParticlesDialoginline
particlespnxmipp.viewer.particlepicker.ParticlesDialogprotected
resetParticlesDialog()xmipp.viewer.particlepicker.ParticlesDialoginlineprotected
spxmipp.viewer.particlepicker.ParticlesDialogprotected
widthxmipp.viewer.particlepicker.ParticlesDialogprotected
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-Generated by   -doxygen - 1.8.13 -
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Xmipp -  v20.07 -
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-Public Member Functions | -Static Public Attributes | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.viewer.particlepicker.ParticlesDialog Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.ParticlesDialog:
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-Collaboration diagram for xmipp.viewer.particlepicker.ParticlesDialog:
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-Public Member Functions

 ParticlesDialog (ParticlePickerJFrame frame)
 
void loadParticles (boolean resize)
 
void close ()
 
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-Static Public Attributes

static final int maxHeight = (int)(0.9 * XmippWindowUtil.getScreenRectangle().height)
 
static final int minWidth = 600
 
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-Protected Member Functions

void resetParticlesDialog ()
 
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-Protected Attributes

ParticlePickerJFrame frame
 
Panel particlespn
 
ScrollPane sp
 
GridBagConstraints constraints
 
int width
 
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Detailed Description

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Definition at line 17 of file ParticlesDialog.java.

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Constructor & Destructor Documentation

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◆ ParticlesDialog()

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xmipp.viewer.particlepicker.ParticlesDialog.ParticlesDialog (ParticlePickerJFrame frame)
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Definition at line 28 of file ParticlesDialog.java.

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29  {
30  super(frame);
31  this.frame = frame;
32  initComponents();
33 
34  addWindowListener(new WindowAdapter()
35  {
36  public void windowClosing(WindowEvent winEvt)
37  {
38  resetParticlesDialog();
39  close();
40  }
41 
42  });
43  }
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Member Function Documentation

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◆ close()

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void xmipp.viewer.particlepicker.ParticlesDialog.close ()
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Definition at line 139 of file ParticlesDialog.java.

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140  {
141  setVisible(false);
142  dispose();
143 
144  }
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◆ loadParticles()

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void xmipp.viewer.particlepicker.ParticlesDialog.loadParticles (boolean resize)
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Definition at line 51 of file ParticlesDialog.java.

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52  {
53 
54  List<? extends PickerParticle> particles = frame.getAvailableParticles();
55  side = frame.getSide();
56 
57  if (side == 0)
58  throw new IllegalArgumentException(XmippMessage.getOutOfBoundsMsg("side"));
59 
60  if (particles.isEmpty())
61  {
62  particlespn.removeAll();
63  width = minWidth;
64  height = maxHeight;
65  sp.setPreferredSize(new Dimension(width, height));
66  pack();
67  return;
68  }
69 
70  if (resize) // first time or keep size
71  {
72  columns = Math.min(minWidth, particles.size() * side) / side;
73  rows = (int) Math.ceil(particles.size() / (float) columns);
74  width = side * columns + 20;
75  height = Math.min(side * rows, maxHeight);
76 
77  }
78  else//size changed by user
79  {
80  Dimension d = sp.getSize();
81  width = (int) d.getWidth();
82  height = (int)d.getHeight();
83  columns = width / side;
84  rows = (int) Math.ceil((particles.size() / (float) columns));
85 
86  }
87  sp.setPreferredSize(new Dimension(width, height));
88  particlespn.removeAll();
89 
90  particles = frame.getAvailableParticles();
91  int index = 0;
92  ParticleCanvas c;
93  PickerParticle p;
94  for (int i = 0; i < rows; i++)
95  for (int j = 0; j < columns; j++, index++)
96  {
97 
98  if (index == particles.size())
99  break;
100  p = particles.get(index);
101  c = p.getParticleCanvas(frame);
102 
103  particlespn.add(c, XmippWindowUtil.getConstraints(constraints, j, i, 1));
104  }
105  // particlespn.revalidate();
106  sp.getVAdjustable().setValue(sp.getVAdjustable().getMaximum());
107  sp.getHAdjustable().setValue(sp.getHAdjustable().getMaximum());
108  pack();
109 
110  }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.getAvailableParticles
abstract List<? extends PickerParticle > getAvailableParticles()
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◆ resetParticlesDialog()

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void xmipp.viewer.particlepicker.ParticlesDialog.resetParticlesDialog ()
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Definition at line 45 of file ParticlesDialog.java.

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46  {
47  frame.particlesdialog = null;
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49  }
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Member Data Documentation

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◆ constraints

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GridBagConstraints xmipp.viewer.particlepicker.ParticlesDialog.constraints
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Definition at line 23 of file ParticlesDialog.java.

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◆ frame

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ParticlePickerJFrame xmipp.viewer.particlepicker.ParticlesDialog.frame
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Definition at line 20 of file ParticlesDialog.java.

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◆ maxHeight

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final int xmipp.viewer.particlepicker.ParticlesDialog.maxHeight = (int)(0.9 * XmippWindowUtil.getScreenRectangle().height)
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Definition at line 25 of file ParticlesDialog.java.

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◆ minWidth

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final int xmipp.viewer.particlepicker.ParticlesDialog.minWidth = 600
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Definition at line 26 of file ParticlesDialog.java.

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◆ particlespn

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Panel xmipp.viewer.particlepicker.ParticlesDialog.particlespn
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Definition at line 21 of file ParticlesDialog.java.

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◆ sp

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ScrollPane xmipp.viewer.particlepicker.ParticlesDialog.sp
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Definition at line 22 of file ParticlesDialog.java.

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◆ width

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int xmipp.viewer.particlepicker.ParticlesDialog.width
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Definition at line 24 of file ParticlesDialog.java.

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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.PickerParticle Member List
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This is the complete list of members for xmipp.viewer.particlepicker.PickerParticle, including all inherited members.

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compareTo(Particle p)xmipp.jni.Particleinline
contains(int x2, int y2, int size)xmipp.jni.Particleinline
costxmipp.jni.Particleprotected
getCost()xmipp.jni.Particleinline
getMicrograph()xmipp.viewer.particlepicker.PickerParticleinline
getParticleCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.PickerParticleinline
getPosition()xmipp.jni.Particleinline
getX()xmipp.jni.Particleinline
getX0(int size)xmipp.viewer.particlepicker.PickerParticleinline
getY()xmipp.jni.Particleinline
getY0(int size)xmipp.viewer.particlepicker.PickerParticleinline
micrographxmipp.viewer.particlepicker.PickerParticleprotected
Particle(int x, int y)xmipp.jni.Particleinline
Particle(int x, int y, double cost)xmipp.jni.Particleinline
PickerParticle(int x, int y, Micrograph m)xmipp.viewer.particlepicker.PickerParticleinline
PickerParticle(int x, int y, Micrograph m, double cost)xmipp.viewer.particlepicker.PickerParticleinline
resetParticleCanvas()xmipp.viewer.particlepicker.PickerParticleinline
setCost(double cost)xmipp.jni.Particleinline
setMicrograph(Micrograph micrograph)xmipp.viewer.particlepicker.PickerParticleinline
setPosition(int x, int y)xmipp.jni.Particleinline
setX(int x)xmipp.jni.Particleinline
setY(int y)xmipp.jni.Particleinline
toString()xmipp.jni.Particleinline
xxmipp.jni.Particleprotected
yxmipp.jni.Particleprotected
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1PickerParticle.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1PickerParticle.html deleted file mode 100644 index caec73cc..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1PickerParticle.html +++ /dev/null @@ -1,460 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.PickerParticle Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Attributes | -List of all members
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xmipp.viewer.particlepicker.PickerParticle Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.PickerParticle:
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-Public Member Functions

 PickerParticle (int x, int y, Micrograph m)
 
 PickerParticle (int x, int y, Micrograph m, double cost)
 
int getX0 (int size)
 
int getY0 (int size)
 
ParticleCanvas getParticleCanvas (ParticlePickerJFrame frame)
 
void resetParticleCanvas ()
 
Micrograph getMicrograph ()
 
void setMicrograph (Micrograph micrograph)
 
- Public Member Functions inherited from xmipp.jni.Particle
 Particle (int x, int y)
 
 Particle (int x, int y, double cost)
 
int getX ()
 
void setX (int x)
 
int getY ()
 
void setY (int y)
 
double getCost ()
 
void setCost (double cost)
 
boolean contains (int x2, int y2, int size)
 
void setPosition (int x, int y)
 
Point getPosition ()
 
String toString ()
 
int compareTo (Particle p)
 
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-Protected Attributes

Micrograph micrograph
 
- Protected Attributes inherited from xmipp.jni.Particle
int x
 
int y
 
double cost
 
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Detailed Description

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Definition at line 5 of file PickerParticle.java.

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Constructor & Destructor Documentation

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◆ PickerParticle() [1/2]

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xmipp.viewer.particlepicker.PickerParticle.PickerParticle (int x,
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Definition at line 11 of file PickerParticle.java.

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12  {
13  super(x, y);
14  this.micrograph = m;
15  // TODO Auto-generated constructor stub
16  }
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◆ PickerParticle() [2/2]

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xmipp.viewer.particlepicker.PickerParticle.PickerParticle (int x,
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Definition at line 18 of file PickerParticle.java.

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19  {
20  super(x, y, cost);
21  this.micrograph = m;
22  // TODO Auto-generated constructor stub
23  }
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◆ getMicrograph()

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Micrograph xmipp.viewer.particlepicker.PickerParticle.getMicrograph ()
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Definition at line 51 of file PickerParticle.java.

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51  {
52  return micrograph;
53  }
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◆ getParticleCanvas()

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ParticleCanvas xmipp.viewer.particlepicker.PickerParticle.getParticleCanvas (ParticlePickerJFrame frame)
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Definition at line 38 of file PickerParticle.java.

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39  {
40  if(canvas == null)
41  canvas = new ParticleCanvas(this, frame);
42  return canvas;
43  }
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◆ getX0()

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int xmipp.viewer.particlepicker.PickerParticle.getX0 (int size)
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Definition at line 25 of file PickerParticle.java.

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26  {
27  int radius = size/2;
28  return getX() - radius;
29  }
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◆ getY0()

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Definition at line 31 of file PickerParticle.java.

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32  {
33  int radius = size/2;
34  return getY() - radius;
35  }
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◆ resetParticleCanvas()

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void xmipp.viewer.particlepicker.PickerParticle.resetParticleCanvas ()
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Definition at line 45 of file PickerParticle.java.

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46  {
47  canvas = null;
48  }
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◆ setMicrograph()

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void xmipp.viewer.particlepicker.PickerParticle.setMicrograph (Micrograph micrograph)
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Definition at line 56 of file PickerParticle.java.

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56  {
57  this.micrograph = micrograph;
58  }
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Member Data Documentation

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◆ micrograph

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Micrograph xmipp.viewer.particlepicker.PickerParticle.micrograph
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Definition at line 9 of file PickerParticle.java.

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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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xmipp.viewer.particlepicker.extract.ExtractCanvas Member List
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This is the complete list of members for xmipp.viewer.particlepicker.extract.ExtractCanvas, including all inherited members.

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activexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activemovedxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activestxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
adjustMagnification()xmipp.ij.commons.XmippImageCanvasinline
captureWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
continuousstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
customScrollSetup(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
dashedstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
doCustomPaint(Graphics2D g2)xmipp.viewer.particlepicker.extract.ExtractCanvasinlineprotected
drawLine(double alpha, Graphics2D g2)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
erase(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
eraserCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
ExtractCanvas(ExtractPickerJFrame frame)xmipp.viewer.particlepicker.extract.ExtractCanvasinline
framexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
getActive()xmipp.viewer.particlepicker.extract.ExtractCanvasinline
getFrame()xmipp.viewer.particlepicker.extract.ExtractCanvasinline
getIw()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getLastParticle()xmipp.viewer.particlepicker.extract.ExtractCanvasinlineprotected
getMicrograph()xmipp.viewer.particlepicker.extract.ExtractCanvasinline
getParticlePicker()xmipp.viewer.particlepicker.extract.ExtractCanvasinline
getPreferredMagnification()xmipp.ij.commons.XmippImageCanvasinline
getTool()xmipp.ij.commons.XmippImageCanvasinline
getXOnImage(int x)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getYOnImage(int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
hasActiveParticle()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
isDragImage(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinlineprotected
isKeyPressed(int keyCode)xmipp.ij.commons.XmippImageCanvasinlineprotected
iwxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
keyPressed(KeyEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
keyReleased(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyTyped(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
linearCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
loadData(XmippIJWindow xiw)xmipp.ij.commons.XmippImageCanvasinline
manageActive(int x, int y)xmipp.viewer.particlepicker.extract.ExtractCanvasinlineprotected
micrographxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
mouseDragged(MouseEvent e)xmipp.viewer.particlepicker.extract.ExtractCanvasinline
mouseEntered(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseExited(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseMoved(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mousePressed(MouseEvent e)xmipp.viewer.particlepicker.extract.ExtractCanvasinline
mouseReleased(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseWheelMoved(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
moveActiveParticle(int x, int y)xmipp.viewer.particlepicker.extract.ExtractCanvasinlineprotected
moveTo(PickerParticle p)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
offScreenX(int x)xmipp.ij.commons.XmippImageCanvasinline
offScreenY(int y)xmipp.ij.commons.XmippImageCanvasinline
paint(Graphics g)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
paintEraser(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
ParticlePickerCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
ParticlePickerCanvas(ParticlePickerJFrame frame, Micrograph micrograph)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
pickerxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
pickingCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
refresh()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
refreshActive(PickerParticle p)xmipp.viewer.particlepicker.extract.ExtractCanvasinline
removeParticle(PickerParticle particleToRemove)xmipp.viewer.particlepicker.extract.ExtractCanvasinlineprotected
xmipp::viewer::particlepicker::ParticlePickerCanvas.removeParticle(P particleToRemove)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
restoreWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setActiveMoved(boolean b)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setCustomCursor()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
setCustomCursor(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setInvertX(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setInvertY(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
thinContinuousStxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
updateMicrograph()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
updateMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
XmippImageCanvas(ImagePlus imp)xmipp.ij.commons.XmippImageCanvasinline
zoomIn(int sx, int sy)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
zoomOut(int sx, int sy)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractCanvas.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractCanvas.html deleted file mode 100644 index d0fac973..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractCanvas.html +++ /dev/null @@ -1,750 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.extract.ExtractCanvas Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.particlepicker.extract.ExtractCanvas Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.extract.ExtractCanvas:
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-Public Member Functions

 ExtractCanvas (ExtractPickerJFrame frame)
 
void refreshActive (PickerParticle p)
 
ExtractParticle getActive ()
 
ExtractMicrograph getMicrograph ()
 
void mousePressed (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
ExtractPickerJFrame getFrame ()
 
ExtractParticlePicker getParticlePicker ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
void setMicrograph (Micrograph m)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame, Micrograph micrograph)
 
void keyPressed (KeyEvent e)
 
void zoomIn (int sx, int sy)
 
void zoomOut (int sx, int sy)
 
boolean hasActiveParticle ()
 
ImageWindow getIw ()
 
void moveTo (PickerParticle p)
 
void mouseEntered (MouseEvent e)
 
void mouseExited (MouseEvent e)
 
void setCustomCursor ()
 
abstract void refreshActive (PickerParticle p)
 
abstract P getActive ()
 
abstract ParticlePickerJFrame getFrame ()
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void updateMicrograph ()
 
void updateMicrograph (Micrograph m)
 
abstract Micrograph getMicrograph ()
 
void paint (Graphics g)
 
void mouseMoved (MouseEvent e)
 
abstract ParticlePicker getParticlePicker ()
 
void mouseWheelMoved (MouseWheelEvent e)
 
- Public Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
Tool getTool ()
 
 XmippImageCanvas (ImagePlus imp)
 
void mousePressed (MouseEvent e)
 
void customScrollSetup (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void mouseWheelMoved (MouseWheelEvent e)
 
void mouseMoved (MouseEvent e)
 
int offScreenX (int x)
 
int offScreenY (int y)
 
void loadData (XmippIJWindow xiw)
 
double getPreferredMagnification ()
 
void adjustMagnification ()
 
void setInvertX (boolean value)
 
void setInvertY (boolean value)
 
void keyTyped (KeyEvent keyEvent)
 
void keyPressed (KeyEvent keyEvent)
 
void keyReleased (KeyEvent keyEvent)
 
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-Protected Member Functions

void doCustomPaint (Graphics2D g2)
 
ExtractParticle getLastParticle ()
 
void moveActiveParticle (int x, int y)
 
void manageActive (int x, int y)
 
void removeParticle (PickerParticle particleToRemove)
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
void captureWindowSize ()
 
void restoreWindowSize ()
 
abstract P getLastParticle ()
 
abstract void manageActive (int x, int y)
 
void setActiveMoved (boolean b)
 
void refresh ()
 
void setCustomCursor (MouseEvent e)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)
 
void drawLine (double alpha, Graphics2D g2)
 
void erase (MouseEvent e)
 
abstract void removeParticle (P particleToRemove)
 
void moveActiveParticle (int x, int y)
 
abstract void doCustomPaint (Graphics2D g2)
 
void paintEraser (MouseEvent e)
 
- Protected Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
boolean isDragImage (MouseEvent e)
 
boolean isKeyPressed (int keyCode)
 
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-Additional Inherited Members

- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
static final BasicStroke dashedst = new BasicStroke(2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 10.0f, new float[] { 10.0f }, 0.0f)
 
static final BasicStroke continuousst = new BasicStroke(2.0f)
 
static final BasicStroke thinContinuousSt = new BasicStroke(1.5f)
 
static final BasicStroke activest = new BasicStroke(1.5f)
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
ParticlePickerJFrame frame
 
Micrograph micrograph
 
ParticlePicker picker
 
XmippImageWindow iw
 
Cursor eraserCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("eraserC.png").getImage(), new Point(3, 31), "Eraser")
 
Cursor linearCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("linearPickingC.png").getImage(), new Point(0, 0), "Linear")
 
Cursor pickingCursor = getPickingCursor(pickingCursorIndex)
 
P active
 
boolean activemoved
 
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Detailed Description

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Definition at line 12 of file ExtractCanvas.java.

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Constructor & Destructor Documentation

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◆ ExtractCanvas()

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xmipp.viewer.particlepicker.extract.ExtractCanvas.ExtractCanvas (ExtractPickerJFrame frame)
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Definition at line 15 of file ExtractCanvas.java.

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16  {
17  super(frame);
18  active = getLastParticle();
19  }
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◆ doCustomPaint()

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void xmipp.viewer.particlepicker.extract.ExtractCanvas.doCustomPaint (Graphics2D g2)
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Definition at line 42 of file ExtractCanvas.java.

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43  {
44  Color color;
45  double score;
46  for (ExtractParticle p : getMicrograph().getParticles())
47  {
48  score = p.getScore(getFrame().getColorHelper().getId());
49  color = getFrame().getColorHelper().getColor(score);
50  if (p.isEnabled())
51  drawShape(g2, p.getX(), p.getY(), getFrame().getParticlePicker().getSize(), false, continuousst, color);
52  else
53  drawShape(g2, p.getX(), p.getY(), getFrame().getParticlePicker().getSize(), false, dashedst, color);
54  }
55  if (active != null)
56  {
57  score = getActive().getScore(getFrame().getColorHelper().getId());
58  color = getFrame().getColorHelper().getColor(score);
59  drawShape(g2, active.getX(), active.getY(), frame.getParticlePicker().getSize(), true, activest, color);
60  }
61  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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◆ getActive()

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Definition at line 30 of file ExtractCanvas.java.

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31  {
32  return (ExtractParticle) active;
33  }
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Definition at line 154 of file ExtractCanvas.java.

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155  {
156  return (ExtractPickerJFrame)frame;
157  }
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Definition at line 63 of file ExtractCanvas.java.

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64  {
65  if (getMicrograph().getParticles().isEmpty())
66  return null;
67  return getMicrograph().getParticles().get(getMicrograph().getParticles().size() - 1);
68  }
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Definition at line 36 of file ExtractCanvas.java.

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37  {
38  return (ExtractMicrograph)micrograph;
39  }
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◆ getParticlePicker()

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Definition at line 165 of file ExtractCanvas.java.

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166  {
167  return (ExtractParticlePicker)picker;
168  }
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◆ manageActive()

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void xmipp.viewer.particlepicker.extract.ExtractCanvas.manageActive (int x,
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Definition at line 142 of file ExtractCanvas.java.

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143  {
144  if(!activemoved)
145  return;
146  if (!micrograph.fits(x, y, picker.getSize()))
147  return;
148  moveActiveParticle(x, y);
149  setActiveMoved(false);
150 
151  }
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ mouseDragged()

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void xmipp.viewer.particlepicker.extract.ExtractCanvas.mouseDragged (MouseEvent e)
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Definition at line 104 of file ExtractCanvas.java.

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105  {
106 
107  super.mouseDragged(e);
108  int x = super.offScreenX(e.getX());
109  int y = super.offScreenY(e.getY());
110  if (frame.isPickingAvailable(e))
111  {
112  if (frame.isEraserMode(e))
113  {
114  getMicrograph().removeParticles(x, y, picker);
115  active = getLastParticle();
116  refresh();
117  return;
118  }
119  if (active == null)
120  return;
121 
122  if (!micrograph.fits(x, y, picker.getSize()))
123  return;
124  moveActiveParticle(x, y);
125  getActive().setEnabled(true);// if it was disabled gets enabled
126  getFrame().refreshActiveOnGallery(getActive());// if enabled propagate info
127  frame.setChanged(true);
128  repaint();
129  }
130  }
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abstract void setChanged(boolean changed)
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void removeParticles(int x, int y, ParticlePicker picker)
Definition: ExtractMicrograph.java:46
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boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ mousePressed()

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Definition at line 70 of file ExtractCanvas.java.

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71  {
72  super.mousePressed(e);
73  int x = super.offScreenX(e.getX());
74  int y = super.offScreenY(e.getY());
75 
76  if (frame.isPickingAvailable(e))
77  {
78  if (frame.isEraserMode(null))
79  {
80  getMicrograph().removeParticles(x, y, picker);
81  active = getLastParticle();
82  refresh();
83 
84  return;
85  }
86  ExtractParticle p = getMicrograph().getParticle(x, y, picker.getSize());
87 
88  if (p != null)
89  {
90  if (SwingUtilities.isLeftMouseButton(e))
91  {
92  if (e.isShiftDown())
93  p.setEnabled(!p.isEnabled());
94  active = p;
95  }
96  getFrame().refreshActiveOnGallery(getActive());
97  }
98 
99  refresh();
100  }
101  }
- - - - - - - - - - -
xmipp.viewer.particlepicker.extract.ExtractMicrograph.getParticle
ExtractParticle getParticle(int x, int y, int size)
Definition: ExtractMicrograph.java:64
- -
xmipp.viewer.particlepicker.extract.ExtractMicrograph.removeParticles
void removeParticles(int x, int y, ParticlePicker picker)
Definition: ExtractMicrograph.java:46
- -
-
-
- -

◆ moveActiveParticle()

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-
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void xmipp.viewer.particlepicker.extract.ExtractCanvas.moveActiveParticle (int x,
int y 
)
- 		-inlineprotected
-
- -

Definition at line 134 of file ExtractCanvas.java.

-
135  {
136  getActive().setEnabled(true);
137  super.moveActiveParticle(x, y);
138  getFrame().refreshActiveOnGallery(getActive());
139  }
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-
-
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◆ refreshActive()

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-
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- - - - - - - - -
void xmipp.viewer.particlepicker.extract.ExtractCanvas.refreshActive (PickerParticle p)
- 		-inline
-
- -

Definition at line 22 of file ExtractCanvas.java.

-
23  {
24  active = p;
25  repaint();
26 
27  }
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-
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◆ removeParticle()

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-
- - - - - -
- - - - - - - - -
void xmipp.viewer.particlepicker.extract.ExtractCanvas.removeParticle (PickerParticle particleToRemove)
- 		-inlineprotected
-
- -

Definition at line 160 of file ExtractCanvas.java.

-
160  {
161  getMicrograph().removeParticle((ExtractParticle) particleToRemove);
162  }
- -
-
-
-
The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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- node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.extract.\lExtractCanvas",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lParticlePickerCanvas\< P\l extends PickerParticle \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerCanvas.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.ij.commons.XmippImage\lCanvas",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1XmippImageCanvas.html"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ImageCanvas",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; 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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.extract.ExtractMicrograph Member List
-
-
- -

This is the complete list of members for xmipp.viewer.particlepicker.extract.ExtractMicrograph, including all inherited members.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
addParticle(ExtractParticle p)xmipp.viewer.particlepicker.extract.ExtractMicrographinline
extxmipp.viewer.particlepicker.Micrographstatic
ExtractMicrograph(String file, CtfInfo ctfInfo)xmipp.viewer.particlepicker.extract.ExtractMicrographinline
fits(int x, int y, int size)xmipp.viewer.particlepicker.Micrographinline
getCTF()xmipp.viewer.particlepicker.Micrographinline
getCTFIcon()xmipp.viewer.particlepicker.Micrographinline
getCtfInfo()xmipp.viewer.particlepicker.Micrographinline
getFile()xmipp.viewer.particlepicker.Micrographinline
getHeigth()xmipp.viewer.particlepicker.Micrographinline
getImagePlus()xmipp.viewer.particlepicker.Micrographinline
getImagePlus(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
getName(String file, int level)xmipp.viewer.particlepicker.Micrographinlinestatic
getName()xmipp.viewer.particlepicker.Micrographinline
getNoImageIcon()xmipp.viewer.particlepicker.Micrographinlinestatic
getParticle(int x, int y, int size)xmipp.viewer.particlepicker.extract.ExtractMicrographinline
getParticleList()xmipp.viewer.particlepicker.extract.ExtractMicrographinline
getParticles()xmipp.viewer.particlepicker.extract.ExtractMicrographinline
getPosFile()xmipp.viewer.particlepicker.Micrographinline
getPosFileFromXmipp24()xmipp.viewer.particlepicker.Micrographinline
getPSD()xmipp.viewer.particlepicker.Micrographinline
getPSDImage()xmipp.viewer.particlepicker.Micrographinline
getWidth()xmipp.viewer.particlepicker.Micrographinline
hasData()xmipp.viewer.particlepicker.extract.ExtractMicrographinline
loadDimensions()xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
releaseImage()xmipp.viewer.particlepicker.Micrographinline
removeParticle(ExtractParticle particle)xmipp.viewer.particlepicker.extract.ExtractMicrographinline
removeParticles(int x, int y, ParticlePicker picker)xmipp.viewer.particlepicker.extract.ExtractMicrographinline
runImageJFilters(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
setPosFileFromXmipp24(String posfile)xmipp.viewer.particlepicker.Micrographinline
toString()xmipp.viewer.particlepicker.Micrographinline
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-Public Member Functions

 ExtractMicrograph (String file, CtfInfo ctfInfo)
 
boolean hasData ()
 
List<? extends PickerParticle > getParticleList ()
 
void addParticle (ExtractParticle p)
 
List< ExtractParticle > getParticles ()
 
void removeParticles (int x, int y, ParticlePicker picker)
 
void removeParticle (ExtractParticle particle)
 
ExtractParticle getParticle (int x, int y, int size)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.Micrograph
void setPosFileFromXmipp24 (String posfile)
 
String getPosFileFromXmipp24 ()
 
 Micrograph (String file)
 
 Micrograph (String file, String name)
 
 Micrograph (String file, CtfInfo ctfInfo)
 
 Micrograph (String file, String name, CtfInfo ctfInfo)
 
String getPSD ()
 
ImagePlus getPSDImage ()
 
Icon getCTFIcon ()
 
String getCTF ()
 
CtfInfo getCtfInfo ()
 
boolean fits (int x, int y, int size)
 
String getPosFile ()
 
void loadDimensions ()
 
ImagePlus getImagePlus ()
 
ImagePlus getImagePlus (List< IJCommand > filters)
 
void runImageJFilters (List< IJCommand > filters)
 
String getFile ()
 
String getName ()
 
String toString ()
 
abstract boolean hasData ()
 
int getWidth ()
 
int getHeigth ()
 
void releaseImage ()
 
List<? extends PickerParticle > getParticleList ()
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.viewer.particlepicker.Micrograph
static Icon getNoImageIcon ()
 
static String getName (String file, int level)
 
- Static Public Attributes inherited from xmipp.viewer.particlepicker.Micrograph
static final String ext = ".pos"
 
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Definition at line 12 of file ExtractMicrograph.java.

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◆ ExtractMicrograph()

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xmipp.viewer.particlepicker.extract.ExtractMicrograph.ExtractMicrograph (String file,
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Definition at line 17 of file ExtractMicrograph.java.

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18  {
19  super(file, ctfInfo);
20  particles = new ArrayList<ExtractParticle>();
21  }
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◆ addParticle()

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void xmipp.viewer.particlepicker.extract.ExtractMicrograph.addParticle (ExtractParticle p)
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Definition at line 35 of file ExtractMicrograph.java.

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36  {
37  particles.add(p);
38 
39  }
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Definition at line 64 of file ExtractMicrograph.java.

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65  {
66  for(ExtractParticle p: particles)
67  if(p.contains(x, y, size))
68  return p;
69  return null;
70  }
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Definition at line 30 of file ExtractMicrograph.java.

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30  {
31  return getParticles();
32  }
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Definition at line 41 of file ExtractMicrograph.java.

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42  {
43  return particles;
44  }
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Definition at line 24 of file ExtractMicrograph.java.

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25  {
26  return !particles.isEmpty();
27  }
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Definition at line 59 of file ExtractMicrograph.java.

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60  {
61  particle.setEnabled(false);
62  }
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Definition at line 46 of file ExtractMicrograph.java.

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47  {
48  List<ExtractParticle> removelist = new ArrayList<ExtractParticle>();
49 
50  for (ExtractParticle p : particles)
51  if (p.contains(x, y, picker.getSize()))
52  removelist.add(p);
53  for (ExtractParticle p : removelist)
54  removeParticle(p);
55 
56 
57  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__coll__graph.dot deleted file mode 100644 index e59b7119..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.extract.ExtractMicrograph" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.extract.\lExtractMicrograph",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__coll__graph.md5 deleted file mode 100644 index 91d1d5df..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -13840ef72c7532ede510a9e85b89c100 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__inherit__graph.dot deleted file mode 100644 index 01c095d8..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.extract.ExtractMicrograph" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.extract.\lExtractMicrograph",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__inherit__graph.md5 deleted file mode 100644 index 0c81a9b0..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractMicrograph__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ab13fb69e53bceb0f740c63dbb3fece2 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractParticle-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractParticle-members.html deleted file mode 100644 index 4027020f..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractParticle-members.html +++ /dev/null @@ -1,119 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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This is the complete list of members for xmipp.viewer.particlepicker.extract.ExtractParticle, including all inherited members.

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compareTo(Particle p)xmipp.jni.Particleinline
contains(int x2, int y2, int size)xmipp.jni.Particleinline
costxmipp.jni.Particleprotected
ExtractParticle(long id, int x, int y, Micrograph m, boolean enabled, double zscore, double zscore_shape1, double zscore_shape2, double zscore_snr1, double zscore_snr2, double zscore_hist)xmipp.viewer.particlepicker.extract.ExtractParticleinline
ExtractParticle(long id, int x, int y, Micrograph m, double zscore, double zscore_shape1, double zscore_shape2, double zscore_snr1, double zscore_snr2, double zscore_hist)xmipp.viewer.particlepicker.extract.ExtractParticleinline
getCost()xmipp.jni.Particleinline
getId()xmipp.viewer.particlepicker.extract.ExtractParticleinline
getMicrograph()xmipp.viewer.particlepicker.PickerParticleinline
getParticleCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.PickerParticleinline
getPosition()xmipp.jni.Particleinline
getScore(int id)xmipp.viewer.particlepicker.extract.ExtractParticleinline
getX()xmipp.jni.Particleinline
getX0(int size)xmipp.viewer.particlepicker.PickerParticleinline
getY()xmipp.jni.Particleinline
getY0(int size)xmipp.viewer.particlepicker.PickerParticleinline
getZscore()xmipp.viewer.particlepicker.extract.ExtractParticleinline
getZscore_hist()xmipp.viewer.particlepicker.extract.ExtractParticleinline
getZscore_shape1()xmipp.viewer.particlepicker.extract.ExtractParticleinline
getZscore_shape2()xmipp.viewer.particlepicker.extract.ExtractParticleinline
getZscore_snr1()xmipp.viewer.particlepicker.extract.ExtractParticleinline
getZscore_snr2()xmipp.viewer.particlepicker.extract.ExtractParticleinline
isEnabled()xmipp.viewer.particlepicker.extract.ExtractParticleinline
micrographxmipp.viewer.particlepicker.PickerParticleprotected
Particle(int x, int y)xmipp.jni.Particleinline
Particle(int x, int y, double cost)xmipp.jni.Particleinline
PickerParticle(int x, int y, Micrograph m)xmipp.viewer.particlepicker.PickerParticleinline
PickerParticle(int x, int y, Micrograph m, double cost)xmipp.viewer.particlepicker.PickerParticleinline
resetParticleCanvas()xmipp.viewer.particlepicker.PickerParticleinline
setCost(double cost)xmipp.jni.Particleinline
setEnabled(boolean b)xmipp.viewer.particlepicker.extract.ExtractParticleinline
setMicrograph(Micrograph micrograph)xmipp.viewer.particlepicker.PickerParticleinline
setPosition(int x, int y)xmipp.jni.Particleinline
setX(int x)xmipp.jni.Particleinline
setY(int y)xmipp.jni.Particleinline
toString()xmipp.jni.Particleinline
xxmipp.jni.Particleprotected
yxmipp.jni.Particleprotected
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-Public Member Functions

 ExtractParticle (long id, int x, int y, Micrograph m, boolean enabled, double zscore, double zscore_shape1, double zscore_shape2, double zscore_snr1, double zscore_snr2, double zscore_hist)
 
long getId ()
 
 ExtractParticle (long id, int x, int y, Micrograph m, double zscore, double zscore_shape1, double zscore_shape2, double zscore_snr1, double zscore_snr2, double zscore_hist)
 
boolean isEnabled ()
 
double getZscore ()
 
double getZscore_shape1 ()
 
double getZscore_shape2 ()
 
double getZscore_snr1 ()
 
double getZscore_snr2 ()
 
double getZscore_hist ()
 
void setEnabled (boolean b)
 
double getScore (int id)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.PickerParticle
 PickerParticle (int x, int y, Micrograph m)
 
 PickerParticle (int x, int y, Micrograph m, double cost)
 
int getX0 (int size)
 
int getY0 (int size)
 
ParticleCanvas getParticleCanvas (ParticlePickerJFrame frame)
 
void resetParticleCanvas ()
 
Micrograph getMicrograph ()
 
void setMicrograph (Micrograph micrograph)
 
- Public Member Functions inherited from xmipp.jni.Particle
 Particle (int x, int y)
 
 Particle (int x, int y, double cost)
 
int getX ()
 
void setX (int x)
 
int getY ()
 
void setY (int y)
 
double getCost ()
 
void setCost (double cost)
 
boolean contains (int x2, int y2, int size)
 
void setPosition (int x, int y)
 
Point getPosition ()
 
String toString ()
 
int compareTo (Particle p)
 
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-Additional Inherited Members

- Protected Attributes inherited from xmipp.viewer.particlepicker.PickerParticle
Micrograph micrograph
 
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int x
 
int y
 
double cost
 
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Definition at line 10 of file ExtractParticle.java.

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◆ ExtractParticle() [1/2]

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xmipp.viewer.particlepicker.extract.ExtractParticle.ExtractParticle (long id,
int x,
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Micrograph m,
boolean enabled,
double zscore,
double zscore_shape1,
double zscore_shape2,
double zscore_snr1,
double zscore_snr2,
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Definition at line 16 of file ExtractParticle.java.

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18  {
19  super(x, y, m);
20  this.enabled = enabled;
21  this.id = id;
22  this.zscore = zscore;
23  this.zscore_hist = zscore_hist;
24  this.zscore_shape1 = zscore_shape1;
25  this.zscore_shape2 = zscore_shape2;
26  this.zscore_snr1 = zscore_snr1;
27  this.zscore_snr2 = zscore_snr2;
28 
29  }
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xmipp.viewer.particlepicker.extract.ExtractParticle.ExtractParticle (long id,
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double zscore,
double zscore_shape1,
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Definition at line 36 of file ExtractParticle.java.

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38  {
39  this(id, x, y, m, true, zscore, zscore_shape1, zscore_shape2, zscore_snr1, zscore_snr2, zscore_hist);
40  }
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Definition at line 31 of file ExtractParticle.java.

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32  {
33  return id;
34  }
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Definition at line 93 of file ExtractParticle.java.

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94  {
95  if(id == MDLabel.MDL_ZSCORE)
96  return getZscore();
97  if(id == MDLabel.MDL_ZSCORE_SHAPE1)
98  return getZscore_shape1();
99  if(id == MDLabel.MDL_ZSCORE_SHAPE2)
100  return getZscore_shape2();
101  if(id == MDLabel.MDL_ZSCORE_SNR1)
102  return getZscore_snr1();
103  if(id == MDLabel.MDL_ZSCORE_SNR2)
104  return getZscore_snr2();
105  if(id == MDLabel.MDL_ZSCORE_HISTOGRAM)
106  return getZscore_hist();
107  return 0;
108  }
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Definition at line 49 of file ExtractParticle.java.

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50  {
51  return zscore;
52  }
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Definition at line 79 of file ExtractParticle.java.

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80  {
81  return zscore_hist;
82  }
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Definition at line 56 of file ExtractParticle.java.

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57  {
58  return zscore_shape1;
59  }
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Definition at line 61 of file ExtractParticle.java.

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62  {
63  return zscore_shape2;
64  }
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Definition at line 66 of file ExtractParticle.java.

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67  {
68  return zscore_snr1;
69  }
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Definition at line 72 of file ExtractParticle.java.

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73  {
74  return zscore_snr2;
75  }
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Definition at line 42 of file ExtractParticle.java.

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43  {
44  return enabled;
45  }
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Definition at line 84 of file ExtractParticle.java.

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85  {
86  enabled = b;
87 
88  }
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xmipp.viewer.particlepicker.extract.ExtractParticlePicker Member List
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This is the complete list of members for xmipp.viewer.particlepicker.extract.ExtractParticlePicker, including all inherited members.

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addFilter(String command, String options)xmipp.viewer.particlepicker.ParticlePickerinline
blockxmipp.viewer.particlepicker.ParticlePickerprotected
changedxmipp.viewer.particlepicker.ParticlePickerprotected
colorxmipp.viewer.particlepicker.ParticlePickerprotected
colorsxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
configfilexmipp.viewer.particlepicker.ParticlePickerprotected
detectFileFormat(String path)xmipp.viewer.particlepicker.ParticlePickerinline
detectFormat(String path, String preffix, StringBuffer suffix)xmipp.viewer.particlepicker.ParticlePickerinline
emextensionsxmipp.viewer.particlepicker.ParticlePicker
ExtractParticlePicker(String selfile, int size, ParticlePickerParams params)xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
ExtractParticlePicker(String block, String selfile, int size, ParticlePickerParams params)xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
fillParticlesMdFromEmanFile(String file, Micrograph m, MetaData md, float scale)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromRelionFile(String file, Micrograph m, MetaData md)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromXmipp301File(String file, Micrograph m, MetaData md)xmipp.viewer.particlepicker.ParticlePickerinline
filtersxmipp.viewer.particlepicker.ParticlePickerprotected
getColor()xmipp.viewer.particlepicker.ParticlePickerinline
getColor(String name)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getColumns()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
getCoordsFiles(String folder)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getDefaultSize()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getExportFile(String path)xmipp.viewer.particlepicker.ParticlePickerinline
getFilters()xmipp.viewer.particlepicker.ParticlePickerinline
getLogger()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getMicrograph()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
xmipp::viewer::particlepicker::ParticlePicker.getMicrograph(String name)xmipp.viewer.particlepicker.ParticlePickerinline
getMicrographIndex()xmipp.viewer.particlepicker.ParticlePickerinline
getMicrographs()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
getMicrographsSelFile()xmipp.viewer.particlepicker.ParticlePickerinline
getMode()xmipp.viewer.particlepicker.ParticlePickerinline
getNextColor()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getOutputDir()xmipp.viewer.particlepicker.ParticlePickerinline
getOutputPath(String file)xmipp.viewer.particlepicker.ParticlePickerinline
getParams()xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesAutoBlock(String file)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesAutoBlock(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesBlock(Format f, String file)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesBlock(String file)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesBlock(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesBlockName(Format f)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesCount()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
getPicker()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getPort()xmipp.viewer.particlepicker.ParticlePickerinline
getPosFileFromXmipp24Project(String projectdir, String mname)xmipp.viewer.particlepicker.ParticlePickerinline
getRadius()xmipp.viewer.particlepicker.ParticlePickerinline
getSize()xmipp.viewer.particlepicker.ParticlePickerinline
getTemplatesFile(String name)xmipp.viewer.particlepicker.ParticlePickerinline
getZoom()xmipp.viewer.particlepicker.ParticlePickerinline
importSize(String path, Format f, double scale)xmipp.viewer.particlepicker.ParticlePickerinline
isChanged()xmipp.viewer.particlepicker.ParticlePickerinline
isFilterAdded(String filter)xmipp.viewer.particlepicker.ParticlePickerinline
isSaved()xmipp.viewer.particlepicker.ParticlePickerinline
isScipionSave()xmipp.viewer.particlepicker.ParticlePickerinline
isShowDeleted()xmipp.viewer.particlepicker.ParticlePickerinline
isValidSize(JFrame parent, int size)xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
loadColumn(int column, String name, MetaData md)xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
loadColumns(MetaData md)xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
loadConfig()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
loadEmptyMicrographs()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
loadParticles()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
loggerxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
macrosfilexmipp.viewer.particlepicker.ParticlePickerprotected
modexmipp.viewer.particlepicker.ParticlePickerprotected
nextcolorxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
open(String block, String filename, int size, GalleryJFrame galleryfr)xmipp.viewer.particlepicker.extract.ExtractParticlePickerinlinestatic
outputdirxmipp.viewer.particlepicker.ParticlePickerprotected
paramsxmipp.viewer.particlepicker.ParticlePickerprotected
ParticlePicker(String selfile, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
ParticlePicker(String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
ParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
particlesAutoBlockxmipp.viewer.particlepicker.ParticlePickerstatic
pickerxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
runXmippProgram(String program, String args)xmipp.viewer.particlepicker.ParticlePickerinline
saveConfig()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
xmipp::viewer::particlepicker::ParticlePicker.saveConfig(MetaData md, long id)xmipp.viewer.particlepicker.ParticlePickerinlineprotected
savedxmipp.viewer.particlepicker.ParticlePickerprotected
saveData()xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
saveData(Micrograph m)xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
selfilexmipp.viewer.particlepicker.ParticlePickerprotected
setChanged(boolean changed)xmipp.viewer.particlepicker.ParticlePickerinline
setColor(Color color)xmipp.viewer.particlepicker.ParticlePickerinline
setFilterOptions(String command, String options)xmipp.viewer.particlepicker.ParticlePickerinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.extract.ExtractParticlePickerinline
setSaved(boolean saved)xmipp.viewer.particlepicker.ParticlePickerinline
setShowDeleted(boolean showDeleted)xmipp.viewer.particlepicker.ParticlePickerinline
setSize(int size)xmipp.viewer.particlepicker.ParticlePickerinline
setZoom(double zoom)xmipp.viewer.particlepicker.ParticlePickerinline
sizexmipp.viewer.particlepicker.ParticlePickerprotected
sizemaxxmipp.viewer.particlepicker.ParticlePickerstatic
toggleShowDeleted()xmipp.viewer.particlepicker.ParticlePickerinline
updateFilters(String command)xmipp.viewer.particlepicker.ParticlePickerinline
validateState(Mode state)xmipp.viewer.particlepicker.ParticlePickerinline
xmippsmoothfilterxmipp.viewer.particlepicker.ParticlePickerstatic
zoomxmipp.viewer.particlepicker.ParticlePickerprotected
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractParticlePicker.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractParticlePicker.html deleted file mode 100644 index 796b789a..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1ExtractParticlePicker.html +++ /dev/null @@ -1,972 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.extract.ExtractParticlePicker Class Reference - - - - - - - - - -
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-Public Member Functions | -Static Public Member Functions | -List of all members
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xmipp.viewer.particlepicker.extract.ExtractParticlePicker Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.extract.ExtractParticlePicker:
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-Public Member Functions

 ExtractParticlePicker (String selfile, int size, ParticlePickerParams params)
 
 ExtractParticlePicker (String block, String selfile, int size, ParticlePickerParams params)
 
void loadEmptyMicrographs ()
 
void loadColumns (MetaData md)
 
void loadColumn (int column, String name, MetaData md)
 
void loadParticles ()
 
List< ExtractMicrograph > getMicrographs ()
 
void saveData ()
 
void saveData (Micrograph m)
 
ExtractMicrograph getMicrograph ()
 
void setMicrograph (Micrograph m)
 
void saveConfig ()
 
void loadConfig ()
 
int getParticlesCount ()
 
ColorHelper [] getColumns ()
 
boolean isValidSize (JFrame parent, int size)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
boolean isShowDeleted ()
 
void setShowDeleted (boolean showDeleted)
 
void toggleShowDeleted ()
 
double getZoom ()
 
void setZoom (double zoom)
 
ParticlePickerParams getParams ()
 
String getParticlesAutoBlock (String file)
 
String getParticlesBlock (Micrograph m)
 
String getParticlesAutoBlock (Micrograph m)
 
 ParticlePicker (String selfile, ParticlePickerParams params)
 
 ParticlePicker (String selfile, String outputdir, ParticlePickerParams params)
 
 ParticlePicker (String block, String selfile, String outputdir, ParticlePickerParams params)
 
void loadConfig ()
 
synchronized void saveConfig ()
 
Format detectFileFormat (String path)
 
Format detectFormat (String path, String preffix, StringBuffer suffix)
 
String getExportFile (String path)
 
String getPosFileFromXmipp24Project (String projectdir, String mname)
 
abstract void loadEmptyMicrographs ()
 
void updateFilters (String command)
 
boolean isFilterAdded (String filter)
 
String getMicrographsSelFile ()
 
void setFilterOptions (String command, String options)
 
void addFilter (String command, String options)
 
List< IJCommand > getFilters ()
 
void setChanged (boolean changed)
 
boolean isChanged ()
 
boolean isSaved ()
 
void setSaved (boolean saved)
 
Mode getMode ()
 
String getOutputPath (String file)
 
String getOutputDir ()
 
abstract List<? extends Micrograph > getMicrographs ()
 
int getMicrographIndex ()
 
String getTemplatesFile (String name)
 
Mode validateState (Mode state)
 
void saveData ()
 
abstract void saveData (Micrograph m)
 
Micrograph getMicrograph (String name)
 
void fillParticlesMdFromFile (String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
 
void fillParticlesMdFromXmipp301File (String file, Micrograph m, MetaData md)
 
void fillParticlesMdFromRelionFile (String file, Micrograph m, MetaData md)
 
void fillParticlesMdFromEmanFile (String file, Micrograph m, MetaData md, float scale)
 
void runXmippProgram (String program, String args)
 
abstract Micrograph getMicrograph ()
 
abstract void setMicrograph (Micrograph m)
 
abstract boolean isValidSize (JFrame parent, int size)
 
int getSize ()
 
void setSize (int size)
 
Color getColor ()
 
void setColor (Color color)
 
int getRadius ()
 
void importSize (String path, Format f, double scale)
 
boolean isScipionSave ()
 
abstract int getParticlesCount ()
 
Integer getPort ()
 
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-Static Public Member Functions

static ExtractPickerJFrame open (String block, String filename, int size, GalleryJFrame galleryfr)
 
- Static Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
static Color getNextColor ()
 
static String getParticlesBlock (Format f, String file)
 
static String getParticlesBlockName (Format f)
 
static String getParticlesBlock (String file)
 
static Logger getLogger ()
 
static Color getColor (String name)
 
static int getDefaultSize ()
 
static File [] getCoordsFiles (String folder)
 
static ParticlePicker getPicker ()
 
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-Additional Inherited Members

- Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
final HashMap< Format, String > emextensions
 
- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
static final String xmippsmoothfilter = "Xmipp Smooth Filter"
 
static final String particlesAutoBlock = "particles_auto"
 
static final int sizemax = 2000
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
void saveConfig (MetaData md, long id)
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
String macrosfile
 
String outputdir = "."
 
boolean changed
 
boolean saved
 
Mode mode
 
List< IJCommand > filters
 
String selfile
 
String configfile
 
Color color
 
int size
 
String block
 
ParticlePickerParams params
 
double zoom = -1.f
 
- Static Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
static Logger logger
 
static Color [] colors = new Color[]{Color.GREEN, Color.BLUE, Color.CYAN, Color.MAGENTA, Color.ORANGE, Color.PINK, Color.YELLOW}
 
static int nextcolor
 
static ParticlePicker picker
 
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Detailed Description

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Definition at line 19 of file ExtractParticlePicker.java.

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Constructor & Destructor Documentation

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◆ ExtractParticlePicker() [1/2]

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xmipp.viewer.particlepicker.extract.ExtractParticlePicker.ExtractParticlePicker (String selfile,
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Definition at line 27 of file ExtractParticlePicker.java.

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28  {
29  super(selfile, params);
30  setSize(size);
31  loadParticles();
32  if (filters.isEmpty())
33  filters.add(new IJCommand(XmippImageJ.gaussianBlurFilter, "sigma=2"));
34  }
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static final String gaussianBlurFilter
Definition: XmippImageJ.java:14
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xmipp.viewer.particlepicker.extract.ExtractParticlePicker.ExtractParticlePicker (String block,
String selfile,
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ParticlePickerParams params 
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Definition at line 36 of file ExtractParticlePicker.java.

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37  {
38  super(block, selfile, ".", params);
39  setSize(size);
40  loadParticles();
41  if (filters.isEmpty())
42  filters.add(new IJCommand(XmippImageJ.gaussianBlurFilter, "sigma=2"));
43  }
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xmipp.ij.commons.XmippImageJ.gaussianBlurFilter
static final String gaussianBlurFilter
Definition: XmippImageJ.java:14
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◆ getColumns()

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ColorHelper [] xmipp.viewer.particlepicker.extract.ExtractParticlePicker.getColumns ()
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Definition at line 246 of file ExtractParticlePicker.java.

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247  {
248  return colorby.toArray(new ColorHelper[]{});
249  }
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Definition at line 195 of file ExtractParticlePicker.java.

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196  {
197  return micrograph;
198  }
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Definition at line 153 of file ExtractParticlePicker.java.

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154  {
155  return micrographs;
156  }
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Definition at line 236 of file ExtractParticlePicker.java.

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237  {
238  int particles = 0;
239  for (ExtractMicrograph m : micrographs)
240  particles += m.getParticles().size();
241  return particles;
242  }
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Definition at line 252 of file ExtractParticlePicker.java.

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253  {
254  for (ExtractParticle p : getMicrograph().getParticles())
255  if (!getMicrograph().fits(p.getX(), p.getY(), size))
256  return false;
257  return true;
258  }
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Definition at line 105 of file ExtractParticlePicker.java.

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106  {
107  boolean exists = md.containsLabel(column);
108  if(exists)
109  {
110  colorby.add(new ColorHelper(column, name, md));
111  }
112  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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Definition at line 90 of file ExtractParticlePicker.java.

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91  {
92  colorby = new ArrayList<ColorHelper>();
93 
94  loadColumn(MDLabel.MDL_ZSCORE, "ZScore", md);
95  loadColumn(MDLabel.MDL_ZSCORE_SHAPE1, "ZScore-Shape1", md);
96  loadColumn(MDLabel.MDL_ZSCORE_SHAPE2, "ZScore-Shape2", md);
97  loadColumn(MDLabel.MDL_ZSCORE_SNR1, "ZScore-SNR1", md);
98  loadColumn(MDLabel.MDL_ZSCORE_SNR2, "ZScore-SNR2", md);
99  loadColumn(MDLabel.MDL_ZSCORE_HISTOGRAM, "ZScore-Hist", md);
100  if(colorby.isEmpty())
101  throw new IllegalArgumentException("No score available to sort particles");
102 
103  }
xmipp.jni.MDLabel.MDL_ZSCORE_SNR1
static final int MDL_ZSCORE_SNR1
< Z Score (double)
Definition: MDLabel.java:444
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static final int MDL_ZSCORE_SHAPE1
< Z Score of the covariance matrix of the residuals (double)
Definition: MDLabel.java:442
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xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE2
static final int MDL_ZSCORE_SHAPE2
< Z Score (double)
Definition: MDLabel.java:443
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static final int MDL_ZSCORE_SNR2
< Z Score (double)
Definition: MDLabel.java:445
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xmipp.jni.MDLabel.MDL_ZSCORE_HISTOGRAM
static final int MDL_ZSCORE_HISTOGRAM
< Z Score (double)
Definition: MDLabel.java:438
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xmipp.jni.MDLabel.MDL_ZSCORE
static final int MDL_ZSCORE
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Definition: MDLabel.java:435
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Definition at line 215 of file ExtractParticlePicker.java.

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216  {
217  setMicrograph(micrographs.get(0));
218  }
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Definition at line 48 of file ExtractParticlePicker.java.

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49  {
50  micrographs = new ArrayList<ExtractMicrograph>();
51  String path = (block == null)? selfile: block + "@" + selfile;
52  MetaData md = new MetaData(path);
53  String fileiter;
54  boolean exists;
55  ExtractMicrograph current = null;
56  boolean existspsd = md.containsLabel(MDLabel.MDL_PSD_ENHANCED);
57  boolean existsctf = md.containsLabel(MDLabel.MDL_CTF_MODEL);
58  String psd = null, ctf = null;
59  CtfInfo ctfInfo;
60 
61  for (long id : md.findObjects())
62  {
63  exists = false;
64  fileiter = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
65  for (ExtractMicrograph iter : micrographs)
66  if (iter.getFile().equals(fileiter))
67  {
68  exists = true;
69  current = iter;
70  break;
71  }
72  if (!exists)
73  {
74  ctfInfo = (existsctf || existspsd) ? new CtfInfo() : null;
75  if (existspsd)
76  ctfInfo.psd = md.getValueString(MDLabel.MDL_PSD_ENHANCED, id);
77  if (existsctf)
78  ctfInfo.ctf = md.getValueString(MDLabel.MDL_CTF_MODEL, id);
79  current = new ExtractMicrograph(fileiter, ctfInfo);
80 
81  micrographs.add(current);
82  }
83 
84  }
85  loadColumns(md);
86  md.destroy();
87 
88  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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static final int MDL_CTF_MODEL
< Parameters file for the CTF Model (std::string)
Definition: MDLabel.java:80
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.jni.MDLabel.MDL_PSD_ENHANCED
static final int MDL_PSD_ENHANCED
< A Power Spectrum Density file name (std::string)
Definition: MDLabel.java:309
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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◆ loadParticles()

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void xmipp.viewer.particlepicker.extract.ExtractParticlePicker.loadParticles ()
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Definition at line 116 of file ExtractParticlePicker.java.

-
117  {
118  String path = (block == null)? selfile: block + "@" + selfile;
119  MetaData md = new MetaData(path);
120  ExtractParticle p;
121  int x, y;
122  String fileiter;
123  boolean enabled;
124  ExtractMicrograph current = null;
125  double zscore, zscore_shape1, zscore_shape2, zscore_snr1, zscore_snr2, zscore_hist;
126  for (long id : md.findObjects())
127  {
128  fileiter = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
129  for (ExtractMicrograph iter : micrographs)
130  if (iter.getFile().equals(fileiter))
131  {
132  current = iter;
133  break;
134  }
135 
136  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
137  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
138  enabled = (md.getValueInt(MDLabel.MDL_ENABLED, id) == 1) ? true : false;
139  zscore = md.getValueDouble(MDLabel.MDL_ZSCORE, id);
140  zscore_shape1 = md.getValueDouble(MDLabel.MDL_ZSCORE_SHAPE1, id);
141  zscore_shape2 = md.getValueDouble(MDLabel.MDL_ZSCORE_SHAPE2, id);
142  zscore_snr1 = md.getValueDouble(MDLabel.MDL_ZSCORE_SNR1, id);
143  zscore_snr2 = md.getValueDouble(MDLabel.MDL_ZSCORE_SNR2, id);
144  zscore_hist = md.getValueDouble(MDLabel.MDL_ZSCORE_HISTOGRAM, id);
145  p = new ExtractParticle(id, x, y, current, enabled, zscore, zscore_shape1, zscore_shape2, zscore_snr1, zscore_snr2, zscore_hist);
146  current.addParticle(p);
147 
148  }
149  md.destroy();
150  }
- -
xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MDLabel.MDL_ZSCORE_SNR1
static final int MDL_ZSCORE_SNR1
< Z Score (double)
Definition: MDLabel.java:444
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE1
static final int MDL_ZSCORE_SHAPE1
< Z Score of the covariance matrix of the residuals (double)
Definition: MDLabel.java:442
-
xmipp.jni.MetaData.destroy
synchronized native void destroy()
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xmipp.jni.MDLabel.MDL_ZSCORE_SHAPE2
static final int MDL_ZSCORE_SHAPE2
< Z Score (double)
Definition: MDLabel.java:443
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xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
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xmipp.jni.MDLabel.MDL_ZSCORE_SNR2
static final int MDL_ZSCORE_SNR2
< Z Score (double)
Definition: MDLabel.java:445
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xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.jni.MDLabel.MDL_ZSCORE_HISTOGRAM
static final int MDL_ZSCORE_HISTOGRAM
< Z Score (double)
Definition: MDLabel.java:438
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xmipp.jni.MDLabel.MDL_ZSCORE
static final int MDL_ZSCORE
< Z component (int)
Definition: MDLabel.java:435
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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◆ open()

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static ExtractPickerJFrame xmipp.viewer.particlepicker.extract.ExtractParticlePicker.open (String block,
String filename,
int size,
GalleryJFrame galleryfr 
)
- 		-inlinestatic
-
- -

Definition at line 220 of file ExtractParticlePicker.java.

-
221  {
222  try
223 
224  {
225  ExtractParticlePicker picker = new ExtractParticlePicker(block, filename, size, new ParticlePickerParams(Mode.Extract));
226  return new ExtractPickerJFrame(picker, galleryfr);
227  }
228  catch(Exception e)
229  {
230  XmippDialog.showError(null,e.getMessage());
231  return null;
232  }
233  }
- - -
xmipp.viewer.particlepicker.extract.ExtractParticlePicker.ExtractParticlePicker
ExtractParticlePicker(String selfile, int size, ParticlePickerParams params)
Definition: ExtractParticlePicker.java:27
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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◆ saveConfig()

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void xmipp.viewer.particlepicker.extract.ExtractParticlePicker.saveConfig ()
- 		-inline
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Definition at line 208 of file ExtractParticlePicker.java.

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209  {
210  // TODO Auto-generated method stub
211 
212  }
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◆ saveData() [1/2]

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void xmipp.viewer.particlepicker.extract.ExtractParticlePicker.saveData ()
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Definition at line 158 of file ExtractParticlePicker.java.

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159  {
160  if (isChanged())
161  for(ExtractMicrograph m: micrographs)
162  saveData(m);
163  }
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void xmipp.viewer.particlepicker.extract.ExtractParticlePicker.saveData (Micrograph m)
- 		-inline
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Definition at line 166 of file ExtractParticlePicker.java.

-
167  {
168  long id;
169  micrograph = (ExtractMicrograph)m;
170  try
171  {
172  MetaData md = new MetaData();
173 
174  for (ExtractParticle p : micrograph.getParticles())
175  {
176  id = p.getId();
177  md.setValueInt(MDLabel.MDL_XCOOR, p.getX(), id);
178  md.setValueInt(MDLabel.MDL_YCOOR, p.getY(), id);
179  md.setValueInt(MDLabel.MDL_ENABLED, p.isEnabled()? 1: -1, id);
180  }
181  String path = (block == null)? selfile: block + "@" + selfile;
182  md.write(path);
183  md.destroy();
184 
185  }
186  catch (Exception e)
187  {
188  getLogger().log(Level.SEVERE, e.getMessage(), e);
189  throw new IllegalArgumentException(e.getMessage());
190  }
191 
192  }
- -
xmipp.jni.MetaData.write
native void write(String filename)
-
xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
-
xmipp.jni.MetaData.destroy
synchronized native void destroy()
-
xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
- - - -
xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
-
xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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◆ setMicrograph()

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void xmipp.viewer.particlepicker.extract.ExtractParticlePicker.setMicrograph (Micrograph m)
- 		-inline
-
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Definition at line 201 of file ExtractParticlePicker.java.

-
202  {
203  micrograph = (ExtractMicrograph) m;
204 
205  }
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-
The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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-
- - - - - - - -
-
Xmipp -  v20.07 -
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- - - - - - - - -
-
- - -
- -
- - -
-
-
-
xmipp.viewer.particlepicker.extract.ExtractPickerJFrame Member List
-
-
- -

This is the complete list of members for xmipp.viewer.particlepicker.extract.ExtractPickerJFrame, including all inherited members.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
actionPerformed(ActionEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateEraseMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateLinearMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateNormalMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activefilterxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
addFilterAppliedListener()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
applyFilter(String filter)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
bundlexmipp.viewer.particlepicker.ParticlePickerJFrameprotected
canExit()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
centerchbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
changeShapes()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
circlechbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
close()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
closebtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorpnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
commandxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
displayZoom(double zoom)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
enableEdition(boolean enable)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
ERASE_ACTIVExmipp.viewer.particlepicker.ParticlePickerJFramestatic
eraseAvailable()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
eSizexmipp.viewer.particlepicker.ParticlePickerJFrameprotected
eSizelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
eSizepnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
executeScipionSaveAndExit()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
exitmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
exportmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
ExtractPickerJFrame(ParticlePicker picker, GalleryJFrame galleryfr)xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
filemnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
filtersmnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
getAvailableParticles()xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
getCanvas()xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
getEraserSize()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getKeyAssist()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getMicrograph()xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
getParticlePicker()xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
getParticlesJDialog()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getResetMsg()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getSide()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getStep()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getTextField(JSpinner spinner)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
hcontentsmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
helpmnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
ijmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
importmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
importpjdxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
initColorPane(Color color)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initEraserSizePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initParticlesJDialog()xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
initShapePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initSizePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initStepPane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initToolBar()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isEraserMode(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isLinearMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isNormalMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isPickingAvailable(MouseEvent e)xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
isShapeSelected(Shape shape)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
linearModeAvailable()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
loadMicrograph()xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinlineprotected
loadParticles(boolean reset)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
micrographstbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
modesgrpxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
moveToNextMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
moveToPreviousMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
NEXT_MICROGRAPH_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
openHelpURl()xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinlineprotected
ParticlePickerJFrame(ParticlePicker picker)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
particlesdialogxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
pmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
positionlbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
PREVIOUS_MICROGRAPH_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
processSizeMouseWheelEvent(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
readSizeFromTextField()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
rectanglechbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
refreshActive(long id, boolean b)xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
refreshActiveOnGallery(ExtractParticle active)xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
reloadImage()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
resetbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
resetMicrograph()xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinlineprotected
saveandexitbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
savebtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
saveData(boolean notify)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
savemixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
setCanvasCursor()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
setChanged(boolean changed)xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
setEraserSize(int newSize)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
setSaved(boolean saved)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
setTitle()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
shapelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
showException(Exception e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
showHideModeParameters()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
showMessage(String message)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
sizelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sizepnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sizetfxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
tbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
TOGGLE_ERASE_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_LINEAR_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_MARKER_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_NORMAL_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
updateColor(Color color)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
updateMicrographsModel(boolean all)xmipp.viewer.particlepicker.extract.ExtractPickerJFrameinline
xmipp::viewer::particlepicker::ParticlePickerJFrame.updateMicrographsModel()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
updateSize(int size)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
usezoombtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
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-Classes | -Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.particlepicker.extract.ExtractPickerJFrame Class Reference
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-Classes

class  ExtractMicrographsTableModel
 
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-Public Member Functions

 ExtractPickerJFrame (ParticlePicker picker, GalleryJFrame galleryfr)
 
boolean isPickingAvailable (MouseEvent e)
 
ParticlePickerCanvas getCanvas ()
 
void updateMicrographsModel (boolean all)
 
ExtractMicrograph getMicrograph ()
 
List<? extends PickerParticle > getAvailableParticles ()
 
ExtractParticlePicker getParticlePicker ()
 
void setChanged (boolean changed)
 
String importParticles (Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
ParticlesDialog initParticlesJDialog ()
 
void refreshActive (long id, boolean b)
 
void refreshActiveOnGallery (ExtractParticle active)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
 ParticlePickerJFrame (ParticlePicker picker)
 
void moveToNextMicrograph ()
 
void moveToPreviousMicrograph ()
 
void processSizeMouseWheelEvent (MouseWheelEvent e)
 
String getResetMsg ()
 
void actionPerformed (ActionEvent e)
 
void applyFilter (String filter)
 
int getSide ()
 
abstract ParticlePickerCanvas getCanvas ()
 
abstract ParticlesDialog initParticlesJDialog ()
 
void loadParticles (boolean reset)
 
void updateMicrographsModel ()
 
abstract void updateMicrographsModel (boolean all)
 
ParticlesDialog getParticlesJDialog ()
 
abstract Micrograph getMicrograph ()
 
abstract List<? extends PickerParticle > getAvailableParticles ()
 
boolean isPickingAvailable (MouseEvent e)
 
void updateColor (Color color)
 
void initToolBar ()
 
boolean isEraserMode (MouseEvent e)
 
void activateEraseMode ()
 
boolean isLinearMode ()
 
boolean isNormalMode ()
 
void activateLinearMode ()
 
void activateNormalMode ()
 
int getEraserSize ()
 
void setEraserSize (int newSize)
 
int getStep ()
 
void changeShapes ()
 
boolean isShapeSelected (Shape shape)
 
abstract ParticlePicker getParticlePicker ()
 
abstract void setChanged (boolean changed)
 
void setSaved (boolean saved)
 
JFormattedTextField getTextField (JSpinner spinner)
 
void updateSize (int size)
 
boolean showMessage (String message)
 
boolean showException (Exception e)
 
void close ()
 
abstract String importParticles (Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
Map< Object, Object > getKeyAssist ()
 
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-Protected Member Functions

void loadMicrograph ()
 
void openHelpURl ()
 
void resetMicrograph ()
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
boolean canExit ()
 
abstract void loadMicrograph ()
 
boolean saveData (boolean notify)
 
void addFilterAppliedListener ()
 
void openHelpURl ()
 
abstract void resetMicrograph ()
 
void enableEdition (boolean enable)
 
void reloadImage ()
 
void initShapePane ()
 
boolean eraseAvailable ()
 
void setCanvasCursor ()
 
boolean linearModeAvailable ()
 
void showHideModeParameters ()
 
void displayZoom (double zoom)
 
void setTitle ()
 
void initColorPane (Color color)
 
void initStepPane ()
 
void initEraserSizePane ()
 
void initSizePane ()
 
void readSizeFromTextField ()
 
void executeScipionSaveAndExit ()
 
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- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
static final int TOGGLE_LINEAR_MODE_KEY = KeyEvent.VK_L
 
static final int TOGGLE_ERASE_MODE_KEY = KeyEvent.VK_E
 
static final int NEXT_MICROGRAPH_KEY = KeyEvent.VK_R
 
static final int PREVIOUS_MICROGRAPH_KEY = KeyEvent.VK_W
 
static final int TOGGLE_MARKER_KEY = KeyEvent.VK_SPACE
 
static final int TOGGLE_NORMAL_MODE_KEY = KeyEvent.VK_P
 
static final int ERASE_ACTIVE = KeyEvent.VK_DELETE
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
ParticlesDialog particlesdialog
 
JMenuItem ijmi
 
JToggleButton circlechb
 
JToggleButton rectanglechb
 
JToggleButton centerchb
 
JLabel shapelb
 
JMenuItem savemi
 
JMenuItem hcontentsmi
 
JMenuItem pmi
 
JMenuItem exportmi
 
JMenu filtersmn
 
String activefilter
 
JPanel sizepn
 
JLabel sizelb
 
JFormattedTextField sizetf
 
JPanel eSizepn
 
JLabel eSizelb
 
JSpinner eSize
 
JMenu filemn
 
JMenuItem importmi
 
JButton colorbt
 
Color color
 
JPanel colorpn
 
JButton resetbt
 
JTable micrographstb
 
ImportParticlesJDialog importpjd = null
 
JMenuItem exitmi
 
JLabel positionlb
 
JToggleButton usezoombt
 
ButtonGroup modesgrp
 
JMenu helpmn
 
JButton savebt
 
JButton saveandexitbt
 
JToolBar tb
 
ResourceBundle bundle
 
String command
 
JButton closebt
 
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Detailed Description

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Definition at line 39 of file ExtractPickerJFrame.java.

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Constructor & Destructor Documentation

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◆ ExtractPickerJFrame()

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xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.ExtractPickerJFrame (ParticlePicker picker,
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Definition at line 58 of file ExtractPickerJFrame.java.

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59  {
60  super(picker);
61  this.picker = (ExtractParticlePicker)picker;
62  this.galleryfr = galleryfr;
63  initComponents();
64  // TODO Auto-generated constructor stub
65  }
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◆ getAvailableParticles()

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List<? extends PickerParticle> xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.getAvailableParticles ()
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Definition at line 294 of file ExtractPickerJFrame.java.

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295  {
296  return getMicrograph().getParticles();
297  }
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ParticlePickerCanvas xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.getCanvas ()
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Definition at line 266 of file ExtractPickerJFrame.java.

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267  {
268  return canvas;
269  }
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◆ getMicrograph()

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Definition at line 288 of file ExtractPickerJFrame.java.

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289  {
290  return picker.getMicrograph();
291  }
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ExtractParticlePicker xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.getParticlePicker ()
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Definition at line 302 of file ExtractPickerJFrame.java.

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303  {
304  return picker;
305  }
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◆ importParticles()

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String xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.importParticles (Format format,
String dir,
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String suffix,
float scale,
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Definition at line 316 of file ExtractPickerJFrame.java.

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317  {
318  throw new UnsupportedOperationException();
319 
320  }
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◆ initParticlesJDialog()

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Definition at line 364 of file ExtractPickerJFrame.java.

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365  {
366  return new ParticlesDialog(this);
367  }
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boolean xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.isPickingAvailable (MouseEvent e)
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Definition at line 98 of file ExtractPickerJFrame.java.

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99  {
100  return false;
101  }
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◆ loadMicrograph()

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Definition at line 219 of file ExtractPickerJFrame.java.

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220  {
221  if (micrographstb.getSelectedRow() == -1)
222  return;// Probably from fireTableDataChanged raised
223  // is same micrograph??
224  if (index == micrographstb.getSelectedRow() && canvas != null && canvas.getIw().isVisible())
225  return;
226  if (picker.isChanged())
227  picker.saveData(getMicrograph());// Saving changes when switching
228  index = micrographstb.getSelectedRow();
229  picker.setMicrograph(picker.getMicrographs().get(index));
230  setChanged(false);
231  initializeCanvas();
232  iconbt.setIcon(picker.getMicrograph().getCTFIcon());
233 
234  pack();
235  }
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Definition at line 247 of file ExtractPickerJFrame.java.

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248  {
249  XmippDialog.showInfo(this, "Not available yet");
250  }
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void xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.refreshActive (long id,
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Definition at line 369 of file ExtractPickerJFrame.java.

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370  {
371  int index = 0;
372  active = null;
373  List<ExtractMicrograph> micrographs = picker.getMicrographs();
374  for(int i = 0; i < micrographs.size(); i ++)
375  for(ExtractParticle p: micrographs.get(i).getParticles())
376  if(p.getId() == id)
377  {
378  index = i;
379  active = p;
380  active.setEnabled(b);
381  break;
382 
383  }
384  if(index != this.index)
385  micrographstb.setRowSelectionInterval(index, index);
386  if(active != null)
387  {
388  canvas.refreshActive(active);
389  canvas.moveTo(active);
390  active = null;
391  }
392 
393  }
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void xmipp.viewer.particlepicker.extract.ExtractPickerJFrame.refreshActiveOnGallery (ExtractParticle active)
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Definition at line 395 of file ExtractPickerJFrame.java.

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396  {
397  if(galleryfr != null)
398  galleryfr.refreshActive(active.getId(), active.isEnabled());
399 
400  }
xmipp.viewer.windows.GalleryJFrame.refreshActive
void refreshActive(long id, boolean enabled)
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◆ resetMicrograph()

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Definition at line 253 of file ExtractPickerJFrame.java.

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254  {
255  picker.getMicrograph().getParticles().clear();
256  canvas.refreshActive(null);
257  updateMicrographsModel();
258 
259  }
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Definition at line 308 of file ExtractPickerJFrame.java.

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309  {
310  picker.setChanged(changed);
311  }
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Definition at line 272 of file ExtractPickerJFrame.java.

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273  {
274  if (particlesdialog != null)
275  loadParticles(false);
276 
277  if (all)
278  micrographsmd.fireTableRowsUpdated(0, micrographsmd.getRowCount() - 1);
279  else
280  micrographsmd.fireTableRowsUpdated(index, index);
281 
282  micrographstb.setRowSelectionInterval(index, index);
283  particleslb.setText(Integer.toString(picker.getParticlesCount()));
284 
285  }
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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
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xmipp.viewer.particlepicker.extract.MicrographCanvas Member List
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This is the complete list of members for xmipp.viewer.particlepicker.extract.MicrographCanvas, including all inherited members.

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adjustMagnification()xmipp.ij.commons.XmippImageCanvasinline
customScrollSetup(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
display()xmipp.viewer.particlepicker.extract.MicrographCanvasinline
doCustomPaint(Graphics2D g2)xmipp.viewer.particlepicker.extract.MicrographCanvasinlineprotected
drawShape(Graphics2D g2, Shape shape, int x, int y, int radius)xmipp.viewer.particlepicker.extract.MicrographCanvasinlineprotected
getPreferredMagnification()xmipp.ij.commons.XmippImageCanvasinline
getTool()xmipp.ij.commons.XmippImageCanvasinline
getXOnImage(int x)xmipp.ij.commons.XmippImageCanvasinline
getYOnImage(int y)xmipp.ij.commons.XmippImageCanvasinline
isDragImage(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinlineprotected
isKeyPressed(int keyCode)xmipp.ij.commons.XmippImageCanvasinlineprotected
iwxmipp.viewer.particlepicker.extract.MicrographCanvasprotected
keyPressed(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyReleased(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyTyped(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
loadData(XmippIJWindow xiw)xmipp.ij.commons.XmippImageCanvasinline
MicrographCanvas(MicrographData loader, int size)xmipp.viewer.particlepicker.extract.MicrographCanvasinline
mouseDragged(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseMoved(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mousePressed(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseReleased(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
mouseWheelMoved(MouseWheelEvent e)xmipp.ij.commons.XmippImageCanvasinline
offScreenX(int x)xmipp.ij.commons.XmippImageCanvasinline
offScreenY(int y)xmipp.ij.commons.XmippImageCanvasinline
paint(Graphics g)xmipp.viewer.particlepicker.extract.MicrographCanvasinline
setInvertX(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setInvertY(boolean value)xmipp.ij.commons.XmippImageCanvasinline
XmippImageCanvas(ImagePlus imp)xmipp.ij.commons.XmippImageCanvasinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1MicrographCanvas.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1MicrographCanvas.html deleted file mode 100644 index b81afaa0..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1extract_1_1MicrographCanvas.html +++ /dev/null @@ -1,381 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.extract.MicrographCanvas Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.viewer.particlepicker.extract.MicrographCanvas Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.extract.MicrographCanvas:
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-Public Member Functions

 MicrographCanvas (MicrographData loader, int size)
 
void display ()
 
void paint (Graphics g)
 
- Public Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
Tool getTool ()
 
 XmippImageCanvas (ImagePlus imp)
 
void mousePressed (MouseEvent e)
 
void customScrollSetup (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void mouseWheelMoved (MouseWheelEvent e)
 
void mouseMoved (MouseEvent e)
 
int offScreenX (int x)
 
int offScreenY (int y)
 
void loadData (XmippIJWindow xiw)
 
double getPreferredMagnification ()
 
void adjustMagnification ()
 
void setInvertX (boolean value)
 
void setInvertY (boolean value)
 
void keyTyped (KeyEvent keyEvent)
 
void keyPressed (KeyEvent keyEvent)
 
void keyReleased (KeyEvent keyEvent)
 
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-Protected Member Functions

void drawShape (Graphics2D g2, Shape shape, int x, int y, int radius)
 
void doCustomPaint (Graphics2D g2)
 
- Protected Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
boolean isDragImage (MouseEvent e)
 
boolean isKeyPressed (int keyCode)
 
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-Protected Attributes

ImageWindow iw
 
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Detailed Description

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Definition at line 15 of file MicrographCanvas.java.

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Constructor & Destructor Documentation

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◆ MicrographCanvas()

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xmipp.viewer.particlepicker.extract.MicrographCanvas.MicrographCanvas (MicrographData loader,
int size 
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Definition at line 23 of file MicrographCanvas.java.

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24  {
25  super(loader.getMicrograph().getImagePlus());
26  this.micdata = loader;
27  this.particles = loader.getParticles();
28  this.size = size;
29  }
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Member Function Documentation

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◆ display()

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void xmipp.viewer.particlepicker.extract.MicrographCanvas.display ()
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Definition at line 33 of file MicrographCanvas.java.

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34  {
35  if (iw != null && iw.isVisible())
36  {
37  iw.setImage(getImage());
38  iw.updateImage(getImage());
39  }
40  else
41  this.iw = new ImageWindow(getImage(), this);// if you don't provide
42  // iw, I init mine
43  // iw.maximize();
44  iw.pack();
45  }
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◆ doCustomPaint()

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void xmipp.viewer.particlepicker.extract.MicrographCanvas.doCustomPaint (Graphics2D g2)
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Definition at line 79 of file MicrographCanvas.java.

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80  {
81  g2.setColor(Color.GREEN);
82  for (Particle p : particles)
83  {
84  drawShape(g2, Shape.Rectangle, getXOnImage(p.getX()), getYOnImage(p.getY()), size);
85  drawShape(g2, Shape.Center, getXOnImage(p.getX()), getYOnImage(p.getY()), size);
86  }
87  }
xmipp.viewer.particlepicker.extract.MicrographCanvas.drawShape
void drawShape(Graphics2D g2, Shape shape, int x, int y, int radius)
Definition: MicrographCanvas.java:63
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void xmipp.viewer.particlepicker.extract.MicrographCanvas.drawShape (Graphics2D g2,
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Definition at line 63 of file MicrographCanvas.java.

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64  {
65  int size = 2 * radius;
66  if (shape == Shape.Rectangle)
67  g2.drawRect(x - radius, y - radius, size, size);
68  else if (shape == Shape.Circle)
69  g2.drawOval(x - radius, y - radius, size, size);
70  else if (shape == Shape.Center)
71  {
72  int distance = (int) (radius / 5. * magnification);
73  g2.drawLine(x, y - distance, x, y + distance);
74  g2.drawLine(x + distance, y, x - distance, y);
75  }
76 
77  }
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◆ paint()

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void xmipp.viewer.particlepicker.extract.MicrographCanvas.paint (Graphics g)
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Definition at line 47 of file MicrographCanvas.java.

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48  {
49  Graphics offgc;//Off screen graphic
50  Image offscreen = null;//Off screen image
51  Dimension d = getSize();
52  // create the offscreen buffer and associated Graphics
53  offscreen = createImage(d.width, d.height);
54  offgc = offscreen.getGraphics();
55  super.paint(offgc);//super paint in off screen
56  //my paint in offscreen
57  Graphics2D g2 = (Graphics2D) offgc;
58  doCustomPaint(g2);
59  //drawing offscreen image
60  g.drawImage(offscreen, 0, 0, this);
61  }
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Member Data Documentation

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◆ iw

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ImageWindow xmipp.viewer.particlepicker.extract.MicrographCanvas.iw
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Definition at line 31 of file MicrographCanvas.java.

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xmipp.viewer.particlepicker.extract.MicrographData Member List
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This is the complete list of members for xmipp.viewer.particlepicker.extract.MicrographData, including all inherited members.

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getMicrograph()xmipp.viewer.particlepicker.extract.MicrographDatainline
getMicrographData(String file)xmipp.viewer.particlepicker.extract.MicrographDatainlinestatic
getMicrographFile()xmipp.viewer.particlepicker.extract.MicrographDatainline
getParticles()xmipp.viewer.particlepicker.extract.MicrographDatainline
MicrographData(String mdfile, String micfile)xmipp.viewer.particlepicker.extract.MicrographDatainline
openMicrographs(String mdfile)xmipp.viewer.particlepicker.extract.MicrographDatainlinestatic
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xmipp.viewer.particlepicker.extract.MicrographData Class Reference
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-Public Member Functions

 MicrographData (String mdfile, String micfile)
 
Micrograph getMicrograph ()
 
List< Particle > getParticles ()
 
String getMicrographFile ()
 
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-Static Public Member Functions

static void openMicrographs (String mdfile)
 
static List< MicrographData > getMicrographData (String file)
 
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Definition at line 11 of file MicrographData.java.

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◆ MicrographData()

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xmipp.viewer.particlepicker.extract.MicrographData.MicrographData (String mdfile,
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Definition at line 18 of file MicrographData.java.

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19  {
20  this.mdfile = mdfile;
21  this.particles = new ArrayList<Particle>();
22  this.micfile = micfile;
23  this.micrograph = new Micrograph(micfile)
24  {
25 
26 
27 
28  @Override
29  public boolean hasData()
30  {
31  return !particles.isEmpty();
32  }
33  };
34  loadData();
35  }
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◆ getMicrograph()

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Micrograph xmipp.viewer.particlepicker.extract.MicrographData.getMicrograph ()
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Definition at line 37 of file MicrographData.java.

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38  {
39  return micrograph;
40  }
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static List<MicrographData> xmipp.viewer.particlepicker.extract.MicrographData.getMicrographData (String file)
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Definition at line 88 of file MicrographData.java.

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89  {
90  List<MicrographData> loaders = new ArrayList<MicrographData>();
91  MetaData md = new MetaData(file);
92  Particle p;
93  int x, y;
94  String micfileiter;
95  boolean exists;
96  MicrographData data = null;
97  for (long id : md.findObjects())
98  {
99  exists = false;
100  micfileiter = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
101  for (MicrographData dataiter : loaders)
102  if (dataiter.getMicrographFile().equals(micfileiter))
103  {
104  exists = true;
105  data = dataiter;
106  break;
107  }
108  if (!exists)
109  {
110  data = new MicrographData(file, micfileiter);
111  loaders.add(data);
112  }
113  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
114  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
115  p = new Particle(x, y);
116  data.addParticle(p);
117  }
118  md.destroy();
119  return loaders;
120  }
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Definition at line 83 of file MicrographData.java.

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84  {
85  return micfile;
86  }
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Definition at line 78 of file MicrographData.java.

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79  {
80  return particles;
81  }
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Definition at line 42 of file MicrographData.java.

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43  {
44 
45 
46  List<MicrographData> micdatas = MicrographData.getMicrographData(mdfile);
47  MicrographCanvas mc;
48  for(MicrographData pl: micdatas)
49  {
50  mc = new MicrographCanvas(pl, 30);
51  mc.display();
52  }
53  }
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xmipp.viewer.particlepicker.tiltpair.TiltPairPickerRunner Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.TiltPairPickerRunner, including all inherited members.

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main(String[] args)xmipp.viewer.particlepicker.tiltpair.TiltPairPickerRunnerinlinestatic
run()xmipp.viewer.particlepicker.tiltpair.TiltPairPickerRunnerinline
TiltPairPickerRunner(String[] args)xmipp.viewer.particlepicker.tiltpair.TiltPairPickerRunnerinline
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 TiltPairPickerRunner (String[] args)
 
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Definition at line 15 of file TiltPairPickerRunner.java.

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◆ TiltPairPickerRunner()

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Definition at line 22 of file TiltPairPickerRunner.java.

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22  {
23 
24  params = new ParticlePickerParams(args);
25 
26  }
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static void xmipp.viewer.particlepicker.tiltpair.TiltPairPickerRunner.main (String [] args)
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Definition at line 54 of file TiltPairPickerRunner.java.

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54  {
55  TiltPairPickerRunner spr = new TiltPairPickerRunner(args);
56  SwingUtilities.invokeLater(spr);
57 
58  }
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void xmipp.viewer.particlepicker.tiltpair.TiltPairPickerRunner.run ()
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Definition at line 35 of file TiltPairPickerRunner.java.

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35  {
36  try {
37 
38  TiltPairPicker ppicker = null;
39  ppicker = new TiltPairPicker(params.inputfile, params.outputdir, params);
40 
41  if(params.isScipion())
42  XmippApplication.setIsScipion(true);
43 
44  new TiltPairPickerJFrame(ppicker);
45  } catch (Exception e) {
46  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
47  if (!e.getMessage().isEmpty())
48  XmippDialog.showError(null, e.getMessage());
49 
50  }
51 
52  }
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xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
browsebtxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
browseDirectory(JTextField sourcetf)xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
formatxmipp.viewer.particlepicker.ImportParticlesJDialog
formatsListxmipp.viewer.particlepicker.ImportParticlesJDialogstatic
formatsStringxmipp.viewer.particlepicker.ImportParticlesJDialogstatic
handleActionPerformed(ActionEvent evt)xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.viewer.particlepicker.ImportParticlesJDialoginline
importParticles()xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialoginlineprotected
ImportParticlesFromFilesTiltPairJDialog(TiltPairPickerJFrame parent)xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialoginline
ImportParticlesJDialog(ParticlePickerJFrame parent)xmipp.viewer.particlepicker.ImportParticlesJDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
invertxcbxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
invertycbxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
jcbFormatxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
pathxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
scaletfxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
sourcetfxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
xfcxmipp.viewer.particlepicker.ImportParticlesJDialogprotected
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1ImportParticlesFromFilesTiltPairJDialog.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1ImportParticlesFromFilesTiltPairJDialog.html deleted file mode 100644 index 7a1a2fae..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1ImportParticlesFromFilesTiltPairJDialog.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog:
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-Public Member Functions

 ImportParticlesFromFilesTiltPairJDialog (TiltPairPickerJFrame parent)
 
void handleActionPerformed (ActionEvent evt)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ImportParticlesJDialog
 ImportParticlesJDialog (ParticlePickerJFrame parent)
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void createContent (JPanel panel)
 
void browseDirectory (JTextField sourcetf)
 
String importParticles ()
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ImportParticlesJDialog
void createContent (JPanel panel)
 
void browseDirectory (JTextField sourcetf)
 
String importParticles ()
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
- Public Attributes inherited from xmipp.viewer.particlepicker.ImportParticlesJDialog
Format format = Format.Auto
 
- Static Public Attributes inherited from xmipp.viewer.particlepicker.ImportParticlesJDialog
static final String [] formatsString = new String[]{Format.Auto.toString(), Format.Xmipp24.toString(), Format.Xmipp30.toString(), Format.Xmipp301.toString(), Format.Eman.toString(), Format.Relion.toString()}
 
static final Format [] formatsList
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ImportParticlesJDialog
ParticlePickerJFrame parent
 
JTextField sourcetf
 
JButton browsebt
 
JComboBox jcbFormat
 
XmippFileChooser xfc = null
 
String path
 
JFormattedTextField scaletf
 
JCheckBox invertxcb
 
JCheckBox invertycb
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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Detailed Description

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Definition at line 25 of file ImportParticlesFromFilesTiltPairJDialog.java.

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Constructor & Destructor Documentation

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◆ ImportParticlesFromFilesTiltPairJDialog()

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xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog.ImportParticlesFromFilesTiltPairJDialog (TiltPairPickerJFrame parent)
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Definition at line 33 of file ImportParticlesFromFilesTiltPairJDialog.java.

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33  {
34  super(parent);
35  }
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Member Function Documentation

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◆ browseDirectory()

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void xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog.browseDirectory (JTextField sourcetf)
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Definition at line 108 of file ImportParticlesFromFilesTiltPairJDialog.java.

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108  {
109  int returnVal = xfc.showOpenDialog(this);
110  try {
111  if (returnVal == XmippFileChooser.APPROVE_OPTION) {
112  path = xfc.getSelectedPath();
113  sourcetf.setText(path);
114  }
115  } catch (Exception ex) {
116  showException(ex);
117  }
118 
119  }
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xmipp.utils.XmippDialog.showException
boolean showException(Exception e)
Definition: XmippDialog.java:217
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void xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog.createContent (JPanel panel)
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Create a combobox with possible formats

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Definition at line 42 of file ImportParticlesFromFilesTiltPairJDialog.java.

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42  {
43  setResizable(false);
44  panel.setLayout(new GridBagLayout());
45  GridBagConstraints gbc = new GridBagConstraints();
46  gbc.insets = new Insets(5, 5, 5, 5);
47 
48  gbc.anchor = GridBagConstraints.EAST;
49  panel.add(new JLabel("Format:"),
50  XmippWindowUtil.getConstraints(gbc, 0, 0, 1));
51  panel.add(new JLabel("Untilted:"),
52  XmippWindowUtil.getConstraints(gbc, 0, 1, 1));
53 
54  panel.add(new JLabel("Tilted:"),
55  XmippWindowUtil.getConstraints(gbc, 0, 2, 1));
56 
57  gbc.anchor = GridBagConstraints.WEST;
59  jcbFormat = new JComboBox(formatsString);
60  jcbFormat.addActionListener(new ActionListener() {
61 
62  @Override
63  public void actionPerformed(ActionEvent arg0) {
64  format = formatsList[jcbFormat.getSelectedIndex()];
65 
66  }
67  });
68  panel.add(jcbFormat, XmippWindowUtil.getConstraints(gbc, 1, 0, 1));
69  sourcetf = new JTextField(20);
70  panel.add(sourcetf, XmippWindowUtil.getConstraints(gbc, 1, 1, 1));
71 
72  sourcetf2 = new JTextField(20);
73  panel.add(sourcetf2, XmippWindowUtil.getConstraints(gbc, 1, 2, 1));
74  browsebt = XmippWindowUtil.getIconButton("folderopen.gif", this);
75  browsebt2 = XmippWindowUtil.getIconButton("folderopen.gif", this);
76  browsebt2.setActionCommand("browse2");
77  panel.add(browsebt, XmippWindowUtil.getConstraints(gbc, 2, 1, 1));
78  panel.add(browsebt2, XmippWindowUtil.getConstraints(gbc, 2, 2, 1));
79  panel.add(new JLabel("Scale To:"),
80  XmippWindowUtil.getConstraints(gbc, 0, 3, 1));
81  scaletf = new JFormattedTextField(NumberFormat.getNumberInstance(Locale.ENGLISH));
82  scaletf.setColumns(3);
83  scaletf.setValue(1);
84  panel.add(scaletf, XmippWindowUtil.getConstraints(gbc, 1, 3));
85 
86  panel.add(new JLabel("Invert X:"),
87  XmippWindowUtil.getConstraints(gbc, 0, 4));
88  invertxcb = new JCheckBox();
89  panel.add(invertxcb, XmippWindowUtil.getConstraints(gbc, 1, 4));
90 
91  panel.add(new JLabel("Invert Y:"),
92  XmippWindowUtil.getConstraints(gbc, 0, 5));
93  invertycb = new JCheckBox();
94  panel.add(invertycb, XmippWindowUtil.getConstraints(gbc, 1, 5));
95 
96 
97  }// function createContent
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xmipp.utils.XmippDialog.actionPerformed
void actionPerformed(ActionEvent evt)
Definition: XmippDialog.java:163
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void xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog.handleActionPerformed (ActionEvent evt)
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Definition at line 100 of file ImportParticlesFromFilesTiltPairJDialog.java.

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100  {
101  Object o = evt.getSource();
102  if (o == browsebt)
103  browseDirectory(sourcetf);
104  else
105  browseDirectory(sourcetf2);
106  }// function actionPerformed
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String xmipp.viewer.particlepicker.tiltpair.gui.ImportParticlesFromFilesTiltPairJDialog.importParticles ()
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Definition at line 122 of file ImportParticlesFromFilesTiltPairJDialog.java.

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122  {
123  path = sourcetf.getText().trim();
124 
125  if (path == null || path.equals("") )
126  showError(XmippMessage.getEmptyFieldMsg("Untilted"));
127  path2 = sourcetf2.getText().trim();
128 
129  if (path2 == null || path2.equals("") )
130  showError(XmippMessage.getEmptyFieldMsg("Tilted"));
131  return ((TiltPairPickerJFrame)parent).importParticlesFromFiles(format, path, path2, ((Number)scaletf.getValue()).floatValue(), invertxcb.isSelected(), invertycb.isSelected());
132 
133  }
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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The documentation for this class was generated from the following file: -
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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel, including all inherited members.

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getColumnCount()xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModelinline
getColumnName(int c)xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModelinline
getParticlesPosition()xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModelinline
getRowCount()xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModelinline
getValueAt(int rowIndex, int columnIndex)xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModelinline
MicrographPairsTableModel(TiltPairPickerJFrame frame)xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModelinline
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xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel:
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-Collaboration diagram for xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel:
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-Public Member Functions

 MicrographPairsTableModel (TiltPairPickerJFrame frame)
 
int getColumnCount ()
 
String getColumnName (int c)
 
int getRowCount ()
 
Object getValueAt (int rowIndex, int columnIndex)
 
int getParticlesPosition ()
 
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Detailed Description

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Definition at line 10 of file MicrographPairsTableModel.java.

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Constructor & Destructor Documentation

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◆ MicrographPairsTableModel()

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xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel.MicrographPairsTableModel (TiltPairPickerJFrame frame)
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Definition at line 17 of file MicrographPairsTableModel.java.

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18  {
19  this.micrographs = frame.getParticlePicker().getMicrographs();
20  }
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Member Function Documentation

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◆ getColumnCount()

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int xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel.getColumnCount ()
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Definition at line 23 of file MicrographPairsTableModel.java.

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23  {
24  return columns.length;
25  }
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String xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel.getColumnName (int c)
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Definition at line 27 of file MicrographPairsTableModel.java.

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28  {
29  return columns[c];
30  }
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◆ getParticlesPosition()

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int xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel.getParticlesPosition ()
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Definition at line 53 of file MicrographPairsTableModel.java.

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54  {
55  return 2;
56  }
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◆ getRowCount()

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int xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel.getRowCount ()
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Definition at line 33 of file MicrographPairsTableModel.java.

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33  {
34  return micrographs.size();
35  }
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◆ getValueAt()

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Object xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel.getValueAt (int rowIndex,
int columnIndex 
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Definition at line 38 of file MicrographPairsTableModel.java.

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38  {
39  UntiltedMicrograph m = micrographs.get(rowIndex);
40  if(columnIndex == 0)
41  return rowIndex + 1;
42  if(columnIndex == 1)
43  return m.getName();
44  if(columnIndex == 2)
45  return m.getTiltedMicrograph().getName();
46  if(columnIndex == 3)
47  return m.getParticles().size();
48  if(columnIndex == 4)
49  return String.format("%.2f", m.getTiltAngle());
50  return null;
51  }
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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__coll__graph.dot deleted file mode 100644 index 30092bf2..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.tiltpair.gui.\lMicrographPairsTableModel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="AbstractTableModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__coll__graph.md5 deleted file mode 100644 index d6c14a17..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -464a50caa5db723acef36c2df8929fdc \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__inherit__graph.dot deleted file mode 100644 index a368db7b..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.gui.MicrographPairsTableModel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.tiltpair.gui.\lMicrographPairsTableModel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="AbstractTableModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__inherit__graph.md5 deleted file mode 100644 index 9ac886cf..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1MicrographPairsTableModel__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -8ac47b054342d31a6b49bd0dbb7889d1 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog-members.html deleted file mode 100644 index 71d26bc8..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog-members.html +++ /dev/null @@ -1,94 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialog Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialog, including all inherited members.

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close()xmipp.viewer.particlepicker.ParticlesDialoginline
constraintsxmipp.viewer.particlepicker.ParticlesDialogprotected
framexmipp.viewer.particlepicker.ParticlesDialogprotected
loadParticles(boolean changesize)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialoginline
maxHeightxmipp.viewer.particlepicker.ParticlesDialogstatic
minWidthxmipp.viewer.particlepicker.ParticlesDialogstatic
ParticlesDialog(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.ParticlesDialoginline
particlespnxmipp.viewer.particlepicker.ParticlesDialogprotected
resetParticlesDialog()xmipp.viewer.particlepicker.ParticlesDialoginlineprotected
spxmipp.viewer.particlepicker.ParticlesDialogprotected
TiltPairParticlesDialog(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialoginline
widthxmipp.viewer.particlepicker.ParticlesDialogprotected
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog.html deleted file mode 100644 index 257c1ab9..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog.html +++ /dev/null @@ -1,206 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialog Class Reference - - - - - - - - - -
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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialog Class Reference
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-Public Member Functions

 TiltPairParticlesDialog (ParticlePickerJFrame frame)
 
void loadParticles (boolean changesize)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlesDialog
 ParticlesDialog (ParticlePickerJFrame frame)
 
void loadParticles (boolean resize)
 
void close ()
 
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- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlesDialog
static final int maxHeight = (int)(0.9 * XmippWindowUtil.getScreenRectangle().height)
 
static final int minWidth = 600
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlesDialog
void resetParticlesDialog ()
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlesDialog
ParticlePickerJFrame frame
 
Panel particlespn
 
ScrollPane sp
 
GridBagConstraints constraints
 
int width
 
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Detailed Description

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Definition at line 14 of file TiltPairParticlesDialog.java.

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Constructor & Destructor Documentation

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◆ TiltPairParticlesDialog()

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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialog.TiltPairParticlesDialog (ParticlePickerJFrame frame)
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Definition at line 18 of file TiltPairParticlesDialog.java.

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19  {
20 
21  super(frame);
22 
23  }
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void xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialog.loadParticles (boolean changesize)
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Definition at line 25 of file TiltPairParticlesDialog.java.

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26  {
27 
28  List<? extends PickerParticle> particles = frame.getAvailableParticles();
29  side = frame.getSide();
30 
31  if (side == 0)
32  throw new IllegalArgumentException(XmippMessage.getOutOfBoundsMsg("side"));
33 
34  if (particles.isEmpty())
35  {
36  particlespn.removeAll();
37  width = side * 6 + 10;
38  height = maxHeight;
39  sp.setPreferredSize(new Dimension(width, height));
40  pack();
41  return;
42  }
43 
44  if (changesize)// first time or keep size
45  {
46  columns = 3;//Math.min(200, particles.size() * side * 2) / (side * 2);
47  rows = (int) Math.ceil(particles.size() / (float) columns);
48  width = side * columns * 2;
49  height = Math.min(maxHeight, side * rows);
50  boolean scroll = (height < rows * side);
51  width = width + (scroll ? 40 : 20);
52  height = height + (scroll ? 0 : 20);
53  sp.setPreferredSize(new Dimension(width, height));
54  }
55  else
56  {
57  Dimension d = sp.getSize();
58  width = (int) d.getWidth();
59  height = (int)d.getHeight();
60  columns = (int) d.getWidth() / (side * 2);
61  rows = (int) Math.ceil((particles.size() / (float) columns));
62  }
63  sp.setPreferredSize(new Dimension(width, height));
64 
65  particlespn.removeAll();
66  particles = frame.getAvailableParticles();
67  int index = 0;
68  ParticleCanvas c;
69  PickerParticle p;
70  UntiltedParticle up;
71 
72  for (int i = 0; i < rows; i++)
73  for (int j = 0; j < columns * 2; j+= 2, index ++)
74  {
75  if (index == particles.size())
76  break;
77  p = particles.get(index);
78  c = p.getParticleCanvas(frame);
79  up = (UntiltedParticle) p;
80  particlespn.add(c, XmippWindowUtil.getConstraints(constraints, j, i, 1));
81 
82  if (up.getTiltedParticle() != null)
83  particlespn.add(up.getTiltedParticle().getParticleCanvas(frame), XmippWindowUtil.getConstraints(constraints, j + 1, i, 1));
84  }
85 
86  sp.getVAdjustable().setValue(sp.getVAdjustable().getMaximum());
87  sp.getHAdjustable().setValue(sp.getHAdjustable().getMaximum());
88 
89  pack();
90 
91  }
xmipp.viewer.particlepicker.ParticlePickerJFrame.getAvailableParticles
abstract List<? extends PickerParticle > getAvailableParticles()
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog__coll__graph.dot deleted file mode 100644 index 6a5c012b..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairParticlesDialog__coll__graph.dot +++ /dev/null @@ -1,76 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.gui.TiltPairParticlesDialog" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node3 [label="xmipp.viewer.particlepicker.tiltpair.gui.\lTiltPairParticlesDialog",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="xmipp.viewer.particlepicker.\lParticlesDialog",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlesDialog.html"]; 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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame, including all inherited members.

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actionPerformed(ActionEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateEraseMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateLinearMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateNormalMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activefilterxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
addFilterAppliedListener()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
applyFilter(String filter)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
bundlexmipp.viewer.particlepicker.ParticlePickerJFrameprotected
canExit()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
centerchbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
changeShapes()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
circlechbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
close()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
closebtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorpnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
commandxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
displayZoom(double zoom)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
drawAngles()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
enableEdition(boolean enable)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinlineprotected
ERASE_ACTIVExmipp.viewer.particlepicker.ParticlePickerJFramestatic
eraseAvailable()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
eSizexmipp.viewer.particlepicker.ParticlePickerJFrameprotected
eSizelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
eSizepnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
executeScipionSaveAndExit()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
exitmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
exportmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
filemnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
filtersmnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
getAvailableParticles()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
getCanvas()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
getColor()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
getEraserSize()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getKeyAssist()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getMicrograph()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
getParticlePicker()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
getParticleSize()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
getParticlesJDialog()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getResetMsg()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getSide()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getStep()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getTextField(JSpinner spinner)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getTiltedCanvas()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
hcontentsmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
helpmnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
ijmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
importmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
importParticlesFromFiles(Format format, String file1, String file2, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
importParticlesFromFolder(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
importpjdxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
initColorPane(Color color)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initEraserSizePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initMenuBar()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
initParticlesJDialog()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
initShapePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initSizePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initStepPane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initToolBar()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isEraserMode(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isLinearMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isNormalMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isPickingAvailable(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isShapeSelected(Shape shape)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
linearModeAvailable()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
loadMicrograph()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinlineprotected
loadParticles(boolean reset)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
micrographstbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
modesgrpxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
moveToNextMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
moveToPreviousMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
NEXT_MICROGRAPH_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
openHelpURl()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
ParticlePickerJFrame(ParticlePicker picker)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
particlesdialogxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
pmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
positionlbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
PREVIOUS_MICROGRAPH_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
processSizeMouseWheelEvent(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
readSizeFromTextField()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
rectanglechbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
reloadImage()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinlineprotected
resetbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
resetMicrograph()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinlineprotected
saveandexitbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
savebtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
saveData(boolean notify)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
savemixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
setCanvasCursor()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinlineprotected
setChanged(boolean changed)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
setEraserSize(int newSize)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
setSaved(boolean saved)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
setTitle()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
shapelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
showException(Exception e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
showHideModeParameters()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
showImportFromFilesDialog()xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinlineprotected
showMessage(String message)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
sizelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sizepnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sizetfxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
tbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
TiltPairPickerJFrame(TiltPairPicker picker)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
TOGGLE_ERASE_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_LINEAR_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_MARKER_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_NORMAL_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
updateColor(Color color)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
updateMicrographsModel(boolean all)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
xmipp::viewer::particlepicker::ParticlePickerJFrame.updateMicrographsModel()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
updateSize(int size)xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrameinline
usezoombtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame:
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Inheritance graph
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-Public Member Functions

TiltPairPicker getParticlePicker ()
 
 TiltPairPickerJFrame (TiltPairPicker picker)
 
void initMenuBar ()
 
void updateSize (int size)
 
void setChanged (boolean changed)
 
void updateMicrographsModel (boolean all)
 
ParticlePickerCanvas getCanvas ()
 
UntiltedMicrograph getMicrograph ()
 
int getParticleSize ()
 
Color getColor ()
 
List<? extends ManualParticle > getAvailableParticles ()
 
TiltedMicrographCanvas getTiltedCanvas ()
 
boolean drawAngles ()
 
void changeShapes ()
 
String importParticlesFromFolder (Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
String importParticlesFromFiles (Format format, String file1, String file2, float scale, boolean invertx, boolean inverty)
 
String importParticles (Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
ParticlesDialog initParticlesJDialog ()
 
void close ()
 
void applyFilter (String filter)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
 ParticlePickerJFrame (ParticlePicker picker)
 
void moveToNextMicrograph ()
 
void moveToPreviousMicrograph ()
 
void processSizeMouseWheelEvent (MouseWheelEvent e)
 
String getResetMsg ()
 
void actionPerformed (ActionEvent e)
 
void applyFilter (String filter)
 
int getSide ()
 
abstract ParticlePickerCanvas getCanvas ()
 
abstract ParticlesDialog initParticlesJDialog ()
 
void loadParticles (boolean reset)
 
void updateMicrographsModel ()
 
abstract void updateMicrographsModel (boolean all)
 
ParticlesDialog getParticlesJDialog ()
 
abstract Micrograph getMicrograph ()
 
abstract List<? extends PickerParticle > getAvailableParticles ()
 
boolean isPickingAvailable (MouseEvent e)
 
void updateColor (Color color)
 
void initToolBar ()
 
boolean isEraserMode (MouseEvent e)
 
void activateEraseMode ()
 
boolean isLinearMode ()
 
boolean isNormalMode ()
 
void activateLinearMode ()
 
void activateNormalMode ()
 
int getEraserSize ()
 
void setEraserSize (int newSize)
 
int getStep ()
 
void changeShapes ()
 
boolean isShapeSelected (Shape shape)
 
abstract ParticlePicker getParticlePicker ()
 
abstract void setChanged (boolean changed)
 
void setSaved (boolean saved)
 
JFormattedTextField getTextField (JSpinner spinner)
 
void updateSize (int size)
 
boolean showMessage (String message)
 
boolean showException (Exception e)
 
void close ()
 
abstract String importParticles (Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
Map< Object, Object > getKeyAssist ()
 
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-Protected Member Functions

void enableEdition (boolean enable)
 
void setCanvasCursor ()
 
void showImportFromFilesDialog ()
 
void resetMicrograph ()
 
void reloadImage ()
 
void loadMicrograph ()
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
boolean canExit ()
 
abstract void loadMicrograph ()
 
boolean saveData (boolean notify)
 
void addFilterAppliedListener ()
 
void openHelpURl ()
 
abstract void resetMicrograph ()
 
void enableEdition (boolean enable)
 
void reloadImage ()
 
void initShapePane ()
 
boolean eraseAvailable ()
 
void setCanvasCursor ()
 
boolean linearModeAvailable ()
 
void showHideModeParameters ()
 
void displayZoom (double zoom)
 
void setTitle ()
 
void initColorPane (Color color)
 
void initStepPane ()
 
void initEraserSizePane ()
 
void initSizePane ()
 
void readSizeFromTextField ()
 
void executeScipionSaveAndExit ()
 
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-Additional Inherited Members

- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
static final int TOGGLE_LINEAR_MODE_KEY = KeyEvent.VK_L
 
static final int TOGGLE_ERASE_MODE_KEY = KeyEvent.VK_E
 
static final int NEXT_MICROGRAPH_KEY = KeyEvent.VK_R
 
static final int PREVIOUS_MICROGRAPH_KEY = KeyEvent.VK_W
 
static final int TOGGLE_MARKER_KEY = KeyEvent.VK_SPACE
 
static final int TOGGLE_NORMAL_MODE_KEY = KeyEvent.VK_P
 
static final int ERASE_ACTIVE = KeyEvent.VK_DELETE
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
ParticlesDialog particlesdialog
 
JMenuItem ijmi
 
JToggleButton circlechb
 
JToggleButton rectanglechb
 
JToggleButton centerchb
 
JLabel shapelb
 
JMenuItem savemi
 
JMenuItem hcontentsmi
 
JMenuItem pmi
 
JMenuItem exportmi
 
JMenu filtersmn
 
String activefilter
 
JPanel sizepn
 
JLabel sizelb
 
JFormattedTextField sizetf
 
JPanel eSizepn
 
JLabel eSizelb
 
JSpinner eSize
 
JMenu filemn
 
JMenuItem importmi
 
JButton colorbt
 
Color color
 
JPanel colorpn
 
JButton resetbt
 
JTable micrographstb
 
ImportParticlesJDialog importpjd = null
 
JMenuItem exitmi
 
JLabel positionlb
 
JToggleButton usezoombt
 
ButtonGroup modesgrp
 
JMenu helpmn
 
JButton savebt
 
JButton saveandexitbt
 
JToolBar tb
 
ResourceBundle bundle
 
String command
 
JButton closebt
 
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Detailed Description

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Definition at line 39 of file TiltPairPickerJFrame.java.

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Constructor & Destructor Documentation

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◆ TiltPairPickerJFrame()

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xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.TiltPairPickerJFrame (TiltPairPicker picker)
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Definition at line 59 of file TiltPairPickerJFrame.java.

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59  {
60  super(picker);
61  tppicker = picker;
62  initComponents();
63  setChanged(false);
64  }
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Member Function Documentation

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◆ applyFilter()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.applyFilter (String filter)
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Definition at line 390 of file TiltPairPickerJFrame.java.

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391  {
392  IJ.run(getMicrograph().getImagePlus(), filter, "");
393  IJ.run(getMicrograph().getTiltedMicrograph().getImagePlus(), filter, "");
394  }
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◆ changeShapes()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.changeShapes ()
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Definition at line 277 of file TiltPairPickerJFrame.java.

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277  {
278  canvas.repaint();
279  tiltedcanvas.repaint();
280  }
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◆ close()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.close ()
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Definition at line 375 of file TiltPairPickerJFrame.java.

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376  {
377  setVisible(false);
378  dispose();
379  if (getCanvas() != null)
380  {
381  getCanvas().getIw().close();
382  if(getTiltedCanvas() != null)
383  getTiltedCanvas().getIw().close();
384  }
385 
386  XmippApplication.removeInstance(false);
387 
388  }
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◆ drawAngles()

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boolean xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.drawAngles ()
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Definition at line 272 of file TiltPairPickerJFrame.java.

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272  {
273  return anglesmi.isSelected();
274  }
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void xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.enableEdition (boolean enable)
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Definition at line 101 of file TiltPairPickerJFrame.java.

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101  {
102  super.enableEdition(enable);
103  importffilesmi.setEnabled(enable);
104  }
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◆ getAvailableParticles()

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List<? extends ManualParticle> xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.getAvailableParticles ()
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Definition at line 264 of file TiltPairPickerJFrame.java.

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264  {
265  return getMicrograph().getParticles();
266  }
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Definition at line 247 of file TiltPairPickerJFrame.java.

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247  {
248  return canvas;
249  }
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Definition at line 259 of file TiltPairPickerJFrame.java.

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259  {
260  return tppicker.getColor();
261  }
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Definition at line 251 of file TiltPairPickerJFrame.java.

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251  {
252  return tppicker.getMicrograph();
253  }
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Definition at line 55 of file TiltPairPickerJFrame.java.

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55  {
56  return tppicker;
57  }
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Definition at line 255 of file TiltPairPickerJFrame.java.

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255  {
256  return (int) sizetf.getValue();
257  }
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Definition at line 268 of file TiltPairPickerJFrame.java.

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268  {
269  return tiltedcanvas;
270  }
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String xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.importParticles (Format format,
String dir,
String preffix,
String suffix,
float scale,
boolean invertx,
boolean inverty 
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Definition at line 364 of file TiltPairPickerJFrame.java.

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365  {
366  return importParticlesFromFolder(format, dir,preffix, suffix, scale, invertx, inverty);
367 
368  }
xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame.importParticlesFromFolder
String importParticlesFromFolder(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPickerJFrame.java:282
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Definition at line 347 of file TiltPairPickerJFrame.java.

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348  {
349 
350  getMicrograph().reset(tppicker);
351  String result = tppicker.importParticlesFromFiles(file1, file2, format,
352  getMicrograph(), scale, invertx, inverty);
353  tppicker.saveData(getMicrograph());
354 
355  getCanvas().repaint();
356  tiltedcanvas.repaint();
357  updateMicrographsModel();
358  updateSize(tppicker.getSize());
359  canvas.refreshActive(null);
360  return result;
361  }
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFiles
String importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPicker.java:351
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Definition at line 282 of file TiltPairPickerJFrame.java.

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283  {
284  String result = tppicker.importParticlesFromFolder(dir, format, preffix, suffix, scale,
285  invertx, inverty);
286  sizetf.setValue(tppicker.getSize());
287  getCanvas().repaint();
288  updateMicrographsModel(true);
289  getCanvas().refreshActive(null);
290  tiltedcanvas.repaint();
291  return result;
292  }
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFolder
String importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPicker.java:308
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Definition at line 106 of file TiltPairPickerJFrame.java.

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106  {
107  mb = new JMenuBar();
108 
109  filemn.add(importmi);
110  if (tppicker.getMode() != Mode.Manual)
111  importmi.setEnabled(false);
112  importffilesmi = new JMenuItem("Import coordinates from files...");
113  importffilesmi.addActionListener(new ActionListener() {
114 
115  @Override
116  public void actionPerformed(ActionEvent arg0) {
117  showImportFromFilesDialog();
118 
119  }
120  });
121  filemn.add(importffilesmi, 1);
122  filemn.add(exitmi);
123  // Setting menus
124  JMenu viewmn = new JMenu("View");
125  mb.add(filemn);
126  mb.add(filtersmn);
127  mb.add(viewmn);
128  mb.add(helpmn);
129 
130  anglesmi = new JCheckBoxMenuItem("Angles");
131  // anglesmi.setEnabled(false);
132  anglesmi.addActionListener(new ActionListener() {
133 
134  @Override
135  public void actionPerformed(ActionEvent e) {
136  if (anglesmi.isSelected()
137  && !tppicker.getMicrograph().anglesAvailable())
138  XmippDialog
139  .showInfo(TiltPairPickerJFrame.this,
140  "Angles will not be accurate until more than 10 pairs are registered");
141  canvas.repaint();
142  tiltedcanvas.repaint();
143  }
144  });
145  viewmn.add(anglesmi);
146  viewmn.add(pmi);
147  viewmn.add(ijmi);
148  }
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Definition at line 371 of file TiltPairPickerJFrame.java.

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371  {
372  return new TiltPairParticlesDialog(this);
373  }
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Definition at line 310 of file TiltPairPickerJFrame.java.

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310  {
311  if (this.micrographstb.getSelectedRow() == -1)
312  return;// Probably from fireTableDataChanged raised
313 
314  int index = tppicker.getMicrographIndex();
315 
316  if (index == micrographstb.getSelectedRow() && canvas != null && canvas.getIw().isVisible())
317  // micrograph open, no need to reopen
318  return;
319 
320  if (tppicker.isChanged()){
321  if (!saveData(false)) {
322  micrographstb.getSelectionModel().setSelectionInterval(index, index);
323  return;
324  }
325  }
326 
327  getMicrograph().releaseImage();
328 
329  index = micrographstb.getSelectedRow();
330  tppicker.setMicrograph(tppicker.getMicrographs().get(index));
331 
332  setChanged(false);
333  // anglesmi.setEnabled(getMicrograph().getAddedCount() >= 4);
334  initializeCanvas();
335 
336  pack();
337  if (particlesdialog != null)
338  loadParticles(false);
339  }
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Definition at line 303 of file TiltPairPickerJFrame.java.

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303  {
304  getCanvas().updateMicrograph();
305  getTiltedCanvas().updateMicrograph();
306 
307  }
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Definition at line 295 of file TiltPairPickerJFrame.java.

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295  {
296  tppicker.resetMicrograph(getMicrograph());
297  canvas.refreshActive(null);
298  updateMicrographsModel();
299 
300  }
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Definition at line 151 of file TiltPairPickerJFrame.java.

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151  {
152  super.setCanvasCursor();
153  tiltedcanvas.setCustomCursor();
154  }
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Definition at line 210 of file TiltPairPickerJFrame.java.

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210  {
211  tppicker.setChanged(changed);
212  savemi.setEnabled(changed);
213  savebt.setEnabled(changed);
214  }
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Definition at line 155 of file TiltPairPickerJFrame.java.

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155  {
156  if (importffilesjd == null)
157  importffilesjd = new ImportParticlesFromFilesTiltPairJDialog(this);
158  importffilesjd.showDialog();
159  }
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Definition at line 216 of file TiltPairPickerJFrame.java.

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216  {
217  if (particlesdialog != null)
218  loadParticles(false);
219  int index = tppicker.getMicrographIndex();
220  if (all)
221  micrographsmd.fireTableRowsUpdated(0,
222  micrographsmd.getRowCount() - 1);
223  else
224  micrographsmd.fireTableRowsUpdated(index, index);
225  micrographstb.setRowSelectionInterval(index, index);
226  upslb.setText(Integer.toString(tppicker.getUntiltedNumber()));
227  // anglesmi.setEnabled(tppicker.getMicrograph().getAddedCount() >= 4);
228  }
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Definition at line 205 of file TiltPairPickerJFrame.java.

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205  {
206  super.updateSize(size);
207  tiltedcanvas.repaint();
208  }
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The documentation for this class was generated from the following file: -
- -
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- Node34 [label="Panel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node35 -> Node31 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" sp" ,fontname="Helvetica"]; - Node35 [label="ScrollPane",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node21 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" sizepn\ncolorpn\neSizepn" ,fontname="Helvetica"]; - Node28 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" sizetf" ,fontname="Helvetica"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__coll__graph.md5 deleted file mode 100644 index 3b308307..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -951e0d0f69e1469d717049f2b63c9a6d \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__inherit__graph.dot deleted file mode 100644 index 8e51f460..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__inherit__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.gui.TiltPairPickerJFrame" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.tiltpair.gui.\lTiltPairPickerJFrame",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lParticlePickerJFrame",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerJFrame.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__inherit__graph.md5 deleted file mode 100644 index 76981ea8..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltPairPickerJFrame__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -d1454ef44dc7af78f22706ea75f4f897 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas-members.html deleted file mode 100644 index 1d8e3aac..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas-members.html +++ /dev/null @@ -1,159 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas, including all inherited members.

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activexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activemovedxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activestxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
adjustMagnification()xmipp.ij.commons.XmippImageCanvasinline
captureWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
continuousstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
customScrollSetup(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
dashedstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
doCustomPaint(Graphics2D g2)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinlineprotected
drawLine(double alpha, Graphics2D g2)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
erase(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
eraserCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
framexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
getActive()xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
getFrame()xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
getIw()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getLastParticle()xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinlineprotected
getMicrograph()xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
getParticlePicker()xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
getPreferredMagnification()xmipp.ij.commons.XmippImageCanvasinline
getTool()xmipp.ij.commons.XmippImageCanvasinline
getXOnImage(int x)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getYOnImage(int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
hasActiveParticle()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
isDragImage(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinlineprotected
isKeyPressed(int keyCode)xmipp.ij.commons.XmippImageCanvasinlineprotected
iwxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
keyPressed(KeyEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
keyReleased(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyTyped(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
linearCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
loadData(XmippIJWindow xiw)xmipp.ij.commons.XmippImageCanvasinline
manageActive(int x, int y)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinlineprotected
micrographxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
mouseDragged(MouseEvent e)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
mouseEntered(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseExited(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseMoved(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mousePressed(MouseEvent e)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
mousePressed(int x, int y)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
mouseReleased(MouseEvent e)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
mouseWheelMoved(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
moveActiveParticle(int x, int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
moveTo(PickerParticle p)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
offScreenX(int x)xmipp.ij.commons.XmippImageCanvasinline
offScreenY(int y)xmipp.ij.commons.XmippImageCanvasinline
paint(Graphics g)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
paintEraser(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
ParticlePickerCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
ParticlePickerCanvas(ParticlePickerJFrame frame, Micrograph micrograph)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
pickerxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
pickingCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
refresh()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
refreshActive(PickerParticle p)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
removeParticle(PickerParticle particleToRemove)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinlineprotected
xmipp::viewer::particlepicker::ParticlePickerCanvas.removeParticle(P particleToRemove)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
restoreWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setActiveMoved(boolean b)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setCustomCursor()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
setCustomCursor(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setInvertX(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setInvertY(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
setupScrollFromUntilted(int sx, int sy)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
syncWithUntiltedCanvas(int x, int y)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
thinContinuousStxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
TiltedMicrographCanvas(TiltPairPickerJFrame frame)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
updateMicrograph()xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
xmipp::viewer::particlepicker::ParticlePickerCanvas.updateMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
XmippImageCanvas(ImagePlus imp)xmipp.ij.commons.XmippImageCanvasinline
zoomIn(int sx, int sy)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
zoomOut(int sx, int sy)xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvasinline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas.html deleted file mode 100644 index efe9e868..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas.html +++ /dev/null @@ -1,984 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas:
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[legend]
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-Public Member Functions

 TiltedMicrographCanvas (TiltPairPickerJFrame frame)
 
TiltPairPickerJFrame getFrame ()
 
TiltedParticle getActive ()
 
TiltedMicrograph getMicrograph ()
 
TiltPairPicker getParticlePicker ()
 
void updateMicrograph ()
 
void zoomIn (int sx, int sy)
 
void zoomOut (int sx, int sy)
 
void refreshActive (PickerParticle p)
 
void mousePressed (MouseEvent e)
 
void mousePressed (int x, int y)
 
void syncWithUntiltedCanvas (int x, int y)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
void setupScrollFromUntilted (int sx, int sy)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
void setMicrograph (Micrograph m)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame, Micrograph micrograph)
 
void keyPressed (KeyEvent e)
 
void zoomIn (int sx, int sy)
 
void zoomOut (int sx, int sy)
 
boolean hasActiveParticle ()
 
ImageWindow getIw ()
 
void moveTo (PickerParticle p)
 
void mouseEntered (MouseEvent e)
 
void mouseExited (MouseEvent e)
 
void setCustomCursor ()
 
abstract void refreshActive (PickerParticle p)
 
abstract P getActive ()
 
abstract ParticlePickerJFrame getFrame ()
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void updateMicrograph ()
 
void updateMicrograph (Micrograph m)
 
abstract Micrograph getMicrograph ()
 
void paint (Graphics g)
 
void mouseMoved (MouseEvent e)
 
abstract ParticlePicker getParticlePicker ()
 
void mouseWheelMoved (MouseWheelEvent e)
 
- Public Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
Tool getTool ()
 
 XmippImageCanvas (ImagePlus imp)
 
void mousePressed (MouseEvent e)
 
void customScrollSetup (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void mouseWheelMoved (MouseWheelEvent e)
 
void mouseMoved (MouseEvent e)
 
int offScreenX (int x)
 
int offScreenY (int y)
 
void loadData (XmippIJWindow xiw)
 
double getPreferredMagnification ()
 
void adjustMagnification ()
 
void setInvertX (boolean value)
 
void setInvertY (boolean value)
 
void keyTyped (KeyEvent keyEvent)
 
void keyPressed (KeyEvent keyEvent)
 
void keyReleased (KeyEvent keyEvent)
 
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-Protected Member Functions

TiltedParticle getLastParticle ()
 
void removeParticle (PickerParticle particleToRemove)
 
void manageActive (int x, int y)
 
void doCustomPaint (Graphics2D g2)
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
void captureWindowSize ()
 
void restoreWindowSize ()
 
abstract P getLastParticle ()
 
abstract void manageActive (int x, int y)
 
void setActiveMoved (boolean b)
 
void refresh ()
 
void setCustomCursor (MouseEvent e)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)
 
void drawLine (double alpha, Graphics2D g2)
 
void erase (MouseEvent e)
 
abstract void removeParticle (P particleToRemove)
 
void moveActiveParticle (int x, int y)
 
abstract void doCustomPaint (Graphics2D g2)
 
void paintEraser (MouseEvent e)
 
- Protected Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
boolean isDragImage (MouseEvent e)
 
boolean isKeyPressed (int keyCode)
 
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-Additional Inherited Members

- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
static final BasicStroke dashedst = new BasicStroke(2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 10.0f, new float[] { 10.0f }, 0.0f)
 
static final BasicStroke continuousst = new BasicStroke(2.0f)
 
static final BasicStroke thinContinuousSt = new BasicStroke(1.5f)
 
static final BasicStroke activest = new BasicStroke(1.5f)
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
ParticlePickerJFrame frame
 
Micrograph micrograph
 
ParticlePicker picker
 
XmippImageWindow iw
 
Cursor eraserCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("eraserC.png").getImage(), new Point(3, 31), "Eraser")
 
Cursor linearCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("linearPickingC.png").getImage(), new Point(0, 0), "Linear")
 
Cursor pickingCursor = getPickingCursor(pickingCursorIndex)
 
P active
 
boolean activemoved
 
-

Detailed Description

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Definition at line 20 of file TiltedMicrographCanvas.java.

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Constructor & Destructor Documentation

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◆ TiltedMicrographCanvas()

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xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.TiltedMicrographCanvas (TiltPairPickerJFrame frame)
- 		-inline
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Definition at line 29 of file TiltedMicrographCanvas.java.

-
30  {
31  super(frame, frame.getMicrograph().getTiltedMicrograph());
32  this.um = frame.getMicrograph();
33  this.uc = (UntiltedMicrographCanvas) frame.getCanvas();
34 
35  }
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Member Function Documentation

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◆ doCustomPaint()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.doCustomPaint (Graphics2D g2)
- 		-inlineprotected
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Definition at line 134 of file TiltedMicrographCanvas.java.

-
135  {
136 
137  g2.setColor(getFrame().getColor());
138  List<TiltedParticle> particles = um.getTiltedMicrograph().getParticles();
139  for (TiltedParticle p : particles)
140  {
141  drawShape(g2, p, false);
142  }
143 
144  if (uc.getActiveTiltedParticle() != null)
145  {
146  g2.setColor(Color.red);
147  drawShape(g2, uc.getActive().getTiltedParticle(), true);
148  }
149  if (getFrame().drawAngles())
150  drawLine(Math.toRadians(um.getTiltedAngle()), g2);
151 
152  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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◆ getActive()

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TiltedParticle xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.getActive ()
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Definition at line 42 of file TiltedMicrographCanvas.java.

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42 { return uc.getActiveTiltedParticle();}
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◆ getFrame()

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TiltPairPickerJFrame xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.getFrame ()
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Definition at line 39 of file TiltedMicrographCanvas.java.

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39 {return (TiltPairPickerJFrame)frame;}
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◆ getLastParticle()

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TiltedParticle xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.getLastParticle ()
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Definition at line 48 of file TiltedMicrographCanvas.java.

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49  {
50  return uc.getLastParticle().getTiltedParticle();
51  }
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◆ getMicrograph()

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TiltedMicrograph xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.getMicrograph ()
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Definition at line 45 of file TiltedMicrographCanvas.java.

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45 {return (TiltedMicrograph)micrograph;}
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◆ getParticlePicker()

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TiltPairPicker xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.getParticlePicker ()
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Definition at line 54 of file TiltedMicrographCanvas.java.

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55  {
56  return (TiltPairPicker)picker;
57  }
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◆ manageActive()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.manageActive (int x,
int y 
)
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Definition at line 124 of file TiltedMicrographCanvas.java.

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125  {
126  if (!activemoved)
127  return;
128  if (uc.getActive().isAdded())
129  um.initAligner();
130  setActiveMoved(false);
131  }
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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.mouseDragged (MouseEvent e)
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Definition at line 230 of file TiltedMicrographCanvas.java.

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231  {
232  super.mouseDragged(e);
233 
234  if (frame.isPickingAvailable(e)){
235 
236  if (frame.isEraserMode(e))
237  {
238  eraseAndSync(e);
239  return;
240  }
241 
242  int x = super.offScreenX(e.getX());
243  int y = super.offScreenY(e.getY());
244 
245  if (uc.getActive().getTiltedParticle() != null && um.fits(x, y, getFrame().getParticleSize())){
246  setActiveMoved(true);
247  moveActiveParticle(x, y);
248  }
249 
250  frame.setChanged(true);
251  repaint();
252  }
253  }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.setChanged
abstract void setChanged(boolean changed)
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ mousePressed() [1/2]

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.mousePressed (MouseEvent e)
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Adds particle or updates its position if onpick. If ondeletepick removes particle. Considers owner for selection to the first particle containing point. Sets dragged if onpick

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Definition at line 161 of file TiltedMicrographCanvas.java.

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162  {
163  super.mousePressed(e);
164 
165  if (frame.isPickingAvailable(e))
166  {
167  if (frame.isEraserMode(e))
168  {
169  eraseAndSync(e);
170  return;
171  }
172 
173  int x = super.offScreenX(e.getX());
174  int y = super.offScreenY(e.getY());
175 
176  TiltedParticle p = um.getTiltedMicrograph().getParticle(x, y, getFrame().getParticleSize());
177  if (p != null)
178  {
179  if (SwingUtilities.isLeftMouseButton(e) && e.isShiftDown())
180  uc.removeParticle(p.getUntiltedParticle());
181  else if (SwingUtilities.isLeftMouseButton(e))
182  refreshActive(p);
183  }
184  else if (SwingUtilities.isLeftMouseButton(e) && um.fits(x, y, getFrame().getParticleSize()))
185  {
186  TiltedParticle tp = getMicrograph().getParticle(x, y, getParticlePicker().getSize());
187  //associate tilted particle for first cases
188  if (um.getAddedCount() < UntiltedMicrograph.getAlignmentMin())
189  {
190  UntiltedParticle uactive = uc.getActive();
191  if (uactive != null && uactive.getTiltedParticle() == null)
192  {
193  p = new TiltedParticle(x, y, uactive);
194  uactive.setTiltedParticle(p);
195  um.getTiltedMicrograph().addParticle(p);
196  um.addParticleToAligner(uactive, true);
197  frame.updateMicrographsModel();
198  }
199  }
200  else if(tp == null)//generate untilted particle
201  addParticle(x, y);
202  }
203  frame.setChanged(true);
204  repaint();
205  }
206  }
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xmipp.viewer.particlepicker.ParticlePickerJFrame.setChanged
abstract void setChanged(boolean changed)
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.addParticleToAligner
void addParticleToAligner(UntiltedParticle up, boolean recalculateAngles)
Definition: UntiltedMicrograph.java:90
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.mousePressed (int x,
int y 
)
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Definition at line 214 of file TiltedMicrographCanvas.java.

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215  {
216  setupScroll(x, y);
217  }
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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.mouseReleased (MouseEvent e)
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Definition at line 255 of file TiltedMicrographCanvas.java.

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256  {
257  super.mouseReleased(e);
258  if (frame.isPickingAvailable(e))
259  {
260  super.mouseReleased(e);
261  int x = super.offScreenX(e.getX());
262  int y = super.offScreenY(e.getY());
263  manageActive(x, y);
264  }
265  }
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◆ refreshActive()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.refreshActive (PickerParticle p)
- 		-inline
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Definition at line 116 of file TiltedMicrographCanvas.java.

-
117  {
118  if (p != null){
119  active = p;
120  frame.getCanvas().refreshActive(((TiltedParticle) p).getUntiltedParticle());
121  }
122  }
- -
xmipp.viewer.particlepicker.ParticlePickerJFrame.getCanvas
abstract ParticlePickerCanvas getCanvas()
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xmipp.viewer.particlepicker.ParticlePickerCanvas.refreshActive
abstract void refreshActive(PickerParticle p)
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◆ removeParticle()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.removeParticle (PickerParticle particleToRemove)
- 		-inlineprotected
-
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Definition at line 108 of file TiltedMicrographCanvas.java.

-
108  {
109 
110  TiltedParticle toRemove = (TiltedParticle) particleToRemove;
111  uc.removeParticle(toRemove.getUntiltedParticle());
112 
113  }
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◆ setupScrollFromUntilted()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.setupScrollFromUntilted (int sx,
int sy 
)
- 		-inline
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Definition at line 267 of file TiltedMicrographCanvas.java.

-
267  {
268 
269  // Calculate the offset coordinates for sx and sy
270  int ox = offScreenX(sx);
271  int oy = offScreenY(sy);
272 
273  setupScroll(ox, oy);
274 
275  }
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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.syncWithUntiltedCanvas (int x,
int y 
)
- 		-inline
-
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Syncs tilted micrograph with untilted

- -

Definition at line 222 of file TiltedMicrographCanvas.java.

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223  {
224 
225  scroll(x,y);
226 
227  }
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◆ updateMicrograph()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.updateMicrograph ()
- 		-inline
-
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Definition at line 60 of file TiltedMicrographCanvas.java.

-
61  {
62  um = getFrame().getMicrograph();
63  TiltedMicrograph m = getFrame().getMicrograph().getTiltedMicrograph();
64  updateMicrograph(m);
65  }
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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.zoomIn (int sx,
int sy 
)
- 		-inline
-
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Definition at line 67 of file TiltedMicrographCanvas.java.

-
68  {
69  super.zoomIn(sx, sy);
70 
71  if(getParticlePicker().getZoom() != uc.getMagnification())
72  uc.zoomIn(sx, sy);
73  }
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◆ zoomOut()

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void xmipp.viewer.particlepicker.tiltpair.gui.TiltedMicrographCanvas.zoomOut (int sx,
int sy 
)
- 		-inline
-
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Definition at line 75 of file TiltedMicrographCanvas.java.

-
76  {
77  super.zoomOut(sx, sy);
78 
79  if(getParticlePicker().getZoom() != uc.getMagnification())
80  uc.zoomOut(sx, sy);
81  }
- -
-
-
-
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- Node4 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="MouseWheelListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="KeyListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas__inherit__graph.md5 deleted file mode 100644 index e9a2831d..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1TiltedMicrographCanvas__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -1b3b1b73227e819b92c8e21f5ab8aa09 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1UntiltedMicrographCanvas-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1UntiltedMicrographCanvas-members.html deleted file mode 100644 index e8af5242..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1UntiltedMicrographCanvas-members.html +++ /dev/null @@ -1,157 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas, including all inherited members.

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activexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activemovedxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activestxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
adjustMagnification()xmipp.ij.commons.XmippImageCanvasinline
captureWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
continuousstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
customScrollSetup(MouseEvent e)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
dashedstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
doCustomPaint(Graphics2D g2)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinlineprotected
drawLine(double alpha, Graphics2D g2)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
erase(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
eraserCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
framexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
getActive()xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
getActiveTiltedParticle()xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
getFrame()xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
getIw()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getLastParticle()xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinlineprotected
getMicrograph()xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
getParticlePicker()xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
getPreferredMagnification()xmipp.ij.commons.XmippImageCanvasinline
getTool()xmipp.ij.commons.XmippImageCanvasinline
getXOnImage(int x)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getYOnImage(int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
hasActiveParticle()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
isDragImage(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinlineprotected
isKeyPressed(int keyCode)xmipp.ij.commons.XmippImageCanvasinlineprotected
iwxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
keyPressed(KeyEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
keyReleased(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyTyped(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
linearCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
loadData(XmippIJWindow xiw)xmipp.ij.commons.XmippImageCanvasinline
manageActive(int x, int y)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinlineprotected
micrographxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
mouseDragged(MouseEvent e)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
mouseEntered(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseExited(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseMoved(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mousePressed(MouseEvent e)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
mouseReleased(MouseEvent e)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
mouseWheelMoved(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
moveActiveParticle(int x, int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
moveTo(PickerParticle p)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
offScreenX(int x)xmipp.ij.commons.XmippImageCanvasinline
offScreenY(int y)xmipp.ij.commons.XmippImageCanvasinline
paint(Graphics g)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
paintEraser(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
ParticlePickerCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
ParticlePickerCanvas(ParticlePickerJFrame frame, Micrograph micrograph)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
pickerxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
pickingCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
refresh()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
refreshActive(PickerParticle up)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
removeParticle(PickerParticle particleToRemove)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinlineprotected
xmipp::viewer::particlepicker::ParticlePickerCanvas.removeParticle(P particleToRemove)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
restoreWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setActiveMoved(boolean b)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setCustomCursor()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
setCustomCursor(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setInvertX(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setInvertY(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
thinContinuousStxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
UntiltedMicrographCanvas(TiltPairPickerJFrame frame)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
updateMicrograph()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
updateMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
XmippImageCanvas(ImagePlus imp)xmipp.ij.commons.XmippImageCanvasinline
zoomIn(int sx, int sy)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
zoomOut(int sx, int sy)xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvasinline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1UntiltedMicrographCanvas.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1UntiltedMicrographCanvas.html deleted file mode 100644 index aa39654e..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1gui_1_1UntiltedMicrographCanvas.html +++ /dev/null @@ -1,902 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas:
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-Public Member Functions

 UntiltedMicrographCanvas (TiltPairPickerJFrame frame)
 
TiltPairPickerJFrame getFrame ()
 
UntiltedParticle getActive ()
 
UntiltedMicrograph getMicrograph ()
 
TiltedParticle getActiveTiltedParticle ()
 
TiltPairPicker getParticlePicker ()
 
void zoomIn (int sx, int sy)
 
void zoomOut (int sx, int sy)
 
void refreshActive (PickerParticle up)
 
void customScrollSetup (MouseEvent e)
 
void mousePressed (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
void setMicrograph (Micrograph m)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame, Micrograph micrograph)
 
void keyPressed (KeyEvent e)
 
void zoomIn (int sx, int sy)
 
void zoomOut (int sx, int sy)
 
boolean hasActiveParticle ()
 
ImageWindow getIw ()
 
void moveTo (PickerParticle p)
 
void mouseEntered (MouseEvent e)
 
void mouseExited (MouseEvent e)
 
void setCustomCursor ()
 
abstract void refreshActive (PickerParticle p)
 
abstract P getActive ()
 
abstract ParticlePickerJFrame getFrame ()
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void updateMicrograph ()
 
void updateMicrograph (Micrograph m)
 
abstract Micrograph getMicrograph ()
 
void paint (Graphics g)
 
void mouseMoved (MouseEvent e)
 
abstract ParticlePicker getParticlePicker ()
 
void mouseWheelMoved (MouseWheelEvent e)
 
- Public Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
Tool getTool ()
 
 XmippImageCanvas (ImagePlus imp)
 
void mousePressed (MouseEvent e)
 
void customScrollSetup (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void mouseWheelMoved (MouseWheelEvent e)
 
void mouseMoved (MouseEvent e)
 
int offScreenX (int x)
 
int offScreenY (int y)
 
void loadData (XmippIJWindow xiw)
 
double getPreferredMagnification ()
 
void adjustMagnification ()
 
void setInvertX (boolean value)
 
void setInvertY (boolean value)
 
void keyTyped (KeyEvent keyEvent)
 
void keyPressed (KeyEvent keyEvent)
 
void keyReleased (KeyEvent keyEvent)
 
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-Protected Member Functions

UntiltedParticle getLastParticle ()
 
void removeParticle (PickerParticle particleToRemove)
 
void manageActive (int x, int y)
 
void doCustomPaint (Graphics2D g2)
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
void captureWindowSize ()
 
void restoreWindowSize ()
 
abstract P getLastParticle ()
 
abstract void manageActive (int x, int y)
 
void setActiveMoved (boolean b)
 
void refresh ()
 
void setCustomCursor (MouseEvent e)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)
 
void drawLine (double alpha, Graphics2D g2)
 
void erase (MouseEvent e)
 
abstract void removeParticle (P particleToRemove)
 
void moveActiveParticle (int x, int y)
 
abstract void doCustomPaint (Graphics2D g2)
 
void paintEraser (MouseEvent e)
 
- Protected Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
boolean isDragImage (MouseEvent e)
 
boolean isKeyPressed (int keyCode)
 
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-Additional Inherited Members

- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
static final BasicStroke dashedst = new BasicStroke(2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 10.0f, new float[] { 10.0f }, 0.0f)
 
static final BasicStroke continuousst = new BasicStroke(2.0f)
 
static final BasicStroke thinContinuousSt = new BasicStroke(1.5f)
 
static final BasicStroke activest = new BasicStroke(1.5f)
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
ParticlePickerJFrame frame
 
Micrograph micrograph
 
ParticlePicker picker
 
XmippImageWindow iw
 
Cursor eraserCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("eraserC.png").getImage(), new Point(3, 31), "Eraser")
 
Cursor linearCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("linearPickingC.png").getImage(), new Point(0, 0), "Linear")
 
Cursor pickingCursor = getPickingCursor(pickingCursorIndex)
 
P active
 
boolean activemoved
 
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Detailed Description

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Definition at line 21 of file UntiltedMicrographCanvas.java.

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Constructor & Destructor Documentation

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◆ UntiltedMicrographCanvas()

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xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.UntiltedMicrographCanvas (TiltPairPickerJFrame frame)
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Definition at line 24 of file UntiltedMicrographCanvas.java.

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25  {
26  super(frame);
27 
28  }
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Member Function Documentation

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◆ customScrollSetup()

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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.customScrollSetup (MouseEvent e)
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Definition at line 192 of file UntiltedMicrographCanvas.java.

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192  {
193 
194  super.customScrollSetup(e);
195  getFrame().getTiltedCanvas().setupScrollFromUntilted(e.getX(),e.getY());
196 
197  }
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◆ doCustomPaint()

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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.doCustomPaint (Graphics2D g2)
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Definition at line 199 of file UntiltedMicrographCanvas.java.

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200  {
201  g2.setColor(getFrame().getColor());
202  for (ManualParticle p : getMicrograph().getParticles())
203  {
204  drawShape(g2, p, false);
205  }
206  if (active != null)
207  {
208  g2.setColor(Color.red);
209  drawShape(g2, getActive(), true);
210  }
211  if (getFrame().drawAngles())
212  drawLine(Math.toRadians(getMicrograph().getUntiltedAngle()), g2);
213 
214  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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◆ getActive()

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UntiltedParticle xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.getActive ()
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Definition at line 38 of file UntiltedMicrographCanvas.java.

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39  {
40  return (UntiltedParticle) active;
41  }
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◆ getActiveTiltedParticle()

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TiltedParticle xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.getActiveTiltedParticle ()
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Definition at line 58 of file UntiltedMicrographCanvas.java.

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59  {
60  if (hasActiveParticle()) {
61  return ((UntiltedParticle) active).getTiltedParticle();
62  }else {
63  return null;
64  }
65  }
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◆ getFrame()

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TiltPairPickerJFrame xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.getFrame ()
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Definition at line 32 of file UntiltedMicrographCanvas.java.

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33  {
34  return (TiltPairPickerJFrame)frame;
35  }
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◆ getLastParticle()

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UntiltedParticle xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.getLastParticle ()
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Definition at line 49 of file UntiltedMicrographCanvas.java.

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50  {
51  if (getMicrograph().getParticles().isEmpty())
52  return null;
53  return getMicrograph().getParticles().get(getMicrograph().getParticles().size() - 1);
54  }
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◆ getMicrograph()

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UntiltedMicrograph xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.getMicrograph ()
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Definition at line 44 of file UntiltedMicrographCanvas.java.

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45  {
46  return (UntiltedMicrograph)micrograph;
47  }
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◆ getParticlePicker()

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Definition at line 70 of file UntiltedMicrographCanvas.java.

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71  {
72  return (TiltPairPicker)picker;
73  }
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◆ manageActive()

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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.manageActive (int x,
int y 
)
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Definition at line 167 of file UntiltedMicrographCanvas.java.

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168  {
169 
170  UntiltedParticle activeParticle = getActive();
171 
172  if (!activemoved)
173  return;
174 
175  if (micrograph.fits(x, y, getFrame().getParticleSize()))
176  {
177  moveActiveParticle(x, y);
178 
179  }
180  if (activeParticle.isAdded())// added particle on matrix has been moved. Matrix
181  // changed and tilted particle has to be
182  // recalculated
183  {
184  activeParticle.setAdded(false);
185  getMicrograph().initAligner();
186  }
187  getFrame().getTiltedCanvas().repaint();
188  setActiveMoved(false);
189  }
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ mouseDragged()

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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.mouseDragged (MouseEvent e)
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Definition at line 274 of file UntiltedMicrographCanvas.java.

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275  {
276  super.mouseDragged(e);
277 
278  // Sync screen view with tilted canvas
279  if (isDragImage(e)){
280  getFrame().getTiltedCanvas().syncWithUntiltedCanvas(e.getX(),e.getY());
281  return;
282  }
283 
284  if (frame.isPickingAvailable(e)){
285 
286  if (frame.isEraserMode(e))
287  {
288  erase(e);
289  return;
290  }
291 
292  int x = super.offScreenX(e.getX());
293  int y = super.offScreenY(e.getY());
294 
295  if (active != null && micrograph.fits(x, y, getFrame().getParticleSize())){
296  setActiveMoved(true);
297  moveActiveParticle(x, y);
298  }
299  frame.setChanged(true);
300  repaint();
301  }
302 
303  }
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abstract void setChanged(boolean changed)
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ mousePressed()

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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.mousePressed (MouseEvent e)
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Adds particle or updates its position if onpick. If ondeletepick removes particle. Considers owner for selection to the first particle containing point. Sets dragged if onpick

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Definition at line 224 of file UntiltedMicrographCanvas.java.

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225  {
226  super.mousePressed(e);
227  if (frame.isPickingAvailable(e))
228  {
229 
230  if (frame.isEraserMode(e))
231  {
232  erase(e);
233  getFrame().getTiltedCanvas().repaint();
234  return;
235 
236  }
237 
238  UntiltedParticle activeParticle = getActive();
239 
240  if (!isDragImage(e)){
241 
242  int x = super.offScreenX(e.getX());
243  int y = super.offScreenY(e.getY());
244 
245  if (active != null && !activeParticle.isAdded() && activeParticle.getTiltedParticle() != null)
246  getMicrograph().addParticleToAligner(activeParticle, true);
247 
248  UntiltedParticle p = getMicrograph().getParticle(x, y, getParticlePicker().getSize());
249 
250  if(p == null && activeParticle != null && activeParticle.contains(x, y))
251  p = activeParticle;
252  if (p != null)
253  {
254  if (SwingUtilities.isLeftMouseButton(e) && e.isShiftDown())
255  removeParticle(p);
256  else if (SwingUtilities.isLeftMouseButton(e))
257  refreshActive(p);
258  }
259  else if (SwingUtilities.isLeftMouseButton(e))
260  {
261  if (micrograph.fits(x, y, getFrame().getParticleSize()))
262  addParticle(x, y);
263  else
264  XmippMessageDialog.showInfo(frame, XmippMessage.getOutOfBoundsMsg(String
265  .format("Particle centered at %s, %s with size %s", x, y, frame.getParticlePicker().getSize())));
266  }
267  }
268  }
269  }
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.addParticleToAligner
void addParticleToAligner(UntiltedParticle up, boolean recalculateAngles)
Definition: UntiltedMicrograph.java:90
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ mouseReleased()

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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.mouseReleased (MouseEvent e)
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Definition at line 306 of file UntiltedMicrographCanvas.java.

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307  {
308  super.mouseReleased(e);
309  if (frame.isPickingAvailable(e))
310  {
311  int x = super.offScreenX(e.getX());
312  int y = super.offScreenY(e.getY());
313  manageActive(x, y);
314  }
315 
316  }
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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.refreshActive (PickerParticle up)
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Definition at line 145 of file UntiltedMicrographCanvas.java.

-
146  {
147 
148  if (up != null)
149  {
150  active = up;
151  TiltedParticle tp = getActive().getTiltedParticle();
152  if (tp != null)
153  {
154  int x = getFrame().getTiltedCanvas().getXOnImage(tp.getX());
155  int y = getFrame().getTiltedCanvas().getYOnImage(tp.getY());
156 
157  if (!micrograph.fits(x, y, getParticlePicker().getSize()))
158  getFrame().getTiltedCanvas().moveTo(tp);
159  }
160  }
161  else
162  active = null;
163  repaint();
164  getFrame().getTiltedCanvas().repaint();
165  }
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ removeParticle()

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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.removeParticle (PickerParticle particleToRemove)
- 		-inlineprotected
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Definition at line 124 of file UntiltedMicrographCanvas.java.

-
124  {
125 
126  UntiltedParticle toRemove = (UntiltedParticle) particleToRemove;
127 
128  getMicrograph().removeParticle(toRemove);
129 
130  if (active != null && active.equals(toRemove))
131  {
132  if (!getMicrograph().getParticles().isEmpty())
133  refreshActive(getMicrograph().getParticles().get(getMicrograph().getParticles().size() - 1));
134  else
135  refreshActive(null);
136  }
137 
138 
139  if (toRemove.isAdded())
140  getMicrograph().initAligner();
141  refresh();
142  getFrame().getTiltedCanvas().repaint();
143  }
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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.zoomIn (int sx,
int sy 
)
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Definition at line 77 of file UntiltedMicrographCanvas.java.

-
78  {
79  super.zoomIn(sx, sy);
80 
81  if(getParticlePicker().getZoom() != getFrame().getTiltedCanvas().getMagnification())
82  getFrame().getTiltedCanvas().zoomIn(sx, sy);
83  }
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void xmipp.viewer.particlepicker.tiltpair.gui.UntiltedMicrographCanvas.zoomOut (int sx,
int sy 
)
- 		-inline
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Definition at line 85 of file UntiltedMicrographCanvas.java.

-
86  {
87  super.zoomOut(sx, sy);
88 
89  if(getParticlePicker().getZoom() != getFrame().getTiltedCanvas().getMagnification())
90  getFrame().getTiltedCanvas().zoomOut(sx, sy);
91  }
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- -
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- node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.tiltpair.gui.\lUntiltedMicrographCanvas",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lParticlePickerCanvas\< P\l extends PickerParticle \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerCanvas.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.ij.commons.XmippImage\lCanvas",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1XmippImageCanvas.html"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ImageCanvas",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; 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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker, including all inherited members.

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addFilter(String command, String options)xmipp.viewer.particlepicker.ParticlePickerinline
blockxmipp.viewer.particlepicker.ParticlePickerprotected
changedxmipp.viewer.particlepicker.ParticlePickerprotected
colorxmipp.viewer.particlepicker.ParticlePickerprotected
colorsxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
configfilexmipp.viewer.particlepicker.ParticlePickerprotected
detectFileFormat(String path)xmipp.viewer.particlepicker.ParticlePickerinline
detectFormat(String path, String preffix, StringBuffer suffix)xmipp.viewer.particlepicker.ParticlePickerinline
emextensionsxmipp.viewer.particlepicker.ParticlePicker
fillParticlesMdFromEmanFile(String file, Micrograph m, MetaData md, float scale)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromRelionFile(String file, Micrograph m, MetaData md)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromXmipp301File(String file, Micrograph m, MetaData md)xmipp.viewer.particlepicker.ParticlePickerinline
filtersxmipp.viewer.particlepicker.ParticlePickerprotected
getColor()xmipp.viewer.particlepicker.ParticlePickerinline
getColor(String name)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getCoordsFiles(String folder)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getDefaultSize()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getExportFile(String path)xmipp.viewer.particlepicker.ParticlePickerinline
getFilters()xmipp.viewer.particlepicker.ParticlePickerinline
getLogger()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getMicrograph()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
xmipp::viewer::particlepicker::ParticlePicker.getMicrograph(String name)xmipp.viewer.particlepicker.ParticlePickerinline
getMicrographIndex()xmipp.viewer.particlepicker.ParticlePickerinline
getMicrographs()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
getMicrographsSelFile()xmipp.viewer.particlepicker.ParticlePickerinline
getMode()xmipp.viewer.particlepicker.ParticlePickerinline
getNextColor()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getNextFreeMicrograph()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
getOutputDir()xmipp.viewer.particlepicker.ParticlePickerinline
getOutputPath(String file)xmipp.viewer.particlepicker.ParticlePickerinline
getParams()xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesAutoBlock(String file)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesAutoBlock(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesBlock(Format f, String file)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesBlock(String file)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesBlock(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesBlockName(Format f)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesCount()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
getPicker()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getPort()xmipp.viewer.particlepicker.ParticlePickerinline
getPosFileFromXmipp24Project(String projectdir, String mname)xmipp.viewer.particlepicker.ParticlePickerinline
getRadius()xmipp.viewer.particlepicker.ParticlePickerinline
getSize()xmipp.viewer.particlepicker.ParticlePickerinline
getTemplatesFile(String name)xmipp.viewer.particlepicker.ParticlePickerinline
getTiltedNumber()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
getUntiltedNumber()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
getZoom()xmipp.viewer.particlepicker.ParticlePickerinline
importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty, MetaData uMd, MetaData tMd)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
importSize(String path, Format f, double scale)xmipp.viewer.particlepicker.ParticlePickerinline
isChanged()xmipp.viewer.particlepicker.ParticlePickerinline
isFilterAdded(String filter)xmipp.viewer.particlepicker.ParticlePickerinline
isSaved()xmipp.viewer.particlepicker.ParticlePickerinline
isScipionSave()xmipp.viewer.particlepicker.ParticlePickerinline
isShowDeleted()xmipp.viewer.particlepicker.ParticlePickerinline
isValidSize(JFrame parent, int size)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
loadConfig()xmipp.viewer.particlepicker.ParticlePickerinline
loadData()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
loadEmptyMicrographs()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
loadMicrographData(UntiltedMicrograph um, String uPosFile, String tPosFile)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
loadMicrographParticles(UntiltedMicrograph micrograph)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
loadMicrographParticles(UntiltedMicrograph um, MetaData uMd, MetaData tMd)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
loggerxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
macrosfilexmipp.viewer.particlepicker.ParticlePickerprotected
micrographsxmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerprotected
modexmipp.viewer.particlepicker.ParticlePickerprotected
nextcolorxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
outputdirxmipp.viewer.particlepicker.ParticlePickerprotected
paramsxmipp.viewer.particlepicker.ParticlePickerprotected
ParticlePicker(String selfile, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
ParticlePicker(String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
ParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
particlesAutoBlockxmipp.viewer.particlepicker.ParticlePickerstatic
pickerxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
resetMicrograph(UntiltedMicrograph m)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
runXmippProgram(String program, String args)xmipp.viewer.particlepicker.ParticlePickerinline
saveConfig(MetaData md, long id)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinlineprotected
xmipp::viewer::particlepicker::ParticlePicker.saveConfig()xmipp.viewer.particlepicker.ParticlePickerinline
savedxmipp.viewer.particlepicker.ParticlePickerprotected
saveData()xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
saveData(Micrograph m)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
saveMicrographAngles(UntiltedMicrograph m)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
selfilexmipp.viewer.particlepicker.ParticlePickerprotected
setChanged(boolean changed)xmipp.viewer.particlepicker.ParticlePickerinline
setColor(Color color)xmipp.viewer.particlepicker.ParticlePickerinline
setFilterOptions(String command, String options)xmipp.viewer.particlepicker.ParticlePickerinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
setSaved(boolean saved)xmipp.viewer.particlepicker.ParticlePickerinline
setShowDeleted(boolean showDeleted)xmipp.viewer.particlepicker.ParticlePickerinline
setSize(int size)xmipp.viewer.particlepicker.ParticlePickerinline
setZoom(double zoom)xmipp.viewer.particlepicker.ParticlePickerinline
sizexmipp.viewer.particlepicker.ParticlePickerprotected
sizemaxxmipp.viewer.particlepicker.ParticlePickerstatic
TiltPairPicker(String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.tiltpair.model.TiltPairPickerinline
toggleShowDeleted()xmipp.viewer.particlepicker.ParticlePickerinline
updateFilters(String command)xmipp.viewer.particlepicker.ParticlePickerinline
validateState(Mode state)xmipp.viewer.particlepicker.ParticlePickerinline
xmippsmoothfilterxmipp.viewer.particlepicker.ParticlePickerstatic
zoomxmipp.viewer.particlepicker.ParticlePickerprotected
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker Class Reference
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-Public Member Functions

 TiltPairPicker (String selfile, String outputdir, ParticlePickerParams params)
 
void loadData ()
 
void loadEmptyMicrographs ()
 
void loadMicrographParticles (UntiltedMicrograph micrograph)
 
String loadMicrographParticles (UntiltedMicrograph um, MetaData uMd, MetaData tMd)
 
void loadMicrographData (UntiltedMicrograph um, String uPosFile, String tPosFile)
 
int getNextFreeMicrograph ()
 
List< UntiltedMicrograph > getMicrographs ()
 
void resetMicrograph (UntiltedMicrograph m)
 
int getUntiltedNumber ()
 
int getTiltedNumber ()
 
void saveData ()
 
void saveMicrographAngles (UntiltedMicrograph m)
 
void saveData (Micrograph m)
 
String importParticlesFromFolder (String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
String importParticlesFromFiles (String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty)
 
String importParticlesFromFiles (String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty, MetaData uMd, MetaData tMd)
 
UntiltedMicrograph getMicrograph ()
 
void setMicrograph (Micrograph m)
 
boolean isValidSize (JFrame parent, int size)
 
int getParticlesCount ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
boolean isShowDeleted ()
 
void setShowDeleted (boolean showDeleted)
 
void toggleShowDeleted ()
 
double getZoom ()
 
void setZoom (double zoom)
 
ParticlePickerParams getParams ()
 
String getParticlesAutoBlock (String file)
 
String getParticlesBlock (Micrograph m)
 
String getParticlesAutoBlock (Micrograph m)
 
 ParticlePicker (String selfile, ParticlePickerParams params)
 
 ParticlePicker (String selfile, String outputdir, ParticlePickerParams params)
 
 ParticlePicker (String block, String selfile, String outputdir, ParticlePickerParams params)
 
void loadConfig ()
 
synchronized void saveConfig ()
 
Format detectFileFormat (String path)
 
Format detectFormat (String path, String preffix, StringBuffer suffix)
 
String getExportFile (String path)
 
String getPosFileFromXmipp24Project (String projectdir, String mname)
 
abstract void loadEmptyMicrographs ()
 
void updateFilters (String command)
 
boolean isFilterAdded (String filter)
 
String getMicrographsSelFile ()
 
void setFilterOptions (String command, String options)
 
void addFilter (String command, String options)
 
List< IJCommand > getFilters ()
 
void setChanged (boolean changed)
 
boolean isChanged ()
 
boolean isSaved ()
 
void setSaved (boolean saved)
 
Mode getMode ()
 
String getOutputPath (String file)
 
String getOutputDir ()
 
abstract List<? extends Micrograph > getMicrographs ()
 
int getMicrographIndex ()
 
String getTemplatesFile (String name)
 
Mode validateState (Mode state)
 
void saveData ()
 
abstract void saveData (Micrograph m)
 
Micrograph getMicrograph (String name)
 
void fillParticlesMdFromFile (String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
 
void fillParticlesMdFromXmipp301File (String file, Micrograph m, MetaData md)
 
void fillParticlesMdFromRelionFile (String file, Micrograph m, MetaData md)
 
void fillParticlesMdFromEmanFile (String file, Micrograph m, MetaData md, float scale)
 
void runXmippProgram (String program, String args)
 
abstract Micrograph getMicrograph ()
 
abstract void setMicrograph (Micrograph m)
 
abstract boolean isValidSize (JFrame parent, int size)
 
int getSize ()
 
void setSize (int size)
 
Color getColor ()
 
void setColor (Color color)
 
int getRadius ()
 
void importSize (String path, Format f, double scale)
 
boolean isScipionSave ()
 
abstract int getParticlesCount ()
 
Integer getPort ()
 
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-Protected Member Functions

synchronized void saveConfig (MetaData md, long id)
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
void saveConfig (MetaData md, long id)
 
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-Protected Attributes

List< UntiltedMicrograph > micrographs
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
String macrosfile
 
String outputdir = "."
 
boolean changed
 
boolean saved
 
Mode mode
 
List< IJCommand > filters
 
String selfile
 
String configfile
 
Color color
 
int size
 
String block
 
ParticlePickerParams params
 
double zoom = -1.f
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
static Color getNextColor ()
 
static String getParticlesBlock (Format f, String file)
 
static String getParticlesBlockName (Format f)
 
static String getParticlesBlock (String file)
 
static Logger getLogger ()
 
static Color getColor (String name)
 
static int getDefaultSize ()
 
static File [] getCoordsFiles (String folder)
 
static ParticlePicker getPicker ()
 
- Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
final HashMap< Format, String > emextensions
 
- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
static final String xmippsmoothfilter = "Xmipp Smooth Filter"
 
static final String particlesAutoBlock = "particles_auto"
 
static final int sizemax = 2000
 
- Static Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
static Logger logger
 
static Color [] colors = new Color[]{Color.GREEN, Color.BLUE, Color.CYAN, Color.MAGENTA, Color.ORANGE, Color.PINK, Color.YELLOW}
 
static int nextcolor
 
static ParticlePicker picker
 
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Detailed Description

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Business object for Tilt Pair Picker GUI. Inherits from ParticlePicker

Author
airen
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Definition at line 26 of file TiltPairPicker.java.

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Constructor & Destructor Documentation

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◆ TiltPairPicker()

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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.TiltPairPicker (String selfile,
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ParticlePickerParams params 
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Definition at line 32 of file TiltPairPicker.java.

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33  {
34  super(selfile, outputdir, params);
35 
36  for (UntiltedMicrograph um : micrographs)
37  loadMicrographParticles(um);
38 
39  }
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographParticles
void loadMicrographParticles(UntiltedMicrograph micrograph)
Definition: TiltPairPicker.java:97
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Member Function Documentation

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◆ getMicrograph()

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Definition at line 373 of file TiltPairPicker.java.

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374  {
375  return micrograph;
376  }
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Definition at line 182 of file TiltPairPicker.java.

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183  {
184  return micrographs;
185  }
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Definition at line 170 of file TiltPairPicker.java.

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171  {
172  int count = 0;
173  for (UntiltedMicrograph m : micrographs)
174  {
175  if (m.hasData())
176  return count;
177  count++;
178  }
179  return -1;
180  }
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Definition at line 408 of file TiltPairPicker.java.

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408  {
409  return getUntiltedNumber();
410 
411  }
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Definition at line 201 of file TiltPairPicker.java.

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202  {
203  int count = 0;
204  for (UntiltedMicrograph um : micrographs)
205  count += um.getTiltedMicrograph().getParticles().size();
206  return count;
207  }
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Definition at line 193 of file TiltPairPicker.java.

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194  {
195  int count = 0;
196  for (UntiltedMicrograph um : micrographs)
197  count += um.getParticles().size();
198  return count;
199  }
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String xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFiles (String uPath,
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Definition at line 351 of file TiltPairPicker.java.

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352  {
353  MetaData uMd = new MetaData();
354  MetaData tMd = new MetaData();
355  String result = importParticlesFromFiles(uPath, tPath, f, um, scale, invertx, inverty, uMd, tMd);
356  uMd.destroy();
357  tMd.destroy();
358  return result;
359 
360  }
xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFiles
String importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPicker.java:351
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String xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFiles (String uPath,
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Format f,
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Definition at line 362 of file TiltPairPicker.java.

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363  {
364  fillParticlesMdFromFile(uPath, f, um, uMd, scale, invertx, inverty);
365  fillParticlesMdFromFile(tPath, f, um.getTiltedMicrograph(), tMd, scale, invertx, inverty);
366  String result = loadMicrographParticles(um, uMd, tMd);
367 
368  return result;
369  }// function importParticlesFromFiles
xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographParticles
void loadMicrographParticles(UntiltedMicrograph micrograph)
Definition: TiltPairPicker.java:97
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xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromFile
void fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
Definition: ParticlePicker.java:497
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String xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.importParticlesFromFolder (String path,
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String suffix,
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Definition at line 308 of file TiltPairPicker.java.

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309  {
310  if (f == Format.Auto)
311  {
312  StringBuffer suffixPtr = new StringBuffer(suffix);
313  f = detectFormat(path, preffix, suffixPtr);
314  suffix = suffixPtr.toString();
315  }
316  if (f == Format.None)
317  throw new IllegalArgumentException("Unable to detect format");
318  System.out.println(suffix);
319  String uFn, tFn, file;
320  String result = "";
321  importSize(path, f, scale);
322 
323  MetaData uMd = new MetaData();
324  MetaData tMd = new MetaData();
325  for(UntiltedMicrograph m: micrographs)
326  {
327  uFn = null; tFn = null;
328  file = Filename.join(path, preffix + m.getName() + suffix);
329  if(new File(file).exists())
330  uFn = file;
331  file = Filename.join(path, preffix + m.getTiltedMicrograph().getName() + suffix);
332  if(new File(file).exists())
333  tFn = file;
334 
335  if(uFn != null && tFn != null)
336  {
337  uMd.clear();
338  tMd.clear();
339  result += importParticlesFromFiles(uFn, tFn, f, m, scale, invertx, inverty, uMd, tMd);
340  saveData(m);
341  }
342  }
343  uMd.destroy();
344  tMd.destroy();
345  super.saveData();
346 
347 
348  return result;
349  }// function importParticlesFromFolder
xmipp.viewer.particlepicker.ParticlePicker.detectFormat
Format detectFormat(String path, String preffix, StringBuffer suffix)
Definition: ParticlePicker.java:295
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String importParticlesFromFiles(String uPath, String tPath, Format f, UntiltedMicrograph um, float scale, boolean invertx, boolean inverty)
Definition: TiltPairPicker.java:351
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void importSize(String path, Format f, double scale)
Definition: ParticlePicker.java:643
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Definition at line 386 of file TiltPairPicker.java.

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387  {
388  boolean valid = true;
389  UntiltedMicrograph um = getMicrograph();
390  for (UntiltedParticle p : um.getParticles())
391  if (!getMicrograph().fits(p.getX(), p.getY(), size))
392  {
393  valid = false;
394  break;
395  }
396  for (TiltedParticle p : um.getTiltedMicrograph().getParticles())
397  if (!um.getTiltedMicrograph().fits(p.getX(), p.getY(), size))
398  {
399  valid = false;
400  break;
401  }
402  if (!valid)
403  XmippDialog.showInfo(parent, String.format("Particles out of bounds, %s not allowed.", size));
404  return valid;
405  }
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boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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Definition at line 41 of file TiltPairPicker.java.

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42  {
43  try
44  {
45  loadEmptyMicrographs();
46  for (UntiltedMicrograph um : micrographs)
47  loadMicrographParticles(um);
48 
49  }
50  catch (Exception e)
51  {
52  getLogger().log(Level.SEVERE, e.getMessage(), e);
53  throw new IllegalArgumentException(e);
54  }
55 
56  }
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographParticles
void loadMicrographParticles(UntiltedMicrograph micrograph)
Definition: TiltPairPicker.java:97
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Definition at line 58 of file TiltPairPicker.java.

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59  {
60  try
61  {
62  MetaData md = new MetaData(selfile);
63  // md.readPlain(pairsfile, "image tilted_image");
64  if (micrographs == null)
65  this.micrographs = new ArrayList<UntiltedMicrograph>();
66  else
67  micrographs.clear();
68  UntiltedMicrograph untiltedmicrograph;
69  TiltedMicrograph tiltedmicrograph;
70  String image, tiltedimage;
71 
72  long[] ids = md.findObjects();
73  for (long id : ids)
74  {
75  image = md.getValueString(MDLabel.MDL_MICROGRAPH, id);
76  tiltedimage = md.getValueString(MDLabel.MDL_MICROGRAPH_TILTED, id);
77  tiltedmicrograph = new TiltedMicrograph(tiltedimage);
78  untiltedmicrograph = new UntiltedMicrograph(image, tiltedmicrograph);
79  tiltedmicrograph.setUntiltedMicrograph(untiltedmicrograph);
80  micrographs.add(untiltedmicrograph);
81 
82  }
83  md.destroy();
84  if (micrographs.isEmpty())
85  throw new IllegalArgumentException(String.format("No micrographs specified on %s", selfile));
86 
87 
88  }
89  catch (Exception e)
90  {
91  getLogger().log(Level.SEVERE, e.getMessage(), e);
92  throw new IllegalArgumentException(e);
93  }
94 
95  }
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void xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographData (UntiltedMicrograph um,
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Definition at line 153 of file TiltPairPicker.java.

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154  {
155  try
156  {
157  MetaData uMd = new MetaData(getParticlesBlock(uPosFile));
158  MetaData tMd = new MetaData(getParticlesBlock(tPosFile));
159  loadMicrographParticles(um, uMd, tMd);
160  uMd.destroy();
161  tMd.destroy();
162  }
163  catch (Exception e)
164  {
165  getLogger().log(Level.SEVERE, e.getMessage(), e);
166  throw new IllegalArgumentException(e.getMessage());
167  }
168  }
xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographParticles
void loadMicrographParticles(UntiltedMicrograph micrograph)
Definition: TiltPairPicker.java:97
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Definition at line 97 of file TiltPairPicker.java.

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98  {
99  String ufile = getOutputPath(micrograph.getPosFile());
100  String tfile = getOutputPath(micrograph.getTiltedMicrograph().getPosFile());
101  if (Filename.exists(ufile) && Filename.exists(tfile))
102  loadMicrographData(micrograph, ufile, tfile);
103  }
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xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographData
void loadMicrographData(UntiltedMicrograph um, String uPosFile, String tPosFile)
Definition: TiltPairPicker.java:153
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String xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.loadMicrographParticles (UntiltedMicrograph um,
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Definition at line 106 of file TiltPairPicker.java.

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107  {
108  String result = "";
109  um.reset(this);
110  UntiltedParticle up;
111  TiltedParticle tp;
112  TiltedMicrograph tm = um.getTiltedMicrograph();
113  int x, y;
114  long[] uIds = uMd.findObjects();
115  long[] tIds = tMd.findObjects();
116  long id;
117  for (int i = 0; i < uIds.length; ++i)
118  {
119  // Add untilted particle
120  id = uIds[i];
121  x = uMd.getValueInt(MDLabel.MDL_XCOOR, id);
122  y = uMd.getValueInt(MDLabel.MDL_YCOOR, id);
123 
124  // Set tilted pair particle
125  if (i < tIds.length)
126  {
127  up = new UntiltedParticle(x, y, um, this);
128  um.addParticle(up);
129  id = tIds[i];
130  x = tMd.getValueInt(MDLabel.MDL_XCOOR, id);
131  y = tMd.getValueInt(MDLabel.MDL_YCOOR, id);
132  if (x <= 0 || y <= 0)
133  {
134  result += String.format("Tilted particle at %s centered on %s,%s with negative coordinates dismissed.\n", getMicrograph()
135  .getName(), x, y);
136  continue;
137  }
138  tp = new TiltedParticle(x, y, up);
139  up.setTiltedParticle(tp);
140  tm.addParticle(tp);
141  }
142  else
143  result += String.format("%s centered on (%s,%s), ", getMicrograph().getName(), x, y);
144  }
145  if(!result.isEmpty())
146  result = "Particles at: " + result + "without tilted pairs dismissed";
147 
148  um.initAligner();
149 
150  return result;
151  }// loadMicrographs
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void xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.resetMicrograph (UntiltedMicrograph m)
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Definition at line 187 of file TiltPairPicker.java.

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188  {
189  m.reset(this);
190  saveData(m);
191  }
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synchronized void xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.saveConfig (MetaData md,
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Definition at line 414 of file TiltPairPicker.java.

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415  {
416  try
417  {
418  super.saveConfig(md, id);
419  md.setValueInt(MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE, getParticlesCount(), id);
420 
421 
422  }
423  catch (Exception e)
424  {
425  getLogger().log(Level.SEVERE, e.getMessage(), e);
426  throw new IllegalArgumentException(e.getMessage());
427  }
428  }
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Definition at line 210 of file TiltPairPicker.java.

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211  {
212  super.saveData();
213  saveData(micrograph);//every time you switch micrograph data is saved
214  setChanged(false);
215  }
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Definition at line 256 of file TiltPairPicker.java.

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257  {
258  UntiltedMicrograph um = (UntiltedMicrograph) m;
259  String file = getOutputPath(um.getPosFile());
260  long id;
261 
262  try
263  {
264 
265  if (!m.hasData()){
266  new File(file).delete();
267  }
268  else
269  {
270  TiltedParticle tp;
271  MetaData mdU = new MetaData(); // untilted micrograph particles
272  MetaData mdT = new MetaData(); // tilted micrograph particles
273 
274  for (UntiltedParticle p : um.getParticles())
275  {
276  tp = p.getTiltedParticle();
277  if (tp != null)
278  {
279  id = mdU.addObject();
280  mdU.setValueInt(MDLabel.MDL_XCOOR, p.getX(), id);
281  mdU.setValueInt(MDLabel.MDL_YCOOR, p.getY(), id);
282 
283  id = mdT.addObject();
284  mdT.setValueInt(MDLabel.MDL_XCOOR, tp.getX(), id);
285  mdT.setValueInt(MDLabel.MDL_YCOOR, tp.getY(), id);
286  }
287  }
288 
289  mdU.writeWithException(getParticlesBlock(file));
290  file = getOutputPath(um.getTiltedMicrograph().getPosFile());
291  mdT.writeWithException(getParticlesBlock(file));
292 
293  mdU.destroy();
294  mdT.destroy();
295  }
296  saveMicrographAngles(um);
297  }
298  catch (Exception e)
299  {
300  getLogger().log(Level.SEVERE, e.getMessage(), e);
301  throw new IllegalArgumentException(e.getMessage());
302  }
303 
304  }
xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
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void xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.saveMicrographAngles (UntiltedMicrograph m)
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Definition at line 218 of file TiltPairPicker.java.

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219  {
220  try
221  {
222  MetaData anglesmd;
223  anglesmd = new MetaData(selfile);
224 
225  long micId = -1; //Current micrograph id
226  long [] ids = anglesmd.findObjects();
227  String micFile = m.getFile();
228 
229  for (long mid: ids)
230  {
231  if (micFile.equals(anglesmd.getValueString(MDLabel.MDL_MICROGRAPH, mid)))
232  {
233  micId = mid;
234  break;
235  }
236  }
237 
238  if (micId == -1)
239  throw new Exception("Micrograph " + micrograph.getFile() + " was not found in metadata");
240 
241  anglesmd.setValueDouble(MDLabel.MDL_ANGLE_Y, m.getUntiltedAngle(), micId);
242  anglesmd.setValueDouble(MDLabel.MDL_ANGLE_Y2, m.getTiltedAngle(), micId);
243  anglesmd.setValueDouble(MDLabel.MDL_ANGLE_TILT, m.getTiltAngle(), micId);
244  anglesmd.writeBlock(selfile);
245 
246  }
247  catch (Exception e)
248  {
249  getLogger().log(Level.SEVERE, e.getMessage(), e);
250  throw new IllegalArgumentException(e.getMessage());
251  }
252 
253  }
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Definition at line 379 of file TiltPairPicker.java.

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380  {
381  this.micrograph = (UntiltedMicrograph) m;
382 
383  }
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◆ micrographs

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List<UntiltedMicrograph> xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker.micrographs
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Definition at line 29 of file TiltPairPicker.java.

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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__coll__graph.dot deleted file mode 100644 index 1b3881c6..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__coll__graph.dot +++ /dev/null @@ -1,25 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node2 [label="xmipp.viewer.particlepicker.tiltpair.model.\lTiltPairPicker",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.particlepicker.\lParticlePicker",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePicker.html"]; 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- Node8 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" logger" ,fontname="Helvetica"]; - Node8 [label="Logger",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" params" ,fontname="Helvetica"]; - Node9 [label="xmipp.viewer.particlepicker.\lParticlePickerParams",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerParams.html"]; - Node7 -> Node9 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mode" ,fontname="Helvetica"]; - Node10 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" micrographs" ,fontname="Helvetica"]; - Node10 [label="List\< xmipp.viewer.particlepicker.tiltpair.model.\lUntiltedMicrograph \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__coll__graph.md5 deleted file mode 100644 index fbb3f9d4..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -5e45bcaf9c44f9dd900fbad43deddbb5 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__inherit__graph.dot deleted file mode 100644 index 4fe05a1b..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.TiltPairPicker" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.tiltpair.model.\lTiltPairPicker",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lParticlePicker",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePicker.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__inherit__graph.md5 deleted file mode 100644 index 3caeaa52..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltPairPicker__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -2adc90d5a718f7356d473b6b8fc0f8a2 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph-members.html deleted file mode 100644 index 918612fd..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph-members.html +++ /dev/null @@ -1,119 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph, including all inherited members.

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addParticle(TiltedParticle p)xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
extxmipp.viewer.particlepicker.Micrographstatic
fits(int x, int y, int size)xmipp.viewer.particlepicker.Micrographinline
getCTF()xmipp.viewer.particlepicker.Micrographinline
getCTFIcon()xmipp.viewer.particlepicker.Micrographinline
getCtfInfo()xmipp.viewer.particlepicker.Micrographinline
getFile()xmipp.viewer.particlepicker.Micrographinline
getHeigth()xmipp.viewer.particlepicker.Micrographinline
getImagePlus()xmipp.viewer.particlepicker.Micrographinline
getImagePlus(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
getName(String file, int level)xmipp.viewer.particlepicker.Micrographinlinestatic
getName()xmipp.viewer.particlepicker.Micrographinline
getNoImageIcon()xmipp.viewer.particlepicker.Micrographinlinestatic
getParticle(int x, int y, int size)xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
getParticleList()xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
getParticles()xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
getPosFile()xmipp.viewer.particlepicker.Micrographinline
getPosFileFromXmipp24()xmipp.viewer.particlepicker.Micrographinline
getPSD()xmipp.viewer.particlepicker.Micrographinline
getPSDImage()xmipp.viewer.particlepicker.Micrographinline
getUntiltedMicrograph()xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
getWidth()xmipp.viewer.particlepicker.Micrographinline
hasData()xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
loadDimensions()xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
releaseImage()xmipp.viewer.particlepicker.Micrographinline
removeParticle(UntiltedParticle p)xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
removeParticle(TiltedParticle p)xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
removeParticles(int x, int y)xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
runImageJFilters(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
setPosFileFromXmipp24(String posfile)xmipp.viewer.particlepicker.Micrographinline
setUntiltedMicrograph(UntiltedMicrograph untiltedmicrograph)xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
TiltedMicrograph(String file)xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrographinline
toString()xmipp.viewer.particlepicker.Micrographinline
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph.html deleted file mode 100644 index 0149e7da..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph.html +++ /dev/null @@ -1,526 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph Class Reference - - - - - - - - - -
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-Public Member Functions | -List of all members
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xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph:
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[legend]
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-Public Member Functions

 TiltedMicrograph (String file)
 
boolean hasData ()
 
List<? extends PickerParticle > getParticleList ()
 
List< TiltedParticle > getParticles ()
 
void removeParticle (UntiltedParticle p)
 
void addParticle (TiltedParticle p)
 
TiltedParticle getParticle (int x, int y, int size)
 
void removeParticle (TiltedParticle p)
 
UntiltedMicrograph getUntiltedMicrograph ()
 
void setUntiltedMicrograph (UntiltedMicrograph untiltedmicrograph)
 
void removeParticles (int x, int y)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.Micrograph
void setPosFileFromXmipp24 (String posfile)
 
String getPosFileFromXmipp24 ()
 
 Micrograph (String file)
 
 Micrograph (String file, String name)
 
 Micrograph (String file, CtfInfo ctfInfo)
 
 Micrograph (String file, String name, CtfInfo ctfInfo)
 
String getPSD ()
 
ImagePlus getPSDImage ()
 
Icon getCTFIcon ()
 
String getCTF ()
 
CtfInfo getCtfInfo ()
 
boolean fits (int x, int y, int size)
 
String getPosFile ()
 
void loadDimensions ()
 
ImagePlus getImagePlus ()
 
ImagePlus getImagePlus (List< IJCommand > filters)
 
void runImageJFilters (List< IJCommand > filters)
 
String getFile ()
 
String getName ()
 
String toString ()
 
abstract boolean hasData ()
 
int getWidth ()
 
int getHeigth ()
 
void releaseImage ()
 
List<? extends PickerParticle > getParticleList ()
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.viewer.particlepicker.Micrograph
static Icon getNoImageIcon ()
 
static String getName (String file, int level)
 
- Static Public Attributes inherited from xmipp.viewer.particlepicker.Micrograph
static final String ext = ".pos"
 
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Detailed Description

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Definition at line 10 of file TiltedMicrograph.java.

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Constructor & Destructor Documentation

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◆ TiltedMicrograph()

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Definition at line 16 of file TiltedMicrograph.java.

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17  {
18  super(file, getName(file, 1));
19  particles = new ArrayList<TiltedParticle>();
20  }
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◆ addParticle()

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void xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.addParticle (TiltedParticle p)
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Definition at line 45 of file TiltedMicrograph.java.

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46  {
47  particles.add(p);
48 
49  }
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Definition at line 51 of file TiltedMicrograph.java.

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52  {
53  for (TiltedParticle p : particles)
54  if (p.contains(x, y, size))
55  return p;
56  return null;
57  }
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List<? extends PickerParticle> xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.getParticleList ()
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Definition at line 29 of file TiltedMicrograph.java.

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29  {
30  return getParticles();
31  }
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List<TiltedParticle> xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.getParticles ()
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Definition at line 34 of file TiltedMicrograph.java.

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35  {
36  return particles;
37  }
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◆ getUntiltedMicrograph()

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UntiltedMicrograph xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.getUntiltedMicrograph ()
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Definition at line 68 of file TiltedMicrograph.java.

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69  {
70  return untiltedmicrograph;
71  }
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◆ hasData()

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boolean xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.hasData ()
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Definition at line 23 of file TiltedMicrograph.java.

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24  {
25  return !particles.isEmpty();
26  }
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void xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.removeParticle (UntiltedParticle p)
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Definition at line 39 of file TiltedMicrograph.java.

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40  {
41  particles.remove(p);
42 
43  }
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void xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.removeParticle (TiltedParticle p)
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Definition at line 59 of file TiltedMicrograph.java.

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60  {
61  if (p != null)
62  {
63  particles.remove(p);
64  p.getUntiltedParticle().setTiltedParticle(null);
65  }
66  }
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void xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.removeParticles (int x,
int y 
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Definition at line 78 of file TiltedMicrograph.java.

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79  {
80  List<TiltedParticle> particles = new ArrayList<TiltedParticle>();
81  for(TiltedParticle p: getParticles())
82  if (p.contains(x, y, p.getParticlePicker().getSize()))
83  particles.add(p);
84  for(TiltedParticle p: particles)
85  removeParticle(p);
86  }
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◆ setUntiltedMicrograph()

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void xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph.setUntiltedMicrograph (UntiltedMicrograph untiltedmicrograph)
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Definition at line 73 of file TiltedMicrograph.java.

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74  {
75  this.untiltedmicrograph = untiltedmicrograph;
76  }
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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__coll__graph.dot deleted file mode 100644 index 8866e9c4..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.tiltpair.model.\lTiltedMicrograph",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__coll__graph.md5 deleted file mode 100644 index b8ec75a4..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -e12817929016b5ab9f35df2d4f905f68 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__inherit__graph.dot deleted file mode 100644 index b2e64b22..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.TiltedMicrograph" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.tiltpair.model.\lTiltedMicrograph",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__inherit__graph.md5 deleted file mode 100644 index 21ed2388..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedMicrograph__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -2dcfb4ee2e121e330a4a8b8014935fea \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle-members.html deleted file mode 100644 index 6c720dc5..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle-members.html +++ /dev/null @@ -1,128 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle, including all inherited members.

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compareTo(Particle p)xmipp.jni.Particleinline
contains(int x2, int y2)xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.contains(int x2, int y2, int size)xmipp.jni.Particleinline
costxmipp.jni.Particleprotected
getCost()xmipp.jni.Particleinline
getImageGeneric()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getLastalign()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getMicrograph()xmipp.viewer.particlepicker.PickerParticleinline
getParticleCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.PickerParticleinline
getParticlePicker()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getPosition()xmipp.jni.Particleinline
getSize()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateIndex()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplatePsi()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateRotation()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateTilt()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getUntiltedParticle()xmipp.viewer.particlepicker.tiltpair.model.TiltedParticleinline
getX()xmipp.jni.Particleinline
getX0()xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.getX0(int size)xmipp.viewer.particlepicker.PickerParticleinline
getY()xmipp.jni.Particleinline
getY0()xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.getY0(int size)xmipp.viewer.particlepicker.PickerParticleinline
igxmipp.viewer.particlepicker.training.model.ManualParticleprotected
lastalignxmipp.viewer.particlepicker.training.model.ManualParticleprotected
loadImagePlus()xmipp.viewer.particlepicker.training.model.ManualParticleinlineprotected
ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph)xmipp.viewer.particlepicker.training.model.ManualParticleinline
ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)xmipp.viewer.particlepicker.training.model.ManualParticleinline
micrographxmipp.viewer.particlepicker.PickerParticleprotected
Particle(int x, int y)xmipp.jni.Particleinline
Particle(int x, int y, double cost)xmipp.jni.Particleinline
pickerxmipp.viewer.particlepicker.training.model.ManualParticleprotected
PickerParticle(int x, int y, Micrograph m)xmipp.viewer.particlepicker.PickerParticleinline
PickerParticle(int x, int y, Micrograph m, double cost)xmipp.viewer.particlepicker.PickerParticleinline
resetImage()xmipp.viewer.particlepicker.training.model.ManualParticleinline
resetParticleCanvas()xmipp.viewer.particlepicker.PickerParticleinline
setCost(double cost)xmipp.jni.Particleinline
setLastalign(double[] lastalign)xmipp.viewer.particlepicker.training.model.ManualParticleinline
setMicrograph(Micrograph micrograph)xmipp.viewer.particlepicker.PickerParticleinline
setPosition(int x, int y)xmipp.viewer.particlepicker.training.model.ManualParticleinline
setX(int x)xmipp.jni.Particleinline
setY(int y)xmipp.jni.Particleinline
TiltedParticle(int x, int y, UntiltedParticle untiltedparticle)xmipp.viewer.particlepicker.tiltpair.model.TiltedParticleinline
toString()xmipp.jni.Particleinline
xxmipp.jni.Particleprotected
yxmipp.jni.Particleprotected
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle.html deleted file mode 100644 index 9a96cfd9..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle.html +++ /dev/null @@ -1,287 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle Class Reference - - - - - - - - - -
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-Public Member Functions | -List of all members
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xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle:
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-Public Member Functions

 TiltedParticle (int x, int y, UntiltedParticle untiltedparticle)
 
UntiltedParticle getUntiltedParticle ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
double [] getLastalign ()
 
void setLastalign (double[] lastalign)
 
 ManualParticle (int x, int y, ParticlePicker picker, Micrograph micrograph)
 
 ManualParticle (int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)
 
ParticlePicker getParticlePicker ()
 
int getX0 ()
 
int getY0 ()
 
boolean contains (int x2, int y2)
 
void setPosition (int x, int y)
 
void resetImage ()
 
ImageGeneric getImageGeneric ()
 
double getTemplateRotation ()
 
double getTemplateTilt ()
 
double getTemplatePsi ()
 
int getTemplateIndex ()
 
int getSize ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.PickerParticle
 PickerParticle (int x, int y, Micrograph m)
 
 PickerParticle (int x, int y, Micrograph m, double cost)
 
int getX0 (int size)
 
int getY0 (int size)
 
ParticleCanvas getParticleCanvas (ParticlePickerJFrame frame)
 
void resetParticleCanvas ()
 
Micrograph getMicrograph ()
 
void setMicrograph (Micrograph micrograph)
 
- Public Member Functions inherited from xmipp.jni.Particle
 Particle (int x, int y)
 
 Particle (int x, int y, double cost)
 
int getX ()
 
void setX (int x)
 
int getY ()
 
void setY (int y)
 
double getCost ()
 
void setCost (double cost)
 
boolean contains (int x2, int y2, int size)
 
void setPosition (int x, int y)
 
Point getPosition ()
 
String toString ()
 
int compareTo (Particle p)
 
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-Additional Inherited Members

- Protected Member Functions inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
void loadImagePlus ()
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
ParticlePicker picker
 
ImageGeneric ig
 
double [] lastalign
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.PickerParticle
Micrograph micrograph
 
- Protected Attributes inherited from xmipp.jni.Particle
int x
 
int y
 
double cost
 
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Detailed Description

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Definition at line 5 of file TiltedParticle.java.

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Constructor & Destructor Documentation

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◆ TiltedParticle()

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xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle.TiltedParticle (int x,
int y,
UntiltedParticle untiltedparticle 
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Definition at line 9 of file TiltedParticle.java.

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10  {
11  super(x, y, untiltedparticle.getParticlePicker(), ((UntiltedMicrograph)untiltedparticle.getMicrograph()).getTiltedMicrograph());
12  this.untiltedparticle = untiltedparticle;
13  }
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Member Function Documentation

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◆ getUntiltedParticle()

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UntiltedParticle xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle.getUntiltedParticle ()
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Definition at line 15 of file TiltedParticle.java.

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16  {
17  return untiltedparticle;
18  }
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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__coll__graph.dot deleted file mode 100644 index e208d2d5..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__coll__graph.dot +++ /dev/null @@ -1,35 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node5 [label="xmipp.viewer.particlepicker.tiltpair.model.\lTiltedParticle",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="xmipp.viewer.particlepicker.training.model.\lManualParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle.html"]; - Node7 -> Node6 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="xmipp.viewer.particlepicker.\lPickerParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1PickerParticle.html"]; - Node8 -> Node7 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node8 [label="xmipp.jni.Particle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1Particle.html"]; - Node9 -> Node8 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node9 [label="Comparable\< Particle \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node7 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" micrograph" ,fontname="Helvetica"]; - Node10 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html"]; - Node11 -> Node6 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" picker" ,fontname="Helvetica"]; - Node11 [label="xmipp.viewer.particlepicker.\lParticlePicker",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePicker.html"]; - Node12 -> Node11 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" filters" ,fontname="Helvetica"]; - Node12 [label="List\< xmipp.ij.commons.IJCommand \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node13 -> Node11 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" emextensions" ,fontname="Helvetica"]; - Node13 [label="HashMap\< xmipp.viewer.particlepicker.\lFormat, String \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node14 -> Node11 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" color\ncolors" ,fontname="Helvetica"]; - Node14 [label="Color",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node11 -> Node11 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" picker" ,fontname="Helvetica"]; - Node15 -> Node11 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mode" ,fontname="Helvetica"]; - Node15 [label="xmipp.viewer.particlepicker.training.model.Mode",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$enumxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1Mode.html"]; - Node16 -> Node11 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" logger" ,fontname="Helvetica"]; - Node16 [label="Logger",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node17 -> Node11 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" params" ,fontname="Helvetica"]; - Node17 [label="xmipp.viewer.particlepicker.\lParticlePickerParams",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerParams.html"]; - Node15 -> Node17 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mode" ,fontname="Helvetica"]; - Node18 -> Node6 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ig" ,fontname="Helvetica"]; - Node18 [label="xmipp.jni.ImageGeneric",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1ImageGeneric.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__coll__graph.md5 deleted file mode 100644 index ef71c10b..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -b98745bc691de9fdef633f95be54ee73 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__inherit__graph.dot deleted file mode 100644 index 64a5b130..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__inherit__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.TiltedParticle" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.tiltpair.model.\lTiltedParticle",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.training.model.\lManualParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.viewer.particlepicker.\lPickerParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1PickerParticle.html"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.jni.Particle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1Particle.html"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="Comparable\< Particle \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__inherit__graph.md5 deleted file mode 100644 index 7cd9ea3f..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -25815bc0603ace5b6cd55a73514a4706 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph-members.html deleted file mode 100644 index 1504f71a..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph-members.html +++ /dev/null @@ -1,129 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph, including all inherited members.

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addParticle(UntiltedParticle p)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
addParticleToAligner(UntiltedParticle up, boolean recalculateAngles)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
anglesAvailable()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
extxmipp.viewer.particlepicker.Micrographstatic
fits(int x, int y, int size)xmipp.viewer.particlepicker.Micrographinline
getAddedCount()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getAlignedTiltedParticle(int x, int y)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getAlignedUntiltedParticle(int x, int y)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getAlignmentMin()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinlinestatic
getCTF()xmipp.viewer.particlepicker.Micrographinline
getCTFIcon()xmipp.viewer.particlepicker.Micrographinline
getCtfInfo()xmipp.viewer.particlepicker.Micrographinline
getFile()xmipp.viewer.particlepicker.Micrographinline
getHeigth()xmipp.viewer.particlepicker.Micrographinline
getImagePlus()xmipp.viewer.particlepicker.Micrographinline
getImagePlus(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
getName(String file, int level)xmipp.viewer.particlepicker.Micrographinlinestatic
getName()xmipp.viewer.particlepicker.Micrographinline
getNoImageIcon()xmipp.viewer.particlepicker.Micrographinlinestatic
getParticle(int x, int y, int size)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getParticleList()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getParticles()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getPosFile()xmipp.viewer.particlepicker.Micrographinline
getPosFileFromXmipp24()xmipp.viewer.particlepicker.Micrographinline
getPSD()xmipp.viewer.particlepicker.Micrographinline
getPSDImage()xmipp.viewer.particlepicker.Micrographinline
getTiltAngle()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getTiltedAngle()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getTiltedMicrograph()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getUntiltedAngle()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
getWidth()xmipp.viewer.particlepicker.Micrographinline
hasData()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
initAligner()xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
loadDimensions()xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
releaseImage()xmipp.viewer.particlepicker.Micrographinline
removeParticle(UntiltedParticle p)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
removeParticles(int x, int y)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
reset(TiltPairPicker picker)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
runImageJFilters(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
setAlignedTiltedParticle(UntiltedParticle up)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
setPosFileFromXmipp24(String posfile)xmipp.viewer.particlepicker.Micrographinline
toString()xmipp.viewer.particlepicker.Micrographinline
UntiltedMicrograph(String file, TiltedMicrograph tiltedmicrograph)xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrographinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph.html deleted file mode 100644 index f05b513e..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph.html +++ /dev/null @@ -1,886 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Static Public Member Functions | -List of all members
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph:
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-Public Member Functions

 UntiltedMicrograph (String file, TiltedMicrograph tiltedmicrograph)
 
int getAddedCount ()
 
TiltedMicrograph getTiltedMicrograph ()
 
UntiltedParticle getParticle (int x, int y, int size)
 
boolean hasData ()
 
List<? extends PickerParticle > getParticleList ()
 
void reset (TiltPairPicker picker)
 
void removeParticle (UntiltedParticle p)
 
void addParticle (UntiltedParticle p)
 
List< UntiltedParticle > getParticles ()
 
void addParticleToAligner (UntiltedParticle up, boolean recalculateAngles)
 
void initAligner ()
 
boolean anglesAvailable ()
 
double getUntiltedAngle ()
 
double getTiltedAngle ()
 
double getTiltAngle ()
 
Particle getAlignedTiltedParticle (int x, int y)
 
Particle getAlignedUntiltedParticle (int x, int y)
 
void setAlignedTiltedParticle (UntiltedParticle up)
 
void removeParticles (int x, int y)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.Micrograph
void setPosFileFromXmipp24 (String posfile)
 
String getPosFileFromXmipp24 ()
 
 Micrograph (String file)
 
 Micrograph (String file, String name)
 
 Micrograph (String file, CtfInfo ctfInfo)
 
 Micrograph (String file, String name, CtfInfo ctfInfo)
 
String getPSD ()
 
ImagePlus getPSDImage ()
 
Icon getCTFIcon ()
 
String getCTF ()
 
CtfInfo getCtfInfo ()
 
boolean fits (int x, int y, int size)
 
String getPosFile ()
 
void loadDimensions ()
 
ImagePlus getImagePlus ()
 
ImagePlus getImagePlus (List< IJCommand > filters)
 
void runImageJFilters (List< IJCommand > filters)
 
String getFile ()
 
String getName ()
 
String toString ()
 
abstract boolean hasData ()
 
int getWidth ()
 
int getHeigth ()
 
void releaseImage ()
 
List<? extends PickerParticle > getParticleList ()
 
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-Static Public Member Functions

static int getAlignmentMin ()
 
- Static Public Member Functions inherited from xmipp.viewer.particlepicker.Micrograph
static Icon getNoImageIcon ()
 
static String getName (String file, int level)
 
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-Additional Inherited Members

- Static Public Attributes inherited from xmipp.viewer.particlepicker.Micrograph
static final String ext = ".pos"
 
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Detailed Description

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Definition at line 11 of file UntiltedMicrograph.java.

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Constructor & Destructor Documentation

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◆ UntiltedMicrograph()

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xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.UntiltedMicrograph (String file,
TiltedMicrograph tiltedmicrograph 
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Definition at line 21 of file UntiltedMicrograph.java.

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22  {
23  super(file, getName(file, 1));
24  this.tiltedmicrograph = tiltedmicrograph;
25  particles = new ArrayList<UntiltedParticle>();
26  tpa = new TiltPairAligner();
27 
28  }
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◆ addParticle()

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void xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.addParticle (UntiltedParticle p)
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Definition at line 80 of file UntiltedMicrograph.java.

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81  {
82  particles.add(p);
83  }
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void xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.addParticleToAligner (UntiltedParticle up,
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Definition at line 90 of file UntiltedMicrograph.java.

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91  {
92  if (up.getTiltedParticle() == null)
93  throw new IllegalArgumentException(XmippMessage.getEmptyFieldMsg("TiltedParticle"));
94  tpa.addParticleToAligner(up.getX(), up.getY(), up.getTiltedParticle().getX(), up.getTiltedParticle().getY());
95  up.setAdded(true);
96  added++;
97  if (anglesAvailable() && recalculateAngles)
98  angles = tpa.computeAngles();
99  }
xmipp.jni.TiltPairAligner.addParticleToAligner
native void addParticleToAligner(int x1, int y1, int x2, int y2)
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native double [] computeAngles()
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◆ anglesAvailable()

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boolean xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.anglesAvailable ()
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Definition at line 112 of file UntiltedMicrograph.java.

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113  {
114  return !(added < 10);
115  }
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int xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.getAddedCount ()
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Definition at line 30 of file UntiltedMicrograph.java.

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31  {
32  return added;
33  }
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◆ getAlignedTiltedParticle()

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Particle xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.getAlignedTiltedParticle (int x,
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Definition at line 143 of file UntiltedMicrograph.java.

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144  {
145  if (getAddedCount() < getAlignmentMin())
146  return null;
147  Particle p = tpa.getTiltedParticle(x, y);
148  return p;
149  }
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native Particle getTiltedParticle(int x1, int y1)
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Particle xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph.getAlignedUntiltedParticle (int x,
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Definition at line 151 of file UntiltedMicrograph.java.

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152  {
153  if (getAddedCount() < getAlignmentMin())
154  return null;
155  Particle p = tpa.getUntiltedParticle(x, y);
156  return p;
157  }
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Definition at line 183 of file UntiltedMicrograph.java.

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184  {
185  return alignmentmin;
186  }
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Definition at line 40 of file UntiltedMicrograph.java.

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41  {
42  for (UntiltedParticle p : particles)
43  if (p.contains(x, y, size))
44  return p;
45  return null;
46 
47  }
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Definition at line 56 of file UntiltedMicrograph.java.

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56  {
57  return getParticles();
58  }
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Definition at line 85 of file UntiltedMicrograph.java.

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86  {
87  return particles;
88  }
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Definition at line 136 of file UntiltedMicrograph.java.

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137  {
138  if (angles == null)
139  return 0;
140  return angles[2];
141  }
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Definition at line 129 of file UntiltedMicrograph.java.

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130  {
131  if (angles == null)
132  return 90;
133  return angles[1];
134  }
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Definition at line 35 of file UntiltedMicrograph.java.

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36  {
37  return tiltedmicrograph;
38  }
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Definition at line 122 of file UntiltedMicrograph.java.

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123  {
124  if (angles == null)
125  return 90;
126  return angles[0];
127  }
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Definition at line 50 of file UntiltedMicrograph.java.

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51  {
52  return !particles.isEmpty();
53  }
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Definition at line 101 of file UntiltedMicrograph.java.

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102  {
103  tpa.clear();
104  added = 0;
105  for (UntiltedParticle p : particles)
106  if (p.getTiltedParticle() != null)
107  addParticleToAligner(p, false);
108  if (anglesAvailable())
109  angles = tpa.computeAngles();
110  }
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void addParticleToAligner(UntiltedParticle up, boolean recalculateAngles)
Definition: UntiltedMicrograph.java:90
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Definition at line 74 of file UntiltedMicrograph.java.

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75  {
76  particles.remove(p);
77  tiltedmicrograph.removeParticle(p.getTiltedParticle());
78  }
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Definition at line 173 of file UntiltedMicrograph.java.

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174  {
175  List<UntiltedParticle> particles = new ArrayList<UntiltedParticle>();
176  for (UntiltedParticle p : getParticles())
177  if (p.contains(x, y, p.getParticlePicker().getSize()))
178  particles.add(p);
179  for (UntiltedParticle p : particles)
180  removeParticle(p);
181  }
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Definition at line 61 of file UntiltedMicrograph.java.

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62  {
63  angles = null;
64  for(UntiltedParticle p: particles)
65  p.setTiltedParticle(null);
66  getParticles().clear();
67  getTiltedMicrograph().getParticles().clear();
68  //JMRT: I think is very very dangerous to delete the existing pos files.
69  //new File(picker.getOutputPath(getPosFile())).delete();
70  //new File(picker.getOutputPath(getTiltedMicrograph().getPosFile())).delete();
71  initAligner();
72  }
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Definition at line 159 of file UntiltedMicrograph.java.

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160  {
161  tiltedmicrograph.removeParticle(up.getTiltedParticle());
162  Particle p = getAlignedTiltedParticle(up.getX(), up.getY());
163  if(!tiltedmicrograph.fits(p.getX(), p.getY(), up.getParticlePicker().getSize()))
164  p = null;
165  if (p != null)
166  {
167  TiltedParticle tp = new TiltedParticle(p.getX(), p.getY(), up);
168  getTiltedMicrograph().addParticle(tp);
169  up.setTiltedParticle(tp);
170  }
171  }
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__coll__graph.dot deleted file mode 100644 index e425b368..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.tiltpair.model.\lUntiltedMicrograph",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__coll__graph.md5 deleted file mode 100644 index a13f2ad1..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ce17bd13e2e88c36a3cd19dec6ac8806 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__inherit__graph.dot deleted file mode 100644 index 779b7707..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.UntiltedMicrograph" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.tiltpair.model.\lUntiltedMicrograph",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__inherit__graph.md5 deleted file mode 100644 index 72a74368..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedMicrograph__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -aa900abae0f1f8f1ed4eb9ca0bff105d \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedParticle-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedParticle-members.html deleted file mode 100644 index 9f27c868..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedParticle-members.html +++ /dev/null @@ -1,131 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle Member List
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This is the complete list of members for xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle, including all inherited members.

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compareTo(Particle p)xmipp.jni.Particleinline
contains(int x2, int y2)xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.contains(int x2, int y2, int size)xmipp.jni.Particleinline
costxmipp.jni.Particleprotected
getCost()xmipp.jni.Particleinline
getImageGeneric()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getLastalign()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getMicrograph()xmipp.viewer.particlepicker.PickerParticleinline
getParticleCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.PickerParticleinline
getParticlePicker()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getPosition()xmipp.jni.Particleinline
getSize()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateIndex()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplatePsi()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateRotation()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateTilt()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTiltedParticle()xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticleinline
getX()xmipp.jni.Particleinline
getX0()xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.getX0(int size)xmipp.viewer.particlepicker.PickerParticleinline
getY()xmipp.jni.Particleinline
getY0()xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.getY0(int size)xmipp.viewer.particlepicker.PickerParticleinline
igxmipp.viewer.particlepicker.training.model.ManualParticleprotected
isAdded()xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticleinline
lastalignxmipp.viewer.particlepicker.training.model.ManualParticleprotected
loadImagePlus()xmipp.viewer.particlepicker.training.model.ManualParticleinlineprotected
ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph)xmipp.viewer.particlepicker.training.model.ManualParticleinline
ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)xmipp.viewer.particlepicker.training.model.ManualParticleinline
micrographxmipp.viewer.particlepicker.PickerParticleprotected
Particle(int x, int y)xmipp.jni.Particleinline
Particle(int x, int y, double cost)xmipp.jni.Particleinline
pickerxmipp.viewer.particlepicker.training.model.ManualParticleprotected
PickerParticle(int x, int y, Micrograph m)xmipp.viewer.particlepicker.PickerParticleinline
PickerParticle(int x, int y, Micrograph m, double cost)xmipp.viewer.particlepicker.PickerParticleinline
resetImage()xmipp.viewer.particlepicker.training.model.ManualParticleinline
resetParticleCanvas()xmipp.viewer.particlepicker.PickerParticleinline
setAdded(boolean added)xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticleinline
setCost(double cost)xmipp.jni.Particleinline
setLastalign(double[] lastalign)xmipp.viewer.particlepicker.training.model.ManualParticleinline
setMicrograph(Micrograph micrograph)xmipp.viewer.particlepicker.PickerParticleinline
setPosition(int x, int y)xmipp.viewer.particlepicker.training.model.ManualParticleinline
setTiltedParticle(TiltedParticle tiltedparticle)xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticleinline
setX(int x)xmipp.jni.Particleinline
setY(int y)xmipp.jni.Particleinline
toString()xmipp.jni.Particleinline
UntiltedParticle(int x, int y, UntiltedMicrograph micrograph, ParticlePicker picker)xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticleinline
xxmipp.jni.Particleprotected
yxmipp.jni.Particleprotected
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xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle:
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-Public Member Functions

boolean isAdded ()
 
 UntiltedParticle (int x, int y, UntiltedMicrograph micrograph, ParticlePicker picker)
 
void setTiltedParticle (TiltedParticle tiltedparticle)
 
TiltedParticle getTiltedParticle ()
 
void setAdded (boolean added)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
double [] getLastalign ()
 
void setLastalign (double[] lastalign)
 
 ManualParticle (int x, int y, ParticlePicker picker, Micrograph micrograph)
 
 ManualParticle (int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)
 
ParticlePicker getParticlePicker ()
 
int getX0 ()
 
int getY0 ()
 
boolean contains (int x2, int y2)
 
void setPosition (int x, int y)
 
void resetImage ()
 
ImageGeneric getImageGeneric ()
 
double getTemplateRotation ()
 
double getTemplateTilt ()
 
double getTemplatePsi ()
 
int getTemplateIndex ()
 
int getSize ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.PickerParticle
 PickerParticle (int x, int y, Micrograph m)
 
 PickerParticle (int x, int y, Micrograph m, double cost)
 
int getX0 (int size)
 
int getY0 (int size)
 
ParticleCanvas getParticleCanvas (ParticlePickerJFrame frame)
 
void resetParticleCanvas ()
 
Micrograph getMicrograph ()
 
void setMicrograph (Micrograph micrograph)
 
- Public Member Functions inherited from xmipp.jni.Particle
 Particle (int x, int y)
 
 Particle (int x, int y, double cost)
 
int getX ()
 
void setX (int x)
 
int getY ()
 
void setY (int y)
 
double getCost ()
 
void setCost (double cost)
 
boolean contains (int x2, int y2, int size)
 
void setPosition (int x, int y)
 
Point getPosition ()
 
String toString ()
 
int compareTo (Particle p)
 
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- Protected Member Functions inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
void loadImagePlus ()
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
ParticlePicker picker
 
ImageGeneric ig
 
double [] lastalign
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.PickerParticle
Micrograph micrograph
 
- Protected Attributes inherited from xmipp.jni.Particle
int x
 
int y
 
double cost
 
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Detailed Description

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Definition at line 7 of file UntiltedParticle.java.

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Constructor & Destructor Documentation

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◆ UntiltedParticle()

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xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle.UntiltedParticle (int x,
int y,
UntiltedMicrograph micrograph,
ParticlePicker picker 
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Definition at line 18 of file UntiltedParticle.java.

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19  {
20  super(x, y, picker, micrograph);
21 
22  }
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◆ getTiltedParticle()

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TiltedParticle xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle.getTiltedParticle ()
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Definition at line 29 of file UntiltedParticle.java.

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30  {
31  return tiltedparticle;
32  }
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◆ isAdded()

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Definition at line 13 of file UntiltedParticle.java.

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14  {
15  return added;
16  }
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◆ setAdded()

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void xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle.setAdded (boolean added)
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Definition at line 34 of file UntiltedParticle.java.

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35  {
36  this.added = added;
37  }
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◆ setTiltedParticle()

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void xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle.setTiltedParticle (TiltedParticle tiltedparticle)
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Definition at line 24 of file UntiltedParticle.java.

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25  {
26  this.tiltedparticle = tiltedparticle;
27  }
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The documentation for this class was generated from the following file: -
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedParticle__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedParticle__coll__graph.dot deleted file mode 100644 index 29f9c1ae..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedParticle__coll__graph.dot +++ /dev/null @@ -1,35 +0,0 @@ -digraph "xmipp.viewer.particlepicker.tiltpair.model.UntiltedParticle" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node5 [label="xmipp.viewer.particlepicker.tiltpair.model.\lUntiltedParticle",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="xmipp.viewer.particlepicker.training.model.\lManualParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle.html"]; 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xmipp.viewer.particlepicker.training.AutopickRunnable Member List
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AutopickRunnable(SupervisedPickerJFrame frame, SupervisedPickerMicrograph micrograph)xmipp.viewer.particlepicker.training.AutopickRunnableinline
run()xmipp.viewer.particlepicker.training.AutopickRunnableinline
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-Public Member Functions

 AutopickRunnable (SupervisedPickerJFrame frame, SupervisedPickerMicrograph micrograph)
 
void run ()
 
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Detailed Description

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Definition at line 25 of file AutopickRunnable.java.

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◆ AutopickRunnable()

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xmipp.viewer.particlepicker.training.AutopickRunnable.AutopickRunnable (SupervisedPickerJFrame frame,
SupervisedPickerMicrograph micrograph 
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Definition at line 34 of file AutopickRunnable.java.

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35  {
36  this.frame = frame;
37  this.micrograph = micrograph;
38  this.picker = frame.getParticlePicker();
39  this.classifier = picker.getClassifier();
40  }
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Definition at line 42 of file AutopickRunnable.java.

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43  {
44 
45  micrograph.getAutomaticParticles().clear();
46  boolean isGeneric = !(classifier instanceof PickingClassifier);
47 
48  if (!isGeneric)
49  {
50  micrograph.setState(MicrographState.Supervised);
51  micrograph.setAutopickpercent(picker.getAutopickpercent());
52  autopickRows = ((PickingClassifier)classifier).autopick(micrograph.getFile(), micrograph.getAutopickpercent());
53  picker.loadParticles(micrograph, autopickRows);
54  picker.saveData(micrograph);
55  }
56  else
57  {
58  GenericClassifier gc = (GenericClassifier) classifier;
59  gc.autopick(micrograph);
60  // Despite we run autopick in one micrographs, there are cases
61  // in which the command will pick all of them and we want
62  // to load the particles from all
63  if (gc.doPickAll()) {
64  for (SupervisedPickerMicrograph mic : picker.getMicrographs())
65  picker.loadMicrographData(mic);
66  }
67  else
68  picker.loadMicrographData(micrograph);
69  }
70 
71  final boolean updateAllMicrographs = isGeneric && ((GenericClassifier) classifier).doPickAll();
72  // Runs inside of the Swing UI thread
73  SwingUtilities.invokeLater(new Runnable() {
74  public void run() {
75  frame.setChanged(false);
76 
77  // Select the worse particle as active
78  frame.getCanvas().refreshActive(null);
79 
80  frame.getCanvas().repaint();
81  frame.getCanvas().setEnabled(true);
82  XmippWindowUtil.releaseGUI(frame.getRootPane());
83  frame.updateMicrographsModel(updateAllMicrographs);
84  }
85  });
86  }
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadParticles
void loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
Definition: SupervisedParticlePicker.java:1102
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abstract void refreshActive(PickerParticle p)
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xmipp.viewer.particlepicker.training.CorrectAndAutopickRunnable Member List
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CorrectAndAutopickRunnable(SupervisedPickerJFrame frame, MDRow[] manualRows, MDRow[] automaticRows, SupervisedPickerMicrograph next)xmipp.viewer.particlepicker.training.CorrectAndAutopickRunnableinline
run()xmipp.viewer.particlepicker.training.CorrectAndAutopickRunnableinline
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 CorrectAndAutopickRunnable (SupervisedPickerJFrame frame, MDRow[] manualRows, MDRow[] automaticRows, SupervisedPickerMicrograph next)
 
void run ()
 
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Detailed Description

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Definition at line 28 of file CorrectAndAutopickRunnable.java.

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◆ CorrectAndAutopickRunnable()

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xmipp.viewer.particlepicker.training.CorrectAndAutopickRunnable.CorrectAndAutopickRunnable (SupervisedPickerJFrame frame,
MDRow [] manualRows,
MDRow [] automaticRows,
SupervisedPickerMicrograph next 
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Definition at line 41 of file CorrectAndAutopickRunnable.java.

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43  {
44  this.frame = frame;
45  this.manualRows = manualRows;
46  this.automaticRows = automaticRows;
47  this.next = next;
48  this.picker = frame.getParticlePicker();
49  this.classifier = (PickingClassifier)picker.getClassifier();
50  }
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Definition at line 52 of file CorrectAndAutopickRunnable.java.

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53  {
54  try
55  {
56  classifier.correct(manualRows, automaticRows);
57 
58  if (picker.getMode() == Mode.Supervised && next.getState() == MicrographState.Supervised)
59  {
60  next.getAutomaticParticles().clear();
61  next.setAutopickpercent(picker.getAutopickpercent());
62  autopickRows = classifier.autopick(next.getFile(), next.getAutopickpercent());
63  picker.loadParticles(next, autopickRows);
64  picker.saveData(next);
65  // Runs inside of the Swing UI thread
66  SwingUtilities.invokeLater(new Runnable() {
67  public void run() {
68  frame.setChanged(false);
69  }
70  });
71 
72  }
73 
74 
75  // Runs inside of the Swing UI thread
76  SwingUtilities.invokeLater(new Runnable() {
77  public void run() {
78  // Select the worse particle as active
79  frame.getCanvas().refreshActive(null);
80  frame.getCanvas().repaint();
81  frame.getCanvas().setEnabled(true);
82  XmippWindowUtil.releaseGUI(frame.getRootPane());
83  frame.updateMicrographsModel(true);
84  }
85  });
86 
87  }
88  catch(Exception e)
89  {
90 
91  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
92  SwingUtilities.invokeLater(new Runnable() {
93  public void run() {
94  XmippDialog.showError(frame, "Classifier error");
95  }
96  });
97 
98  }
99  }
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synchronized native void correct(MDRow[] manualRows, MDRow[] automaticRows)
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadParticles
void loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
Definition: SupervisedParticlePicker.java:1102
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xmipp.viewer.particlepicker.ParticlePickerCanvas.refreshActive
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main(String[] args)xmipp.viewer.particlepicker.training.SupervisedPickerRunnerinlinestatic
run()xmipp.viewer.particlepicker.training.SupervisedPickerRunnerinline
SupervisedPickerRunner(String[] args)xmipp.viewer.particlepicker.training.SupervisedPickerRunnerinline
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 SupervisedPickerRunner (String[] args)
 
void run ()
 
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static void main (String[] args)
 
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Definition at line 15 of file SupervisedPickerRunner.java.

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Definition at line 18 of file SupervisedPickerRunner.java.

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18  {
19  params = new ParticlePickerParams(args);
20  }
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40  {
41  SupervisedPickerRunner spr = new SupervisedPickerRunner(args);
42  SwingUtilities.invokeLater(spr);
43  }
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Definition at line 23 of file SupervisedPickerRunner.java.

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23  {
24 
25  try {
26  SupervisedParticlePicker ppicker = null;
27 
28  ppicker = new SupervisedParticlePicker(params.inputfile, params.outputdir, params.threads,
29  params.fast, params.incore, params);
30  if(params.isScipion())
31  XmippApplication.setIsScipion(true);
32  new SupervisedPickerJFrame(ppicker);
33  } catch (Exception e) {
34  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
35  if (!e.getMessage().isEmpty())
36  XmippDialog.showException(null, e);
37  }
38  }
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xmipp.viewer.particlepicker.training.TrainRunnable Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.TrainRunnable, including all inherited members.

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autopickRowsxmipp.viewer.particlepicker.training.TrainRunnableprotected
classifierxmipp.viewer.particlepicker.training.TrainRunnableprotected
framexmipp.viewer.particlepicker.training.TrainRunnableprotected
micrographxmipp.viewer.particlepicker.training.TrainRunnableprotected
pickerxmipp.viewer.particlepicker.training.TrainRunnableprotected
rectanglexmipp.viewer.particlepicker.training.TrainRunnableprotected
run()xmipp.viewer.particlepicker.training.TrainRunnableinline
trainInputxmipp.viewer.particlepicker.training.TrainRunnableprotected
TrainRunnable(SupervisedPickerJFrame frame, MDRow[] trainInput, SupervisedPickerMicrograph trainmic)xmipp.viewer.particlepicker.training.TrainRunnableinline
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Attributes | -List of all members
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xmipp.viewer.particlepicker.training.TrainRunnable Class Reference
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-Public Member Functions

 TrainRunnable (SupervisedPickerJFrame frame, MDRow[] trainInput, SupervisedPickerMicrograph trainmic)
 
void run ()
 
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-Protected Attributes

SupervisedPickerJFrame frame
 
MDRow [] trainInput
 
Rectangle rectangle
 
Particle [] autopickRows
 
SupervisedPickerMicrograph micrograph
 
final SupervisedParticlePicker picker
 
final PickingClassifier classifier
 
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Detailed Description

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Author
airen
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Definition at line 25 of file TrainRunnable.java.

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Constructor & Destructor Documentation

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◆ TrainRunnable()

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xmipp.viewer.particlepicker.training.TrainRunnable.TrainRunnable (SupervisedPickerJFrame frame,
MDRow [] trainInput,
SupervisedPickerMicrograph trainmic 
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Definition at line 36 of file TrainRunnable.java.

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37  {
38  this.frame = frame;
39  this.trainInput = trainInput;
40  this.micrograph = frame.getMicrograph();
41  rectangle = trainmic.getRectangle();
42  if(trainmic != micrograph)
43  trainmic.resetParticlesRectangle();
44  this.picker = frame.getParticlePicker();
45  this.classifier = (PickingClassifier)picker.getClassifier();
46  }
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◆ run()

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void xmipp.viewer.particlepicker.training.TrainRunnable.run ()
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Definition at line 48 of file TrainRunnable.java.

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49  {
50  try
51  {
52  classifier.train(trainInput, (int) rectangle.getX(), (int) rectangle.getY(), (int) rectangle.getWidth(), (int) rectangle.getHeight());// should remove training
53  micrograph.setAutopickpercent(picker.getAutopickpercent());
54  autopickRows = classifier.autopick(micrograph.getFile(), micrograph.getAutopickpercent());
55  picker.loadParticles(micrograph, autopickRows);
56  picker.saveData(micrograph);
57  XmippWindowUtil.releaseGUI(frame.getRootPane());
58  frame.getCanvas().setEnabled(true);
59  frame.getCanvas().repaint();
60  frame.updateMicrographsModel();
61  }
62  catch (Exception e)
63  {
64  ParticlePicker.getLogger().log(Level.SEVERE, e.getMessage(), e);
65  XmippDialog.showError(frame, "Classifier error");
66  }
67  }
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xmipp.jni.PickingClassifier.train
synchronized native void train(MDRow[] micrographs, int x, int y, int width, int height)
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadParticles
void loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
Definition: SupervisedParticlePicker.java:1102
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xmipp.jni.PickingClassifier.autopick
synchronized native Particle [] autopick(String micrograph, int percent)
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◆ autopickRows

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Particle [] xmipp.viewer.particlepicker.training.TrainRunnable.autopickRows
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Definition at line 31 of file TrainRunnable.java.

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◆ classifier

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Definition at line 34 of file TrainRunnable.java.

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◆ frame

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Definition at line 28 of file TrainRunnable.java.

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Definition at line 32 of file TrainRunnable.java.

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◆ picker

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final SupervisedParticlePicker xmipp.viewer.particlepicker.training.TrainRunnable.picker
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Definition at line 33 of file TrainRunnable.java.

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Definition at line 30 of file TrainRunnable.java.

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◆ trainInput

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MDRow [] xmipp.viewer.particlepicker.training.TrainRunnable.trainInput
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Definition at line 29 of file TrainRunnable.java.

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The documentation for this class was generated from the following file: -
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-} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1TrainRunnable__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1TrainRunnable__coll__graph.md5 deleted file mode 100644 index 583e6fd1..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1TrainRunnable__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -4d9a416001b7aa7015160915c8bde154 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1TrainRunnable__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1TrainRunnable__inherit__graph.dot deleted file mode 100644 index 03ad3731..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1TrainRunnable__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.TrainRunnable" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; 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xmipp.viewer.particlepicker.training.gui.MicrographsTableModel Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.gui.MicrographsTableModel, including all inherited members.

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getColumnCount()xmipp.viewer.particlepicker.training.gui.MicrographsTableModelinline
getColumnName(int c)xmipp.viewer.particlepicker.training.gui.MicrographsTableModelinline
getRowCount()xmipp.viewer.particlepicker.training.gui.MicrographsTableModelinline
getValueAt(int rowIndex, int columnIndex)xmipp.viewer.particlepicker.training.gui.MicrographsTableModelinline
MicrographsTableModel(SupervisedPickerJFrame frame)xmipp.viewer.particlepicker.training.gui.MicrographsTableModelinline
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xmipp.viewer.particlepicker.training.gui.MicrographsTableModel Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.training.gui.MicrographsTableModel:
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-Public Member Functions

 MicrographsTableModel (SupervisedPickerJFrame frame)
 
int getColumnCount ()
 
String getColumnName (int c)
 
int getRowCount ()
 
Object getValueAt (int rowIndex, int columnIndex)
 
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Detailed Description

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Definition at line 12 of file MicrographsTableModel.java.

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Constructor & Destructor Documentation

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◆ MicrographsTableModel()

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xmipp.viewer.particlepicker.training.gui.MicrographsTableModel.MicrographsTableModel (SupervisedPickerJFrame frame)
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Definition at line 20 of file MicrographsTableModel.java.

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21  {
22  this.micrographs = frame.getParticlePicker().getMicrographs();
23  CtfInfo ctfInfo = micrographs.get(0).getCtfInfo();
24  if (ctfInfo == null || ctfInfo.defocusU == null)
25  columns = new String[]{"", "Name", "Particles", "State"};
26  else
27  columns = new String[]{"", "Name", "Particles", "State", "DefocusU"};
28  this.frame = frame;
29  }
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◆ getColumnCount()

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int xmipp.viewer.particlepicker.training.gui.MicrographsTableModel.getColumnCount ()
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Definition at line 32 of file MicrographsTableModel.java.

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32  {
33  return columns.length;
34  }
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String xmipp.viewer.particlepicker.training.gui.MicrographsTableModel.getColumnName (int c)
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Definition at line 36 of file MicrographsTableModel.java.

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37  {
38 
39  return columns[c];
40  }
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◆ getRowCount()

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Definition at line 43 of file MicrographsTableModel.java.

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43  {
44  return micrographs.size();
45  }
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◆ getValueAt()

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Object xmipp.viewer.particlepicker.training.gui.MicrographsTableModel.getValueAt (int rowIndex,
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Definition at line 48 of file MicrographsTableModel.java.

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48  {
49  SupervisedPickerMicrograph m = micrographs.get(rowIndex);
50  switch (columnIndex) {
51  case 0: return rowIndex + 1;
52  case 1: return m.getName();
53  case 2:
54  if(m.getStep() == Mode.Manual)
55  return Integer.toString(m.getManualParticles().size());
56  if(m.getStep() == Mode.Available)
57  return "0";
58  if(m.getStep() == Mode.Supervised)
59  return String.format("%s + %s", m.getManualParticles().size(),
60  m.getAutomaticParticlesNumber(m.getThreshold()));
61  case 3: return m.getState();
62  case 4:
63  CtfInfo ctfInfo = m.getCtfInfo();
64  return ctfInfo.defocusU.toString();
65  default:
66  return null;
67  }
68  }
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The documentation for this class was generated from the following file: -
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__coll__graph.dot deleted file mode 100644 index ad280621..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.gui.MicrographsTableModel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.training.gui.\lMicrographsTableModel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="AbstractTableModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__coll__graph.md5 deleted file mode 100644 index 6a05b143..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -d3ec796d0d70586099622d344469e416 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__inherit__graph.dot deleted file mode 100644 index 85199e98..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.gui.MicrographsTableModel" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.training.gui.\lMicrographsTableModel",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="AbstractTableModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__inherit__graph.md5 deleted file mode 100644 index 183dcc53..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1MicrographsTableModel__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ef74b727ef8e63229690a71640eb9c2b \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas-members.html deleted file mode 100644 index 817b1025..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas-members.html +++ /dev/null @@ -1,160 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas, including all inherited members.

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activexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activemovedxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
activestxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
addParticle(int x, int y, boolean refresh)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinlineprotected
adjustMagnification()xmipp.ij.commons.XmippImageCanvasinline
captureWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
continuousstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
customScrollSetup(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinline
dashedstxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
doCustomPaint(Graphics2D g2)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinlineprotected
drawLine(double alpha, Graphics2D g2)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, ManualParticle p, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
drawShape(Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
erase(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
eraserCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
framexmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
getActive()xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
getFrame()xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
getIw()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getLastManualParticle()xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinlineprotected
getLastParticle()xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinlineprotected
getMicrograph()xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
getParticlePicker()xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
getPreferredMagnification()xmipp.ij.commons.XmippImageCanvasinline
getTool()xmipp.ij.commons.XmippImageCanvasinline
getXOnImage(int x)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
getYOnImage(int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
hasActiveParticle()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
isDragImage(MouseEvent e)xmipp.ij.commons.XmippImageCanvasinlineprotected
isKeyPressed(int keyCode)xmipp.ij.commons.XmippImageCanvasinlineprotected
iwxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
keyPressed(KeyEvent e)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
keyReleased(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
keyTyped(KeyEvent keyEvent)xmipp.ij.commons.XmippImageCanvasinline
linearCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
loadData(XmippIJWindow xiw)xmipp.ij.commons.XmippImageCanvasinline
manageActive(int x, int y)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
micrographxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
mouseDragged(MouseEvent e)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
mouseEntered(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseExited(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
mouseMoved(MouseEvent e)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
mousePressed(MouseEvent e)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
mouseReleased(MouseEvent e)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
mouseWheelMoved(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
moveActiveParticle(int x, int y)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
moveTo(PickerParticle p)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
offScreenX(int x)xmipp.ij.commons.XmippImageCanvasinline
offScreenY(int y)xmipp.ij.commons.XmippImageCanvasinline
paint(Graphics g)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
paintEraser(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
ParticlePickerCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
ParticlePickerCanvas(ParticlePickerJFrame frame, Micrograph micrograph)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
pickerxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
pickingCursorxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
POLIGONAL_MODE_KEYxmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasstatic
refresh()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
refreshActive(PickerParticle p)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
removeParticle(PickerParticle particleToRemove)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinlineprotected
xmipp::viewer::particlepicker::ParticlePickerCanvas.removeParticle(P particleToRemove)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >protected
resetLinearPicking()xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
restoreWindowSize()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setActiveMoved(boolean b)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setCustomCursor()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
setCustomCursor(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inlineprotected
setInvertX(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setInvertY(boolean value)xmipp.ij.commons.XmippImageCanvasinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
SupervisedPickerCanvas(SupervisedPickerJFrame frame)xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvasinline
thinContinuousStxmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >static
updateMicrograph()xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
updateMicrograph(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
XmippImageCanvas(ImagePlus imp)xmipp.ij.commons.XmippImageCanvasinline
zoomIn(int sx, int sy)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
zoomOut(int sx, int sy)xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >inline
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-Public Member Functions | -Static Public Attributes | -Protected Member Functions | -List of all members
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas Class Reference
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-Public Member Functions

 SupervisedPickerCanvas (SupervisedPickerJFrame frame)
 
ManualParticle getActive ()
 
void mousePressed (MouseEvent e)
 
void resetLinearPicking ()
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
void manageActive (int x, int y)
 
void refreshActive (PickerParticle p)
 
SupervisedPickerJFrame getFrame ()
 
SupervisedPickerMicrograph getMicrograph ()
 
SupervisedParticlePicker getParticlePicker ()
 
void keyPressed (KeyEvent e)
 
void mouseMoved (MouseEvent e)
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
void setMicrograph (Micrograph m)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame)
 
 ParticlePickerCanvas (ParticlePickerJFrame frame, Micrograph micrograph)
 
void keyPressed (KeyEvent e)
 
void zoomIn (int sx, int sy)
 
void zoomOut (int sx, int sy)
 
boolean hasActiveParticle ()
 
ImageWindow getIw ()
 
void moveTo (PickerParticle p)
 
void mouseEntered (MouseEvent e)
 
void mouseExited (MouseEvent e)
 
void setCustomCursor ()
 
abstract void refreshActive (PickerParticle p)
 
abstract P getActive ()
 
abstract ParticlePickerJFrame getFrame ()
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void updateMicrograph ()
 
void updateMicrograph (Micrograph m)
 
abstract Micrograph getMicrograph ()
 
void paint (Graphics g)
 
void mouseMoved (MouseEvent e)
 
abstract ParticlePicker getParticlePicker ()
 
void mouseWheelMoved (MouseWheelEvent e)
 
- Public Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
Tool getTool ()
 
 XmippImageCanvas (ImagePlus imp)
 
void mousePressed (MouseEvent e)
 
void customScrollSetup (MouseEvent e)
 
void mouseDragged (MouseEvent e)
 
void mouseReleased (MouseEvent e)
 
int getXOnImage (int x)
 
int getYOnImage (int y)
 
void mouseWheelMoved (MouseWheelEvent e)
 
void mouseMoved (MouseEvent e)
 
int offScreenX (int x)
 
int offScreenY (int y)
 
void loadData (XmippIJWindow xiw)
 
double getPreferredMagnification ()
 
void adjustMagnification ()
 
void setInvertX (boolean value)
 
void setInvertY (boolean value)
 
void keyTyped (KeyEvent keyEvent)
 
void keyPressed (KeyEvent keyEvent)
 
void keyReleased (KeyEvent keyEvent)
 
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-Static Public Attributes

static final int POLIGONAL_MODE_KEY = KeyEvent.VK_C
 
- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
static final BasicStroke dashedst = new BasicStroke(2.0f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 10.0f, new float[] { 10.0f }, 0.0f)
 
static final BasicStroke continuousst = new BasicStroke(2.0f)
 
static final BasicStroke thinContinuousSt = new BasicStroke(1.5f)
 
static final BasicStroke activest = new BasicStroke(1.5f)
 
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-Protected Member Functions

ManualParticle getLastManualParticle ()
 
ManualParticle getLastParticle ()
 
void addParticle (int x, int y, boolean refresh)
 
void doCustomPaint (Graphics2D g2)
 
void removeParticle (PickerParticle particleToRemove)
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
void captureWindowSize ()
 
void restoreWindowSize ()
 
abstract P getLastParticle ()
 
abstract void manageActive (int x, int y)
 
void setActiveMoved (boolean b)
 
void refresh ()
 
void setCustomCursor (MouseEvent e)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
 
void drawShape (Graphics2D g2, ManualParticle p, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke, Color color)
 
void drawShape (Graphics2D g2, int x, int y, int size, boolean all, Stroke stroke)
 
void drawLine (double alpha, Graphics2D g2)
 
void erase (MouseEvent e)
 
abstract void removeParticle (P particleToRemove)
 
void moveActiveParticle (int x, int y)
 
abstract void doCustomPaint (Graphics2D g2)
 
void paintEraser (MouseEvent e)
 
- Protected Member Functions inherited from xmipp.ij.commons.XmippImageCanvas
boolean isDragImage (MouseEvent e)
 
boolean isKeyPressed (int keyCode)
 
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-Additional Inherited Members

- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerCanvas< P extends PickerParticle >
ParticlePickerJFrame frame
 
Micrograph micrograph
 
ParticlePicker picker
 
XmippImageWindow iw
 
Cursor eraserCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("eraserC.png").getImage(), new Point(3, 31), "Eraser")
 
Cursor linearCursor = Toolkit.getDefaultToolkit().createCustomCursor(XmippResource.getIcon("linearPickingC.png").getImage(), new Point(0, 0), "Linear")
 
Cursor pickingCursor = getPickingCursor(pickingCursorIndex)
 
P active
 
boolean activemoved
 
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Detailed Description

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Definition at line 20 of file SupervisedPickerCanvas.java.

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Constructor & Destructor Documentation

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◆ SupervisedPickerCanvas()

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xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas.SupervisedPickerCanvas (SupervisedPickerJFrame frame)
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Definition at line 27 of file SupervisedPickerCanvas.java.

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28  {
29  super(frame);
30 
31  active = getLastManualParticle();
32 
33  }
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◆ addParticle()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas.addParticle (int x,
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Definition at line 85 of file SupervisedPickerCanvas.java.

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85  {
86 
87  ManualParticle p;
88  if (micrograph.fits(x, y, frame.getParticlePicker().getSize()))
89  {
90 
91  p = new ManualParticle(x, y, frame.getParticlePicker(), micrograph);
92  getMicrograph().addManualParticle(p, getParticlePicker());
93 
94  if(getFrame().centerParticle())
95  new CenterParticleTask(this, getParticlePicker(), p).execute();
96 
97  active = p;
98  if(picker.getMode() == Mode.Manual)
99  new ParticleToTemplatesTask(getActive()).execute();
100 
101  if (refresh) refresh();
102  }
103  }
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.addManualParticle
void addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:122
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boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas.doCustomPaint (Graphics2D g2)
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Definition at line 282 of file SupervisedPickerCanvas.java.

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283  {
284 
285  List<ManualParticle> particles;
286  int index;
287  SupervisedParticlePicker picker = getParticlePicker();
288  Color color = picker.getColor();
289  Color autoColor = picker.getAutomaticColor();
290  Color delColor = picker.getDeletedColor();
291  if (!getMicrograph().isEmpty()) {
292  particles = getMicrograph().getManualParticles();
293  g2.setColor(color);
294 
295  for (index = 0; index < particles.size(); index++)
296  drawShape(g2, particles.get(index), false, thinContinuousSt);
297 
298  List<AutomaticParticle> autoparticles = getMicrograph().getAutomaticParticles();
299  for (AutomaticParticle autoparticle : autoparticles)
300  if (!autoparticle.isDeleted() && autoparticle.getCost() >= getFrame().getThreshold()){
301  g2.setColor(autoColor);
302  drawShape(g2, autoparticle, false, thinContinuousSt);
303  }else if (autoparticle.isUnavailable() && picker.isShowDeleted()) {
304  g2.setColor(delColor);
305  drawShape(g2, autoparticle, false, thinContinuousSt);
306  }
307  }
308  if (active != null)
309  {
310  boolean isauto = active instanceof AutomaticParticle;
311 
312  color = isauto? Color.red.darker(): Color.red;
313  g2.setColor(color);
314  drawShape(g2, getActive(), true, activest);
315  }
316  Rectangle autopickout = getMicrograph().getRectangle();
317  if (autopickout != null && getMicrograph().hasManualParticles())
318  {
319  g2.setColor(Color.yellow);
320  g2.setStroke(continuousst);
321  int x = getXOnImage((int) autopickout.getX());
322  int y = getYOnImage((int) autopickout.getY());
323  g2.drawRect(x, y, (int) (autopickout.getWidth() * magnification), (int) (autopickout.getHeight() * magnification));
324  }
325  }
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xmipp.viewer.particlepicker.ParticlePickerCanvas.drawShape
void drawShape(Graphics2D g2, ManualParticle p, boolean all, Stroke stroke)
Definition: ParticlePickerCanvas.java:303
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◆ getActive()

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ManualParticle xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas.getActive ()
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Definition at line 42 of file SupervisedPickerCanvas.java.

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42  {
43  return (ManualParticle) active;
44  }
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Definition at line 342 of file SupervisedPickerCanvas.java.

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343  {
344  return (SupervisedPickerJFrame)frame;
345  }
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Definition at line 35 of file SupervisedPickerCanvas.java.

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35  {
36 
37  if (getMicrograph().getParticles().isEmpty())
38  return null;
39  return getMicrograph().getLastAvailableParticle(getFrame().getThreshold());
40  }
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Definition at line 46 of file SupervisedPickerCanvas.java.

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46  {
47  return getLastManualParticle();
48  }
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Definition at line 353 of file SupervisedPickerCanvas.java.

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354  {
355  return (SupervisedPickerMicrograph)micrograph;
356  }
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Definition at line 360 of file SupervisedPickerCanvas.java.

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361  {
362  // TODO Auto-generated method stub
363  return (SupervisedParticlePicker)picker;
364  }
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Definition at line 367 of file SupervisedPickerCanvas.java.

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367  {
368 
369  super.keyPressed(e);
370 
371  if (e.getKeyCode() == KeyEvent.VK_ESCAPE){
372 
373  if (haveFirstPoint()){
374  resetLinearPicking();
375  }
376  }
377  }
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Definition at line 253 of file SupervisedPickerCanvas.java.

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254  {
255 
256  ManualParticle activeParticle = getActive();
257 
258  if (!activemoved)
259  return;
260 
261  if (!micrograph.fits(x, y, activeParticle.getSize()))
262  return;
263 
264  if (active instanceof AutomaticParticle && !((AutomaticParticle) active).isDeleted())
265  {
266 
267  getMicrograph().removeParticle(activeParticle, getParticlePicker());
268  active = new ManualParticle(activeParticle.getX(), activeParticle.getY(), activeParticle.getParticlePicker(), micrograph);
269  getMicrograph().addManualParticle(activeParticle, getParticlePicker());
270  repaint();
271  }
272  else
273  {
274  //changing particle position requires to remove it from template and add it again
275  moveActiveParticle(x, y);
276  repaint();
277 
278  }
279  frame.setChanged(true);
280  }
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abstract void setChanged(boolean changed)
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Definition: SupervisedPickerMicrograph.java:122
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void removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:140
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Definition: Micrograph.java:129
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Definition at line 179 of file SupervisedPickerCanvas.java.

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180  {
181 
182  super.mouseDragged(e);
183  if (SwingUtilities.isLeftMouseButton(e))
184  {
185  int x = offScreenX(e.getX());
186  int y = offScreenY(e.getY());
187  if (frame.isPickingAvailable(e))
188  {
189  if (frame.isEraserMode(e))
190  {
191  erase(e);
192  return;
193  }
194  if (active == null)
195  return;
196 
197  ManualParticle activeParticle = getActive();
198 
199  if (!micrograph.fits(x, y, activeParticle.getParticlePicker().getSize()))
200  return;
201  if (active instanceof AutomaticParticle)
202  {
203  getMicrograph().removeParticle(activeParticle, getParticlePicker());
204  active = new ManualParticle(activeParticle.getX(), activeParticle.getY(), picker, micrograph);
205  getMicrograph().addManualParticle((ManualParticle) active, getParticlePicker());
206  refresh();
207 
208  }else{
209  setActiveMoved(true);
210  moveActiveParticle(x, y);
211  }
212 
213  manageActive(x, y);
214 
215  }
216  }
217  }
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void addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:122
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void removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:140
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Definition: Micrograph.java:129
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Definition at line 379 of file SupervisedPickerCanvas.java.

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379  {
380  super.mouseMoved(e);
381 
382  if (getFrame().isLinearMode())
383  paintLine(e);
384  }
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Definition at line 51 of file SupervisedPickerCanvas.java.

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52  {
53  super.mousePressed(e);
54 
55  int x = offScreenX(e.getX());
56  int y = offScreenY(e.getY());
57 
58  if (frame.isPickingAvailable(e))
59  {
60  if (frame.isEraserMode(e)){
61  erase(e);
62  return;
63  }
64 
65  // Filament/linear picking
66  if (frame.isLinearMode()) {
67  linearPickingMousePressed(x,y, isKeyPressed(POLIGONAL_MODE_KEY));
68  return;
69  }
70 
71  ManualParticle p = getMicrograph().getParticle(x, y);
72  if (p == null)
73  p = getMicrograph().getAutomaticParticle(x, y, getFrame().getThreshold());
74 
75  if (p != null && SwingUtilities.isLeftMouseButton(e)){
76  active = p;
77  repaint();
78 
79  }else if (SwingUtilities.isLeftMouseButton(e)){
80  addParticle(x, y, true);
81  }
82  }
83  }
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Definition at line 220 of file SupervisedPickerCanvas.java.

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221  {
222 
223  super.mouseReleased(e);
224  int x = offScreenX(e.getX());
225  int y = offScreenY(e.getY());
226  if (frame.isPickingAvailable(e))
227  {
228  if (frame.isEraserMode(e))
229  {
230  erase(e);
231  return;
232  }
233  //deleting when mouse released, takes less updates to templates and frame
234  if (active != null && SwingUtilities.isLeftMouseButton(e) && e.isShiftDown())
235  {
236  getMicrograph().removeParticle(getActive(), getParticlePicker());
237  active = getLastManualParticle();
238  refresh();
239 
240  }
241  else
242  manageActive(x, y);
243  if (activemoved)
244  {
245  setActiveMoved(false);
246  if(picker.getMode() == Mode.Manual)
247 // TasksManager.getInstance().addTask(new ParticleToTemplatesTask(active));
248  new ParticleToTemplatesTask(getActive()).execute();
249  }
250  }
251  }
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void removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:140
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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas.refreshActive (PickerParticle p)
- 		-inline
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Definition at line 330 of file SupervisedPickerCanvas.java.

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331  {
332  if (p == null)
333  // active = null;
334  active = getLastParticle();
335  else
336  active = p;
337  repaint();
338 
339  }
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◆ removeParticle()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas.removeParticle (PickerParticle particleToRemove)
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Definition at line 348 of file SupervisedPickerCanvas.java.

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348  {
349  getMicrograph().removeParticle(particleToRemove,getParticlePicker());
350  }
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.removeParticle
void removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:140
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◆ resetLinearPicking()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas.resetLinearPicking ()
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-
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Definition at line 138 of file SupervisedPickerCanvas.java.

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138  {
139  this.linearPickingStartPoint = null;
140  }
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Member Data Documentation

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◆ POLIGONAL_MODE_KEY

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final int xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas.POLIGONAL_MODE_KEY = KeyEvent.VK_C
- 		-static
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Definition at line 23 of file SupervisedPickerCanvas.java.

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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__coll__graph.dot deleted file mode 100644 index b5dc2c6e..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__coll__graph.dot +++ /dev/null @@ -1,118 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node6 [label="xmipp.viewer.particlepicker.training.gui.\lSupervisedPickerCanvas",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node7 -> Node6 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="xmipp.viewer.particlepicker.\lParticlePickerCanvas\< P\l extends PickerParticle \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerCanvas.html"]; 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- Node74 [label="BasicStroke",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__coll__graph.md5 deleted file mode 100644 index 3e5cdc76..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -cedde3150fcc973f48382b29b9a5a024 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__inherit__graph.dot deleted file mode 100644 index 8daa59f2..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1SupervisedPickerCanvas__inherit__graph.dot +++ /dev/null @@ -1,16 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.gui.SupervisedPickerCanvas" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.training.gui.\lSupervisedPickerCanvas",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lParticlePickerCanvas\< P\l extends PickerParticle \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerCanvas.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.ij.commons.XmippImage\lCanvas",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1ij_1_1commons_1_1XmippImageCanvas.html"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ImageCanvas",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; 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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame Member List
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-
- -

This is the complete list of members for xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame, including all inherited members.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
actionPerformed(ActionEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateEraseMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateLinearMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activateNormalMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
activefilterxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
addFilterAppliedListener()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
applyFilter(String filter)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
autolbxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
autopickchbxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
autopickpercenttfxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
bundlexmipp.viewer.particlepicker.ParticlePickerJFrameprotected
canExit()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
canvasxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
centerchbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
centerParticle()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
centerparticlebtxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
changeShapes()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
checkpercentlbxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
circlechbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
close()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
closebtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
colorpnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
commandxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
displayZoom(double zoom)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
enableEdition(boolean isenable)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
enableSupervised(boolean selected)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
ERASE_ACTIVExmipp.viewer.particlepicker.ParticlePickerJFramestatic
eraseAvailable()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
eSizexmipp.viewer.particlepicker.ParticlePickerJFrameprotected
eSizelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
eSizepnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
executeScipionSaveAndExit()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
exitmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
exportmixmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
filemnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
filtersmnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
formatMicrographsTable()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
getAvailableParticles()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
getCanvas()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
getEraserSize()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getKeyAssist()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getMicrograph()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
getParticlePicker()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
getParticlesJDialog()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getResetMsg()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
getSide()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getStep()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getTextField(JSpinner spinner)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
getThreshold()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
getTrainMic()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
gpickerpnxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
hasThresholdChanged()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
hcontentsmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
helpmnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
iconbtxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
ijmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
importmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
importMicrographParticles(Format format, String file, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
importParticles(Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
importParticlesFromFile(Format format, String file, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
importpjdxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
initColorPane(Color color)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initEraserSizePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initGenericPickerPane()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
initializeCanvas()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
initMenuBar()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
initParticlesJDialog()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
initShapePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initSizePane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initStepPane()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
initToolBar()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isCenterParticle()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
isEraserMode(MouseEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isLinearMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isNormalMode()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isPickingAvailable(MouseEvent e)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
isShapeSelected(Shape shape)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
isSupervised()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
linearModeAvailable()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
loadMicrograph()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
loadParticles(boolean reset)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
manuallbxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
mbxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
micrographpnxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
micrographsmdxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
micrographstbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
modesgrpxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
moveToNextMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
moveToPreviousMicrograph()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
NEXT_MICROGRAPH_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
openHelpURl()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
ParticlePickerJFrame(ParticlePicker picker)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
particlesdialogxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
pmixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
positionlbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
positionxxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
ppickerxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
PREVIOUS_MICROGRAPH_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
processSizeMouseWheelEvent(MouseWheelEvent e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
readSizeFromTextField()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
rectanglechbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
reloadImage()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
resetbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
resetMicrograph()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
saveandexitbtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
savebtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
saveData(boolean notify)xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
savedlbxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
savemixmipp.viewer.particlepicker.ParticlePickerJFrameprotected
setAutopickPercent()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
setCanvasCursor()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
setChanged(boolean changed)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
setEraserSize(int newSize)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
setSaved(boolean saved)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
setThresholdChanged(boolean changed)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
setTitle()xmipp.viewer.particlepicker.ParticlePickerJFrameinlineprotected
shapelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
showException(Exception e)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
showHideModeParameters()xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
showMessage(String message)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
sizelbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sizepnxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sizetfxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
sppickerpnxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
SupervisedPickerJFrame(SupervisedParticlePicker picker)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
tbxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
templatesmixmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
THRESHOLD_LABEL_CHANGE_COLORxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFramestatic
thresholdlbxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
thresholdpnxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
thresholdslxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
thresholdtfxmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameprotected
TOGGLE_ERASE_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_LINEAR_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_MARKER_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
TOGGLE_NORMAL_MODE_KEYxmipp.viewer.particlepicker.ParticlePickerJFramestatic
xmipp::viewer::particlepicker::ParticlePickerJFrame.updateColor(Color color)xmipp.viewer.particlepicker.ParticlePickerJFrameinline
updateMicrographsModel(boolean all)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
xmipp::viewer::particlepicker::ParticlePickerJFrame.updateMicrographsModel()xmipp.viewer.particlepicker.ParticlePickerJFrameinline
updateParam(JTextField tf)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinlineprotected
updateSize(int size)xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrameinline
usezoombtxmipp.viewer.particlepicker.ParticlePickerJFrameprotected
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame Class Reference
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-Public Member Functions

SupervisedParticlePicker getParticlePicker ()
 
 SupervisedPickerJFrame (SupervisedParticlePicker picker)
 
boolean isCenterParticle ()
 
boolean centerParticle ()
 
ParticlesDialog initParticlesJDialog ()
 
SupervisedPickerMicrograph getMicrograph ()
 
double getThreshold ()
 
List<? extends ManualParticle > getAvailableParticles ()
 
String importParticlesFromFile (Format format, String file, float scale, boolean invertx, boolean inverty)
 
String importMicrographParticles (Format format, String file, float scale, boolean invertx, boolean inverty)
 
void updateSize (int size)
 
String importParticles (Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
void setChanged (boolean changed)
 
void setThresholdChanged (boolean changed)
 
boolean hasThresholdChanged ()
 
void setSaved (boolean saved)
 
void updateMicrographsModel (boolean all)
 
ParticlePickerCanvas getCanvas ()
 
boolean isSupervised ()
 
void initMenuBar ()
 
boolean isPickingAvailable (MouseEvent e)
 
SupervisedPickerMicrograph getTrainMic ()
 
void close ()
 
String getResetMsg ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
 ParticlePickerJFrame (ParticlePicker picker)
 
void moveToNextMicrograph ()
 
void moveToPreviousMicrograph ()
 
void processSizeMouseWheelEvent (MouseWheelEvent e)
 
String getResetMsg ()
 
void actionPerformed (ActionEvent e)
 
void applyFilter (String filter)
 
int getSide ()
 
abstract ParticlePickerCanvas getCanvas ()
 
abstract ParticlesDialog initParticlesJDialog ()
 
void loadParticles (boolean reset)
 
void updateMicrographsModel ()
 
abstract void updateMicrographsModel (boolean all)
 
ParticlesDialog getParticlesJDialog ()
 
abstract Micrograph getMicrograph ()
 
abstract List<? extends PickerParticle > getAvailableParticles ()
 
boolean isPickingAvailable (MouseEvent e)
 
void updateColor (Color color)
 
void initToolBar ()
 
boolean isEraserMode (MouseEvent e)
 
void activateEraseMode ()
 
boolean isLinearMode ()
 
boolean isNormalMode ()
 
void activateLinearMode ()
 
void activateNormalMode ()
 
int getEraserSize ()
 
void setEraserSize (int newSize)
 
int getStep ()
 
void changeShapes ()
 
boolean isShapeSelected (Shape shape)
 
abstract ParticlePicker getParticlePicker ()
 
abstract void setChanged (boolean changed)
 
void setSaved (boolean saved)
 
JFormattedTextField getTextField (JSpinner spinner)
 
void updateSize (int size)
 
boolean showMessage (String message)
 
boolean showException (Exception e)
 
void close ()
 
abstract String importParticles (Format format, String dir, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
Map< Object, Object > getKeyAssist ()
 
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-Static Public Attributes

static final Color THRESHOLD_LABEL_CHANGE_COLOR = Color.DARK_GRAY
 
- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
static final int TOGGLE_LINEAR_MODE_KEY = KeyEvent.VK_L
 
static final int TOGGLE_ERASE_MODE_KEY = KeyEvent.VK_E
 
static final int NEXT_MICROGRAPH_KEY = KeyEvent.VK_R
 
static final int PREVIOUS_MICROGRAPH_KEY = KeyEvent.VK_W
 
static final int TOGGLE_MARKER_KEY = KeyEvent.VK_SPACE
 
static final int TOGGLE_NORMAL_MODE_KEY = KeyEvent.VK_P
 
static final int ERASE_ACTIVE = KeyEvent.VK_DELETE
 
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-Protected Member Functions

void initializeCanvas ()
 
void formatMicrographsTable ()
 
void setAutopickPercent ()
 
void enableSupervised (boolean selected)
 
void enableEdition (boolean isenable)
 
synchronized void loadMicrograph ()
 
void resetMicrograph ()
 
void initGenericPickerPane ()
 
void updateParam (JTextField tf)
 
void showHideModeParameters ()
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
boolean canExit ()
 
abstract void loadMicrograph ()
 
boolean saveData (boolean notify)
 
void addFilterAppliedListener ()
 
void openHelpURl ()
 
abstract void resetMicrograph ()
 
void enableEdition (boolean enable)
 
void reloadImage ()
 
void initShapePane ()
 
boolean eraseAvailable ()
 
void setCanvasCursor ()
 
boolean linearModeAvailable ()
 
void showHideModeParameters ()
 
void displayZoom (double zoom)
 
void setTitle ()
 
void initColorPane (Color color)
 
void initStepPane ()
 
void initEraserSizePane ()
 
void initSizePane ()
 
void readSizeFromTextField ()
 
void executeScipionSaveAndExit ()
 
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-Protected Attributes

SupervisedPickerCanvas canvas
 
JMenuBar mb
 
SupervisedParticlePicker ppicker
 
JPanel micrographpn
 
MicrographsTableModel micrographsmd
 
float positionx
 
JButton iconbt
 
JLabel manuallb
 
JLabel autolb
 
JLabel savedlb
 
JSlider thresholdsl
 
JPanel thresholdpn
 
JFormattedTextField thresholdtf
 
JToggleButton centerparticlebt
 
JMenuItem exportmi
 
JToggleButton autopickchb
 
JPanel sppickerpn
 
JMenuItem templatesmi
 
JLabel checkpercentlb
 
JFormattedTextField autopickpercenttf
 
JLabel thresholdlb
 
JPanel gpickerpn
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePickerJFrame
ParticlesDialog particlesdialog
 
JMenuItem ijmi
 
JToggleButton circlechb
 
JToggleButton rectanglechb
 
JToggleButton centerchb
 
JLabel shapelb
 
JMenuItem savemi
 
JMenuItem hcontentsmi
 
JMenuItem pmi
 
JMenuItem exportmi
 
JMenu filtersmn
 
String activefilter
 
JPanel sizepn
 
JLabel sizelb
 
JFormattedTextField sizetf
 
JPanel eSizepn
 
JLabel eSizelb
 
JSpinner eSize
 
JMenu filemn
 
JMenuItem importmi
 
JButton colorbt
 
Color color
 
JPanel colorpn
 
JButton resetbt
 
JTable micrographstb
 
ImportParticlesJDialog importpjd = null
 
JMenuItem exitmi
 
JLabel positionlb
 
JToggleButton usezoombt
 
ButtonGroup modesgrp
 
JMenu helpmn
 
JButton savebt
 
JButton saveandexitbt
 
JToolBar tb
 
ResourceBundle bundle
 
String command
 
JButton closebt
 
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Definition at line 23 of file SupervisedPickerJFrame.java.

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Constructor & Destructor Documentation

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◆ SupervisedPickerJFrame()

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Definition at line 61 of file SupervisedPickerJFrame.java.

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61  {
62 
63  super(picker);
64  try {
65  this.ppicker = picker;
66  initComponents();
67  setChanged(false);
68  Classifier c = ppicker.getClassifier();
69  if(c instanceof GenericClassifier) {
70  GenericClassifier gc = (GenericClassifier)c;
71  if (!gc.hasInitialCoordinates())
72  ppicker.autopick(this, getMicrograph());
73  }
74  } catch (IllegalArgumentException ex) {
75  //close();
76  throw ex;
77  }
78  }
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.autopick
void autopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph next)
Definition: SupervisedParticlePicker.java:1124
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◆ centerParticle()

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Definition at line 84 of file SupervisedPickerJFrame.java.

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84  {
85  return centerparticlebt.isSelected() && isNormalMode();
86  }
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Definition at line 867 of file SupervisedPickerJFrame.java.

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867  {
868  if (ppicker.isCorrectPending()) {
869  boolean iscorrect = XmippDialog.showQuestion(this, "Would you like to correct training with added and deleted particles?");
870  if (iscorrect) {
871  ppicker.correct();
872  }
873  }
874  super.close();
875  }
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static boolean showQuestion(JFrame parent, String message)
Definition: XmippDialog.java:258
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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.enableEdition (boolean isenable)
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Definition at line 461 of file SupervisedPickerJFrame.java.

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461  {
462  super.enableEdition(isenable);
463  centerparticlebt.setEnabled(isenable);
464  if (ppicker.getMode() != Mode.Review) {
465  autopickchb.setEnabled(isenable);
466  thresholdpn.setEnabled(isenable);
467  }
468  saveandexitbt.setEnabled(isenable);
469  if(ppicker.isScipionSave())
470  {
471  Color color = isenable? XmippWindowUtil.firebrick: XmippWindowUtil.LIGHT_BLUE;
472  Color forecolor = isenable? Color.WHITE: Color.GRAY;
473  saveandexitbt.setBackground(color);
474  saveandexitbt.setForeground(forecolor);
475  }
476 
477  }
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Definition: XmippWindowUtil.java:57
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Definition: XmippWindowUtil.java:61
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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.enableSupervised (boolean selected)
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Definition at line 441 of file SupervisedPickerJFrame.java.

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441  {
442 
443  thresholdsl.setEnabled(selected);
444  thresholdlb.setEnabled(selected);
445  thresholdtf.setEnabled(selected);
446  sizelb.setEnabled(!selected);
447  // in sup mode size cannot be changed
448  sizetf.setEnabled(!selected);
449  sizelb.setEnabled(!selected);
450  importmi.setEnabled(!selected);
451  //autopickpercenttf.setEnabled(selected);
452 
453  pack();
454 
455  }
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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.formatMicrographsTable ()
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Definition at line 193 of file SupervisedPickerJFrame.java.

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193  {
194  int totalWidth = 630;
195  int micWidth = 440;
196 
197  if (ppicker.containsPSD()) // shrink columns to make space for PSD
198  {
199  totalWidth -= 115;
200  micWidth -= 115;
201  }
202 
203  micrographstb.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
204 
205  TableColumnModel tcm = micrographstb.getColumnModel();
206  tcm.getColumn(0).setPreferredWidth(40);
207 
208  if (ppicker.hasDefocusU())
209  {
210  micWidth -= 70;
211  tcm.getColumn(4).setPreferredWidth(70);
212  }
213 
214  tcm.getColumn(1).setPreferredWidth(micWidth);
215  tcm.getColumn(2).setPreferredWidth(70);
216  tcm.getColumn(3).setPreferredWidth(80);
217  micrographstb.setPreferredScrollableViewportSize(new Dimension(totalWidth, 304));
218  micrographstb.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
219  int index = ppicker.getMicrographIndex();
220  if (index != -1) {
221  micrographstb.setRowSelectionInterval(index, index);
222  }
223  }
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Definition at line 105 of file SupervisedPickerJFrame.java.

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105  {
106  return getMicrograph().getAvailableParticles(getThreshold());
107  }
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Definition at line 271 of file SupervisedPickerJFrame.java.

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271  {
272  return canvas;
273  }
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Definition at line 93 of file SupervisedPickerJFrame.java.

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93  {
94  return ppicker.getMicrograph();
95  }
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◆ getParticlePicker()

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SupervisedParticlePicker xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.getParticlePicker ()
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Definition at line 57 of file SupervisedPickerJFrame.java.

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57  {
58  return ppicker;
59  }
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◆ getResetMsg()

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String xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.getResetMsg ()
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Definition at line 877 of file SupervisedPickerJFrame.java.

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877  {
878  String msg = super.getResetMsg();
879  if (ppicker.getMode() == Mode.Supervised) {
880  msg += "\nParticles will be automatically picked again";
881  }
882  return msg;
883  }
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◆ getThreshold()

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Definition at line 97 of file SupervisedPickerJFrame.java.

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97  {
98  if (thresholdsl == null) {
99  return 0;
100  }
101  return thresholdsl.getValue() / 100.0;
102  }
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◆ getTrainMic()

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SupervisedPickerMicrograph xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.getTrainMic ()
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Definition at line 794 of file SupervisedPickerJFrame.java.

-
794  {
795  String trainmsg = "Classifier training for autopick requires that the previous micrographs and the particle's region detected to be fully picked. "
796  + "Are you sure you want to continue?";
797  if (ppicker.getManualParticlesNumber() < ppicker.getParticlesThreshold()) {
798  XmippDialog.showInfo(this, String
799  .format("You should have at least %s particles to go to %s mode", ppicker.getParticlesThreshold(), Mode.Supervised));
800  return null;
801  }
802  boolean isvalidrect = false;
803  int index = micrographstb.getSelectedRow();
804  SupervisedPickerMicrograph rectmic = null;
805  while (index >= 0)
806  {
807  rectmic = ppicker.getMicrographs().get(index);
808  if (rectmic.hasManualParticles())
809  {
810  rectmic.initParticlesRectangle(ppicker);
811  isvalidrect = rectmic.isValid(ppicker);
812  if(isvalidrect)
813  break;
814  else
815  rectmic.resetParticlesRectangle();
816  }
817  index --;
818  }
819  if(index < 0)
820  {
821  index = micrographstb.getSelectedRow() + 1;
822  while (index < ppicker.getMicrographs().size())
823  {
824  rectmic = ppicker.getMicrographs().get(index);
825  if (rectmic.hasManualParticles())
826  {
827  rectmic.initParticlesRectangle(ppicker);
828  isvalidrect = rectmic.isValid(ppicker);
829  if(isvalidrect)
830  break;
831  }
832  index ++;
833  }
834  }
835 
836  if(index < 0 || index == ppicker.getMicrographs().size())
837  {
838  canvas.repaint();
839  XmippDialog.showError(this, "No valid training rectangle could be found in micrographs picked. Particles might be too few.");
840  rectmic.resetParticlesRectangle();
841  canvas.repaint();
842  return null;
843  }
844  trainmsg = "";
845  if(rectmic.equals(getMicrograph()))
846  {
847  canvas.repaint();
848  trainmsg += "Classifier requires that the region detected and the micrographs previously picked to be fully picked. "
849  + "Are you sure you want to continue?";
850  }
851  else
852  trainmsg += "Classifier requires that the micrographs previously picked to be fully picked. "
853  + "Are you sure you want to continue?";
854  int result = XmippDialog
855  .showQuestionYesNoCancel(this, trainmsg);
856  if (result == XmippQuestionDialog.CANCEL_OPTION) {
857  canvas.repaint();
858  rectmic.resetParticlesRectangle();
859  }
860  if(result != XmippQuestionDialog.YES_OPTION)
861  rectmic = null;
862  return rectmic;
863  }
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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xmipp.utils.XmippDialog.showQuestionYesNoCancel
static int showQuestionYesNoCancel(JFrame parent, String message)
Definition: XmippDialog.java:274
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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◆ hasThresholdChanged()

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boolean xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.hasThresholdChanged ()
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Definition at line 246 of file SupervisedPickerJFrame.java.

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246  {
247  return this.thresholdlb.getForeground() == THRESHOLD_LABEL_CHANGE_COLOR;
248  }
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◆ importMicrographParticles()

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String xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.importMicrographParticles (Format format,
String file,
float scale,
boolean invertx,
boolean inverty 
)
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Definition at line 129 of file SupervisedPickerJFrame.java.

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129  {
130 
131  String filename = Micrograph.getName(file, 1);
132  // validating you want use this file for this micrograph with different
133  // name
134  if (!filename.equals(getMicrograph().getName())) {
135  String msg = String.format("Are you sure you want to import data from file\n%s to micrograph %s ?", file, getMicrograph().getName());
136  boolean importdata = XmippDialog.showQuestion(this, msg);
137  if (!importdata) {
138  return null;
139  }
140  }
141  ppicker.resetMicrograph(getMicrograph());
142  String result = ppicker.importParticlesFromFile(file, format, getMicrograph(), scale, invertx, inverty);
143  ppicker.saveData(getMicrograph());
144  return result;
145  }
xmipp.viewer.particlepicker.Micrograph.getName
static String getName(String file, int level)
Definition: Micrograph.java:140
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xmipp.utils.XmippDialog.showQuestion
static boolean showQuestion(JFrame parent, String message)
Definition: XmippDialog.java:258
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFile
String importParticlesFromFile(String path, Format f, SupervisedPickerMicrograph m, float scale, boolean invertx, boolean inverty)
Definition: SupervisedParticlePicker.java:817
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◆ importParticles()

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String xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.importParticles (Format format,
String dir,
String preffix,
String suffix,
float scale,
boolean invertx,
boolean inverty 
)
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Definition at line 161 of file SupervisedPickerJFrame.java.

-
161  {
162  String result = "";
163 
164  if (new File(dir).isDirectory()) {
165  result = ppicker.importParticlesFromFolder(dir, format, preffix, suffix, scale, invertx, inverty);
166  boolean resize = ((Integer)sizetf.getValue()).intValue() != ppicker.getSize();
167  sizetf.setValue(ppicker.getSize());
168  getCanvas().repaint();
169  updateMicrographsModel(true);
170  getCanvas().refreshActive(null);
171  ppicker.updateTemplatesStack(resize);
172 
173 
174  } else // only can choose file if TrainingPickerJFrame instance
175  {
176  result = importParticlesFromFile(format, dir, scale, invertx, inverty);
177  }
178  return result;
179 
180  }
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFolder
String importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
Definition: SupervisedParticlePicker.java:777
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.importParticlesFromFile
String importParticlesFromFile(Format format, String file, float scale, boolean invertx, boolean inverty)
Definition: SupervisedPickerJFrame.java:109
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xmipp.viewer.particlepicker.ParticlePickerCanvas.refreshActive
abstract void refreshActive(PickerParticle p)
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◆ importParticlesFromFile()

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String xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.importParticlesFromFile (Format format,
String file,
float scale,
boolean invertx,
boolean inverty 
)
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Definition at line 109 of file SupervisedPickerJFrame.java.

-
109  {
110  if (!new File(file).exists()) {
111  throw new IllegalArgumentException(XmippMessage.getNoSuchFieldValueMsg("file", file));
112  }
113  String result = "";
114  if (ppicker.isReviewFile(file)) {
115  result = ppicker.importAllParticles(file, scale, invertx, inverty);
116  ppicker.saveAllData();
117  } else {
118  result = importMicrographParticles(format, file, scale, invertx, inverty);
119  }
120  setChanged(false);
121  getCanvas().repaint();
122  updateMicrographsModel();
123  updateSize(ppicker.getSize());//will also update templates
124  canvas.refreshActive(null);
125 
126  return result;
127  }
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xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.importMicrographParticles
String importMicrographParticles(Format format, String file, float scale, boolean invertx, boolean inverty)
Definition: SupervisedPickerJFrame.java:129
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xmipp.utils.XmippMessage.getNoSuchFieldValueMsg
static String getNoSuchFieldValueMsg(String field, Object value)
Definition: XmippMessage.java:52
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◆ initGenericPickerPane()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.initGenericPickerPane ()
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Definition at line 887 of file SupervisedPickerJFrame.java.

-
888  {
889  gpickerpn = new JPanel(new FlowLayout(FlowLayout.LEFT));
890  gpickerpn.setBorder(BorderFactory.createTitledBorder("Autopick"));
891  List<Classifier.Parameter> parameters = ppicker.getClassifier().getParams();
892  paramtfs = new HashMap<JTextField, Classifier.Parameter>();
893  JTextField tf;
894  JLabel lb;
895  for(Classifier.Parameter param: parameters)
896  {
897  lb = new JLabel(param.label);
898  lb.setToolTipText(param.help);
899  gpickerpn.add(lb);
900  tf = new JTextField(3);
901  tf.setToolTipText(param.help);
902  tf.setText(param.value);
903  tf.setActionCommand(param.name);
904  tf.addFocusListener(new FocusListener()
905  {
906 
907  @Override
908  public void focusLost(FocusEvent e)
909  {
910  if(e.isTemporary())
911  return;
912  JTextField tf = (JTextField)e.getComponent();
913  updateParam(tf);
914  }
915 
916  @Override
917  public void focusGained(FocusEvent e)
918  {
919  // TODO Auto-generated method stub
920 
921  }
922  });
923  tf.addActionListener(new ActionListener()
924  {
925  @Override
926  public void actionPerformed(ActionEvent e)
927  {
928  JTextField tf = (JTextField)e.getSource();
929  updateParam(tf);
930  for(SupervisedPickerMicrograph m: ppicker.getMicrographs())
931  ppicker.resetMicrograph(m);
932  ppicker.autopick(SupervisedPickerJFrame.this, getMicrograph());
933 
934  }
935  });
936  gpickerpn.add(tf);
937  paramtfs.put(tf, param);
938  if(param.name.equals("diameter") || param.name.equals("boxSize"))//classifier diameter and particle size are the same
939  updateSize(Integer.parseInt(tf.getText()));
940  }
941  autopickbt = XmippWindowUtil.getTextButton("Run", new ActionListener(){
942 
943  @Override
944  public void actionPerformed(ActionEvent arg0)
945  {
946  for(SupervisedPickerMicrograph m: ppicker.getMicrographs())
947  ppicker.resetMicrograph(m);
948  ppicker.autopick(SupervisedPickerJFrame.this, getMicrograph());
949 
950  }});
951  autopickbt.setBackground(XmippWindowUtil.firebrick);
952  autopickbt.setForeground(Color.WHITE);
953  gpickerpn.add(autopickbt);
954  }
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xmipp.jni.Classifier.getParams
List< Classifier.Parameter > getParams()
Definition: Classifier.java:42
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static final Color firebrick
Definition: XmippWindowUtil.java:57
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xmipp.utils.XmippWindowUtil.getTextButton
static JButton getTextButton(String text, ActionListener listener)
Definition: XmippWindowUtil.java:140
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.autopick
void autopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph next)
Definition: SupervisedParticlePicker.java:1124
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◆ initializeCanvas()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.initializeCanvas ()
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Definition at line 183 of file SupervisedPickerJFrame.java.

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183  {
184 
185  if (canvas == null) {
186  canvas = new SupervisedPickerCanvas(this);
187  } else {
188  canvas.updateMicrograph();
189  }
190 
191  }
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◆ initMenuBar()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.initMenuBar ()
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Definition at line 479 of file SupervisedPickerJFrame.java.

-
479  {
480  mb = new JMenuBar();
481 
482  // Setting menus
483  exportmi = new JMenuItem("Export coordinates...", XmippResource.getIcon("export_wiz.gif"));
484 
485  exportmi.addActionListener(new ActionListener() {
486 
487  @Override
488  public void actionPerformed(ActionEvent e) {
489  XmippFileChooser fc = new XmippFileChooser();
490  int returnVal = fc.showOpenDialog(SupervisedPickerJFrame.this);
491 
492  try {
493  if (returnVal == XmippFileChooser.APPROVE_OPTION) {
494  File file = fc.getSelectedFile();
495  ppicker.exportParticles(file.getAbsolutePath());
496  showMessage("Export successful");
497  }
498  } catch (Exception ex) {
499  showException(ex);
500  }
501  }
502  });
503  filemn.add(importmi);
504  if (ppicker.getMode() != Mode.Manual) {
505  importmi.setEnabled(false);
506  }
507  filemn.add(exportmi);
508  filemn.add(exitmi);
509 
510  JMenu windowmn = new JMenu(bundle.getString("window"));
511 
512  mb.add(filemn);
513  mb.add(filtersmn);
514  mb.add(windowmn);
515  mb.add(helpmn);
516  // importffilemi.setText("Import from File...");
517 
518  windowmn.add(pmi);
519  windowmn.add(ijmi);
520 
521 
522  templatesmi = new JMenuItem("Templates");
523  templatesmi.addActionListener(new ActionListener() {
524 
525  @Override
526  public void actionPerformed(ActionEvent arg0) {
527  loadTemplates();
528  }
529  });
530  windowmn.add(templatesmi);
531 
532  }
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static ImageIcon getIcon(String name)
Definition: XmippResource.java:78
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◆ initParticlesJDialog()

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ParticlesDialog xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.initParticlesJDialog ()
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Definition at line 89 of file SupervisedPickerJFrame.java.

-
89  {
90  return new ParticlesDialog(this);
91  }
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◆ isCenterParticle()

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Definition at line 80 of file SupervisedPickerJFrame.java.

-
80  {
81  return centerparticlebt.isSelected();
82  }
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◆ isPickingAvailable()

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boolean xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.isPickingAvailable (MouseEvent e)
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Definition at line 787 of file SupervisedPickerJFrame.java.

-
787  {
788  if (!super.isPickingAvailable(e)) {
789  return false;
790  }
791  return getMicrograph().getState() != MicrographState.Corrected;
792  }
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◆ isSupervised()

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boolean xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.isSupervised ()
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Definition at line 457 of file SupervisedPickerJFrame.java.

-
457  {
458  return autopickchb.isSelected();
459  }
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◆ loadMicrograph()

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synchronized void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.loadMicrograph ()
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Definition at line 684 of file SupervisedPickerJFrame.java.

-
684  {
685 
686  if (micrographstb.getSelectedRow() == -1) {
687  return;// Probably from fireTableDataChanged raised
688  } // is same micrograph??
689  int micindex = ppicker.getMicrographIndex();
690 
691  int index = micrographstb.getSelectedRow();
692  if (micindex == index && canvas != null && canvas.getIw().isVisible()) {
693  return;
694  }
695 
696  // Save particles first before moving and loading the clicked micrograph.
697  if (ppicker.isChanged() && ppicker.getMode() != Mode.Supervised)
698  {
699  if (!saveData(false)) {
700  micrographstb.getSelectionModel().setSelectionInterval(micindex,micindex);
701  return;
702  }
703  }
704 
705  SupervisedPickerMicrograph next = ppicker.getMicrographs().get(index);
706  SupervisedPickerMicrograph current = getMicrograph();
707  current.resetParticlesRectangle();
708  if (!current.equals(next))// app just started
709  {
710  int result = tryCorrectAndAutopick(current, next);
711 
712  if (result == XmippQuestionDialog.CANCEL_OPTION) {
713  micrographstb.setRowSelectionInterval(micindex, micindex);
714  return;
715  }
716 
717  }
718  ppicker.setMicrograph(next);
719  ppicker.saveConfig();
720  Mode mode = ppicker.getMode();
721 
722  if (mode == Mode.Supervised) {
723  resetbt.setEnabled(next.getState() != MicrographState.Manual);
724  double threshold = next.getThreshold();
725  if(threshold == 0 && next.getAutomaticParticlesNumber() == 0)
726  {
727  threshold = current.getThreshold();
728  next.setThreshold(threshold);
729  this.setThresholdChanged(true);
730  }else{
731  this.setThresholdChanged(false);
732  }
733  thresholdsl.setValue((int) (threshold * 100));
734  thresholdtf.setValue(threshold);
735  }
736  else if (mode == Mode.Automatic) {
737  resetbt.setEnabled(false);
738  }
739 
740  initializeCanvas();
741  if(ppicker.containsPSD())
742  iconbt.setIcon(next.getCTFIcon());
743 
744  pack();
745 
746  if (particlesdialog != null) {
747  loadParticles(false);
748  }
749 
750  }
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◆ resetMicrograph()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.resetMicrograph ()
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Definition at line 776 of file SupervisedPickerJFrame.java.

-
776  {
777  ppicker.resetMicrograph(getMicrograph());
778  canvas.refreshActive(null);
779  updateMicrographsModel();
780  ppicker.updateTemplatesStack(false);
781 
782  if (ppicker.getMode() == Mode.Supervised) {
783  ppicker.autopick(this, getMicrograph());
784  }
785  }
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.autopick
void autopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph next)
Definition: SupervisedParticlePicker.java:1124
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◆ setAutopickPercent()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.setAutopickPercent ()
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Definition at line 426 of file SupervisedPickerJFrame.java.

-
427  {
428  if (autopickpercenttf.getValue() == null || ((Number)autopickpercenttf.getValue()).intValue() <= 0)
429  {
430  XmippDialog.showInfo(this, XmippMessage.getEmptyFieldMsg("Check (%)"));
431  autopickpercenttf.setValue(getMicrograph().getAutopickpercent());
432  return;
433  }
434 
435  int autopickpercent = ((Number) autopickpercenttf.getValue()).intValue();
436  getMicrograph().setAutopickpercent(autopickpercent);
437  ppicker.setAutopickpercent(autopickpercent);
438  ppicker.saveConfig();
439  }
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xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
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static String getEmptyFieldMsg(String field)
Definition: XmippMessage.java:44
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◆ setChanged()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.setChanged (boolean changed)
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Definition at line 231 of file SupervisedPickerJFrame.java.

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231  {
232  ppicker.setChanged(changed);
233  savemi.setEnabled(changed);
234  savebt.setEnabled(changed);
235  }
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◆ setSaved()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.setSaved (boolean saved)
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Definition at line 250 of file SupervisedPickerJFrame.java.

-
250  {
251  ppicker.setSaved(saved);
252  // Do not print anything: for debugging --> savedlb.setText(saved?"Saved":"");
253  }
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◆ setThresholdChanged()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.setThresholdChanged (boolean changed)
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Definition at line 237 of file SupervisedPickerJFrame.java.

-
237  {
238 
239  if (changed){
240  this.thresholdlb.setForeground(THRESHOLD_LABEL_CHANGE_COLOR);
241  this.setChanged(true);
242  } else {
243  this.thresholdlb.setForeground(Color.BLACK);
244  }
245  }
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◆ showHideModeParameters()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.showHideModeParameters ()
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Definition at line 966 of file SupervisedPickerJFrame.java.

-
966  {
967  super.showHideModeParameters();
968  centerparticlebt.setVisible(isNormalMode());
969  }
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◆ updateMicrographsModel()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.updateMicrographsModel (boolean all)
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Definition at line 255 of file SupervisedPickerJFrame.java.

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255  {
256 
257  if (particlesdialog != null)
258  loadParticles(false);
259  int index = ppicker.getMicrographIndex();
260 
261  if (all)
262  micrographsmd.fireTableRowsUpdated(0, micrographsmd.getRowCount() - 1);
263  else
264  micrographsmd.fireTableRowsUpdated(index, index);
265 
266  micrographstb.setRowSelectionInterval(index, index);
267  manuallb.setText(Integer.toString(ppicker.getManualParticlesNumber()));
268  autolb.setText(Integer.toString(ppicker.getAutomaticParticlesNumber()));
269  }
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◆ updateParam()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.updateParam (JTextField tf)
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Definition at line 956 of file SupervisedPickerJFrame.java.

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957  {
958  Classifier.Parameter param = paramtfs.get(tf);
959  if(param.value.equals(tf.getText()))
960  return;
961  if(param.name.equals("diameter") || param.name.equals("boxSize"))//classifier diameter and particle size are the same
962  updateSize(Integer.parseInt(tf.getText()));
963  param.value = tf.getText();
964  }
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◆ updateSize()

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void xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.updateSize (int size)
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Definition at line 147 of file SupervisedPickerJFrame.java.

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147  {
148  try {
149 
150  super.updateSize(size);
151  ppicker.updateTemplatesStack(true);
152 
153 
154  } catch (Exception e) {
155  e.printStackTrace();
156  XmippDialog.showError(this, e.getMessage());
157  }
158  }
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xmipp.utils.XmippDialog.showError
boolean showError(String message)
Definition: XmippDialog.java:211
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Member Data Documentation

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◆ autolb

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JLabel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.autolb
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Definition at line 35 of file SupervisedPickerJFrame.java.

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◆ autopickchb

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JToggleButton xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.autopickchb
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Definition at line 44 of file SupervisedPickerJFrame.java.

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◆ autopickpercenttf

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JFormattedTextField xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.autopickpercenttf
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Definition at line 50 of file SupervisedPickerJFrame.java.

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◆ canvas

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SupervisedPickerCanvas xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.canvas
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Definition at line 26 of file SupervisedPickerJFrame.java.

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◆ centerparticlebt

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JToggleButton xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.centerparticlebt
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Definition at line 42 of file SupervisedPickerJFrame.java.

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◆ checkpercentlb

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JLabel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.checkpercentlb
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Definition at line 49 of file SupervisedPickerJFrame.java.

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◆ exportmi

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JMenuItem xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.exportmi
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Definition at line 43 of file SupervisedPickerJFrame.java.

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◆ gpickerpn

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JPanel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.gpickerpn
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Definition at line 52 of file SupervisedPickerJFrame.java.

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◆ iconbt

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JButton xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.iconbt
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Definition at line 33 of file SupervisedPickerJFrame.java.

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◆ manuallb

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JLabel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.manuallb
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Definition at line 34 of file SupervisedPickerJFrame.java.

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◆ mb

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JMenuBar xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.mb
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Definition at line 27 of file SupervisedPickerJFrame.java.

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◆ micrographpn

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JPanel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.micrographpn
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Definition at line 29 of file SupervisedPickerJFrame.java.

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◆ micrographsmd

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MicrographsTableModel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.micrographsmd
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Definition at line 30 of file SupervisedPickerJFrame.java.

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◆ positionx

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float xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.positionx
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Definition at line 32 of file SupervisedPickerJFrame.java.

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◆ ppicker

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SupervisedParticlePicker xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.ppicker
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Definition at line 28 of file SupervisedPickerJFrame.java.

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◆ savedlb

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JLabel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.savedlb
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Definition at line 36 of file SupervisedPickerJFrame.java.

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◆ sppickerpn

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JPanel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.sppickerpn
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Definition at line 45 of file SupervisedPickerJFrame.java.

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◆ templatesmi

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JMenuItem xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.templatesmi
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Definition at line 47 of file SupervisedPickerJFrame.java.

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◆ THRESHOLD_LABEL_CHANGE_COLOR

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final Color xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.THRESHOLD_LABEL_CHANGE_COLOR = Color.DARK_GRAY
- 		-static
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Definition at line 25 of file SupervisedPickerJFrame.java.

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◆ thresholdlb

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JLabel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.thresholdlb
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Definition at line 51 of file SupervisedPickerJFrame.java.

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◆ thresholdpn

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JPanel xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.thresholdpn
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Definition at line 39 of file SupervisedPickerJFrame.java.

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◆ thresholdsl

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JSlider xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.thresholdsl
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Definition at line 38 of file SupervisedPickerJFrame.java.

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◆ thresholdtf

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JFormattedTextField xmipp.viewer.particlepicker.training.gui.SupervisedPickerJFrame.thresholdtf
- 		-protected
-
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Definition at line 40 of file SupervisedPickerJFrame.java.

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-
The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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xmipp.viewer.particlepicker.training.gui.TemplatesJDialog Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.gui.TemplatesJDialog, including all inherited members.

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close()xmipp.viewer.particlepicker.training.gui.TemplatesJDialoginline
framexmipp.viewer.particlepicker.training.gui.TemplatesJDialogprotected
loadTemplates(boolean resize)xmipp.viewer.particlepicker.training.gui.TemplatesJDialoginline
setTemplates()xmipp.viewer.particlepicker.training.gui.TemplatesJDialoginlineprotected
TemplatesJDialog(SupervisedPickerJFrame frame)xmipp.viewer.particlepicker.training.gui.TemplatesJDialoginline
templatespnxmipp.viewer.particlepicker.training.gui.TemplatesJDialogprotected
widthxmipp.viewer.particlepicker.training.gui.TemplatesJDialogprotected
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-Public Member Functions | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.viewer.particlepicker.training.gui.TemplatesJDialog Class Reference
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-Public Member Functions

 TemplatesJDialog (SupervisedPickerJFrame frame)
 
void loadTemplates (boolean resize)
 
void close ()
 
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-Protected Member Functions

void setTemplates ()
 
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-Protected Attributes

SupervisedPickerJFrame frame
 
JPanel templatespn
 
int width
 
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Detailed Description

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Definition at line 24 of file TemplatesJDialog.java.

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Constructor & Destructor Documentation

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◆ TemplatesJDialog()

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xmipp.viewer.particlepicker.training.gui.TemplatesJDialog.TemplatesJDialog (SupervisedPickerJFrame frame)
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Definition at line 32 of file TemplatesJDialog.java.

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33  {
34  super(frame);
35  this.frame = frame;
36  initComponents();
37  }
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◆ close()

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void xmipp.viewer.particlepicker.training.gui.TemplatesJDialog.close ()
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Definition at line 103 of file TemplatesJDialog.java.

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104  {
105  setVisible(false);
106  dispose();
107 
108  }
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◆ loadTemplates()

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void xmipp.viewer.particlepicker.training.gui.TemplatesJDialog.loadTemplates (boolean resize)
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Definition at line 39 of file TemplatesJDialog.java.

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40  {
41  try
42  {
43  ImageGeneric templates = frame.getParticlePicker().getTemplates();
44  int size = frame.getParticlePicker().getSize();
45  templatespn.removeAll();
46  templatespn.setPreferredSize(new Dimension((int) (size * templates.getNDim() + 50), size + 5));
47 
48  if(frame.getParticlePicker().hasManualParticles())
49  {
50  ImagePlus template;
51  for (int i = 0; i < frame.getParticlePicker().getTemplatesNumber(); i ++)
52  {
53  template = XmippImageConverter.convertToImagePlus(templates, ImageGeneric.FIRST_IMAGE + i);
54  templatespn.add(new JLabel(new ImageIcon(template.getImage()), SwingConstants.CENTER));
55  }
56  }
57  }
58  catch (Exception e)
59  {
60  // TODO Auto-generated catch block
61  e.printStackTrace();
62 
63  }
64  templatespn.repaint();
65  pack();
66  }
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void xmipp.viewer.particlepicker.training.gui.TemplatesJDialog.setTemplates ()
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Definition at line 110 of file TemplatesJDialog.java.

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111  {
112  if (templatestf.getValue() == null || ((Number)templatestf.getValue()).intValue() <= 0)
113  {
114  XmippDialog.showInfo(frame, XmippMessage.getOutOfBoundsMsg("Templates"));
115  templatestf.setValue(frame.getParticlePicker().getTemplatesNumber());
116  return;
117  }
118 
119  int templates = ((Number) templatestf.getValue()).intValue();
120  if (templates != frame.getParticlePicker().getTemplatesNumber())
121  {
122  frame.getParticlePicker().setTemplatesNumber(templates);
123  frame.loadTemplates();
124  }
125 
126  }
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◆ frame

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SupervisedPickerJFrame xmipp.viewer.particlepicker.training.gui.TemplatesJDialog.frame
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Definition at line 27 of file TemplatesJDialog.java.

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JPanel xmipp.viewer.particlepicker.training.gui.TemplatesJDialog.templatespn
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Definition at line 28 of file TemplatesJDialog.java.

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int xmipp.viewer.particlepicker.training.gui.TemplatesJDialog.width
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Definition at line 29 of file TemplatesJDialog.java.

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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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- node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.training.gui.\lTemplatesJDialog",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JDialog",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1TemplatesJDialog__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1TemplatesJDialog__inherit__graph.md5 deleted file mode 100644 index f989d391..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1gui_1_1TemplatesJDialog__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -b81178ab55c6ce46f95fb55cc8569427 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1AutomaticParticle-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1AutomaticParticle-members.html deleted file mode 100644 index 773d231b..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1AutomaticParticle-members.html +++ /dev/null @@ -1,131 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.training.model.AutomaticParticle Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.model.AutomaticParticle, including all inherited members.

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aboveThreshold()xmipp.viewer.particlepicker.training.model.AutomaticParticleinline
AutomaticParticle(int x, int y, ParticlePicker picker, SupervisedPickerMicrograph micrograph, double cost, boolean deleted)xmipp.viewer.particlepicker.training.model.AutomaticParticleinline
compareTo(Particle p)xmipp.jni.Particleinline
contains(int x2, int y2)xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.contains(int x2, int y2, int size)xmipp.jni.Particleinline
costxmipp.jni.Particleprotected
getCost()xmipp.jni.Particleinline
getImageGeneric()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getLastalign()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getMicrograph()xmipp.viewer.particlepicker.PickerParticleinline
getParticleCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.PickerParticleinline
getParticlePicker()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getPosition()xmipp.jni.Particleinline
getSize()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateIndex()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplatePsi()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateRotation()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateTilt()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getX()xmipp.jni.Particleinline
getX0()xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.getX0(int size)xmipp.viewer.particlepicker.PickerParticleinline
getY()xmipp.jni.Particleinline
getY0()xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.getY0(int size)xmipp.viewer.particlepicker.PickerParticleinline
igxmipp.viewer.particlepicker.training.model.ManualParticleprotected
isDeleted()xmipp.viewer.particlepicker.training.model.AutomaticParticleinline
isUnavailable()xmipp.viewer.particlepicker.training.model.AutomaticParticleinline
lastalignxmipp.viewer.particlepicker.training.model.ManualParticleprotected
loadImagePlus()xmipp.viewer.particlepicker.training.model.ManualParticleinlineprotected
ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph)xmipp.viewer.particlepicker.training.model.ManualParticleinline
ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)xmipp.viewer.particlepicker.training.model.ManualParticleinline
micrographxmipp.viewer.particlepicker.PickerParticleprotected
Particle(int x, int y)xmipp.jni.Particleinline
Particle(int x, int y, double cost)xmipp.jni.Particleinline
pickerxmipp.viewer.particlepicker.training.model.ManualParticleprotected
PickerParticle(int x, int y, Micrograph m)xmipp.viewer.particlepicker.PickerParticleinline
PickerParticle(int x, int y, Micrograph m, double cost)xmipp.viewer.particlepicker.PickerParticleinline
resetImage()xmipp.viewer.particlepicker.training.model.ManualParticleinline
resetParticleCanvas()xmipp.viewer.particlepicker.PickerParticleinline
setCost(double cost)xmipp.jni.Particleinline
setDeleted(boolean deleted)xmipp.viewer.particlepicker.training.model.AutomaticParticleinline
setLastalign(double[] lastalign)xmipp.viewer.particlepicker.training.model.ManualParticleinline
setMicrograph(Micrograph micrograph)xmipp.viewer.particlepicker.PickerParticleinline
setPosition(int x, int y)xmipp.viewer.particlepicker.training.model.ManualParticleinline
setX(int x)xmipp.jni.Particleinline
setY(int y)xmipp.jni.Particleinline
toString()xmipp.jni.Particleinline
xxmipp.jni.Particleprotected
yxmipp.jni.Particleprotected
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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.training.model.AutomaticParticle Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.training.model.AutomaticParticle:
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-Collaboration diagram for xmipp.viewer.particlepicker.training.model.AutomaticParticle:
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-Public Member Functions

 AutomaticParticle (int x, int y, ParticlePicker picker, SupervisedPickerMicrograph micrograph, double cost, boolean deleted)
 
void setDeleted (boolean deleted)
 
boolean isDeleted ()
 
boolean isUnavailable ()
 
boolean aboveThreshold ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
double [] getLastalign ()
 
void setLastalign (double[] lastalign)
 
 ManualParticle (int x, int y, ParticlePicker picker, Micrograph micrograph)
 
 ManualParticle (int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)
 
ParticlePicker getParticlePicker ()
 
int getX0 ()
 
int getY0 ()
 
boolean contains (int x2, int y2)
 
void setPosition (int x, int y)
 
void resetImage ()
 
ImageGeneric getImageGeneric ()
 
double getTemplateRotation ()
 
double getTemplateTilt ()
 
double getTemplatePsi ()
 
int getTemplateIndex ()
 
int getSize ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.PickerParticle
 PickerParticle (int x, int y, Micrograph m)
 
 PickerParticle (int x, int y, Micrograph m, double cost)
 
int getX0 (int size)
 
int getY0 (int size)
 
ParticleCanvas getParticleCanvas (ParticlePickerJFrame frame)
 
void resetParticleCanvas ()
 
Micrograph getMicrograph ()
 
void setMicrograph (Micrograph micrograph)
 
- Public Member Functions inherited from xmipp.jni.Particle
 Particle (int x, int y)
 
 Particle (int x, int y, double cost)
 
int getX ()
 
void setX (int x)
 
int getY ()
 
void setY (int y)
 
double getCost ()
 
void setCost (double cost)
 
boolean contains (int x2, int y2, int size)
 
void setPosition (int x, int y)
 
Point getPosition ()
 
String toString ()
 
int compareTo (Particle p)
 
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-Additional Inherited Members

- Protected Member Functions inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
void loadImagePlus ()
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.training.model.ManualParticle
ParticlePicker picker
 
ImageGeneric ig
 
double [] lastalign
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.PickerParticle
Micrograph micrograph
 
- Protected Attributes inherited from xmipp.jni.Particle
int x
 
int y
 
double cost
 
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Detailed Description

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Definition at line 6 of file AutomaticParticle.java.

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Constructor & Destructor Documentation

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◆ AutomaticParticle()

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xmipp.viewer.particlepicker.training.model.AutomaticParticle.AutomaticParticle (int x,
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ParticlePicker picker,
SupervisedPickerMicrograph micrograph,
double cost,
boolean deleted 
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Definition at line 10 of file AutomaticParticle.java.

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10  {
11  super(x, y, picker, micrograph, cost);
12  if(cost> 1)
13  throw new IllegalArgumentException(XmippMessage.getNoSuchFieldValueMsg("cost", cost));
14  this.deleted = deleted;
15  }
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Member Function Documentation

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◆ aboveThreshold()

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boolean xmipp.viewer.particlepicker.training.model.AutomaticParticle.aboveThreshold ()
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Definition at line 30 of file AutomaticParticle.java.

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31  {
32  return getCost() >= ((SupervisedPickerMicrograph)micrograph).getThreshold();
33  }
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double getCost()
Definition: Particle.java:42
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◆ isDeleted()

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boolean xmipp.viewer.particlepicker.training.model.AutomaticParticle.isDeleted ()
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Definition at line 22 of file AutomaticParticle.java.

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23  {
24  return deleted;
25  }
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◆ isUnavailable()

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boolean xmipp.viewer.particlepicker.training.model.AutomaticParticle.isUnavailable ()
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Definition at line 26 of file AutomaticParticle.java.

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27  {
28  return deleted || ! aboveThreshold();
29  }
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◆ setDeleted()

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void xmipp.viewer.particlepicker.training.model.AutomaticParticle.setDeleted (boolean deleted)
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Definition at line 17 of file AutomaticParticle.java.

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18  {
19  this.deleted = deleted;
20  }
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The documentation for this class was generated from the following file: -
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xmipp.viewer.particlepicker.training.model.CenterParticleTask Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.model.CenterParticleTask, including all inherited members.

- - - - -
CenterParticleTask(SupervisedPickerCanvas canvas, SupervisedParticlePicker ppicker, ManualParticle particle)xmipp.viewer.particlepicker.training.model.CenterParticleTaskinline
doInBackground()xmipp.viewer.particlepicker.training.model.CenterParticleTaskinlineprotected
done()xmipp.viewer.particlepicker.training.model.CenterParticleTaskinlineprotected
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask.html deleted file mode 100644 index d8eb92c0..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask.html +++ /dev/null @@ -1,217 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.training.model.CenterParticleTask Class Reference - - - - - - - - - -
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xmipp.viewer.particlepicker.training.model.CenterParticleTask Class Reference
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-Public Member Functions

 CenterParticleTask (SupervisedPickerCanvas canvas, SupervisedParticlePicker ppicker, ManualParticle particle)
 
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-Protected Member Functions

String doInBackground () throws Exception
 
void done ()
 
-

Detailed Description

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Definition at line 7 of file CenterParticleTask.java.

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Constructor & Destructor Documentation

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◆ CenterParticleTask()

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xmipp.viewer.particlepicker.training.model.CenterParticleTask.CenterParticleTask (SupervisedPickerCanvas canvas,
SupervisedParticlePicker ppicker,
ManualParticle particle 
)
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Definition at line 15 of file CenterParticleTask.java.

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16  {
17  this.canvas = canvas;
18  this.ppicker = ppicker;
19  this.particle = particle;
20  }
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Member Function Documentation

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◆ doInBackground()

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String xmipp.viewer.particlepicker.training.model.CenterParticleTask.doInBackground () throws Exception
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Definition at line 25 of file CenterParticleTask.java.

-
26  {
27  try
28  {
29 
30  ppicker.centerParticle(particle);
31 
32  }
33  catch (Exception e)
34  {
35  throw new IllegalArgumentException(e);
36  }
37 
38  return "";
39  }
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◆ done()

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void xmipp.viewer.particlepicker.training.model.CenterParticleTask.done ()
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Definition at line 42 of file CenterParticleTask.java.

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42  {
43  canvas.repaint();
44  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__coll__graph.dot deleted file mode 100644 index 4521d6b1..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.CenterParticleTask" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.training.model.\lCenterParticleTask",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="javax::swing::SwingWorker\l\< String, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__coll__graph.md5 deleted file mode 100644 index 6b9deddc..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -ebd52b0a95dffd7f64e1433c24cf4495 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__inherit__graph.dot deleted file mode 100644 index 6718029f..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.CenterParticleTask" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.training.model.\lCenterParticleTask",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="javax::swing::SwingWorker\l\< String, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__inherit__graph.md5 deleted file mode 100644 index 382a5ec1..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1CenterParticleTask__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -04f44b74b98cb8ebdcde81d14aa9823d \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1GenericClassifier-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1GenericClassifier-members.html deleted file mode 100644 index 68201843..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1GenericClassifier-members.html +++ /dev/null @@ -1,97 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.training.model.GenericClassifier Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.model.GenericClassifier, including all inherited members.

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applyChangesxmipp.jni.Classifierprotected
autopick(SupervisedPickerMicrograph micrograph)xmipp.viewer.particlepicker.training.model.GenericClassifierinline
classifierPropertiesxmipp.viewer.particlepicker.training.model.GenericClassifierprotected
doPickAll()xmipp.viewer.particlepicker.training.model.GenericClassifierinline
GenericClassifier(String classifierProperties)xmipp.viewer.particlepicker.training.model.GenericClassifierinline
getParams()xmipp.jni.Classifierinline
getTrainingParticlesMinimum()xmipp.viewer.particlepicker.training.model.GenericClassifierinline
hasInitialCoordinates()xmipp.viewer.particlepicker.training.model.GenericClassifierinline
isApplyChanges()xmipp.jni.Classifierinline
needsTraining()xmipp.viewer.particlepicker.training.model.GenericClassifierinline
paramsxmipp.jni.Classifierprotected
propertiesxmipp.viewer.particlepicker.training.model.GenericClassifierprotected
setApplyChanges(boolean applyChanges)xmipp.viewer.particlepicker.training.model.GenericClassifierinline
setSize(int psize)xmipp.viewer.particlepicker.training.model.GenericClassifierinline
writeProperties()xmipp.viewer.particlepicker.training.model.GenericClassifierinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1GenericClassifier.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1GenericClassifier.html deleted file mode 100644 index 9407ee22..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1GenericClassifier.html +++ /dev/null @@ -1,464 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.training.model.GenericClassifier Class Reference - - - - - - - - - -
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xmipp.viewer.particlepicker.training.model.GenericClassifier Class Reference
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 GenericClassifier (String classifierProperties)
 
void autopick (SupervisedPickerMicrograph micrograph)
 
int getTrainingParticlesMinimum ()
 
void setSize (int psize)
 
boolean needsTraining ()
 
void writeProperties ()
 
void setApplyChanges (boolean applyChanges)
 
boolean hasInitialCoordinates ()
 
boolean doPickAll ()
 
- Public Member Functions inherited from xmipp.jni.Classifier
abstract int getTrainingParticlesMinimum ()
 
abstract void setSize (int psize)
 
boolean isApplyChanges ()
 
void setApplyChanges (boolean applyChanges)
 
List< Classifier.Parameter > getParams ()
 
abstract boolean needsTraining ()
 
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-Protected Attributes

String classifierProperties
 
Properties properties
 
- Protected Attributes inherited from xmipp.jni.Classifier
List< Classifier.Parameter > params
 
boolean applyChanges
 
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Detailed Description

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Definition at line 22 of file GenericClassifier.java.

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Constructor & Destructor Documentation

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◆ GenericClassifier()

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xmipp.viewer.particlepicker.training.model.GenericClassifier.GenericClassifier (String classifierProperties)
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Definition at line 29 of file GenericClassifier.java.

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30  {
31  try
32  {
33  this.classifierProperties = classifierProperties;
34  // create and load properties
35  properties = new Properties();
36  FileInputStream in = new FileInputStream(classifierProperties);
37  properties.load(in);
38 
39  in.close();
40  properties.setProperty("applyChanges", String.valueOf(applyChanges));
41  String[] paramNames = properties.getProperty("parameters").split(",");
42  Parameter param;
43  String label, help, value;
44  params = new ArrayList<Classifier.Parameter>();
45  for(String paramName : paramNames)
46  {
47  label = properties.getProperty(paramName + ".label");
48  help = properties.getProperty(paramName + ".help");
49  value = properties.getProperty(paramName + ".value");
50  param = new Parameter(paramName, label, help, value);
51  params.add(param);
52  }
53  if (hasInitialCoordinates())
54  convert();
55  }
56  catch (Exception e)
57  {
58  throw new IllegalArgumentException(e.getMessage());
59  }
60  }
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xmipp.jni.Classifier.params
List< Classifier.Parameter > params
Definition: Classifier.java:7
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◆ autopick()

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void xmipp.viewer.particlepicker.training.model.GenericClassifier.autopick (SupervisedPickerMicrograph micrograph)
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Definition at line 86 of file GenericClassifier.java.

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87  {
88  String preprocessCommand = properties.getProperty("preprocessCommand");
89  String autopickCommand = properties.getProperty("autopickCommand");
90  String runDir = properties.getProperty("runDir");
91 
92  for(Classifier.Parameter param: params)
93  {
94  if(preprocessCommand != null)
95  preprocessCommand = preprocessCommand.replace("%(" + param.name + ")", param.value);
96  autopickCommand = autopickCommand.replace("%(" + param.name + ")", param.value);
97  }
98 
99  String micPath = micrograph.getFile();
100 
101  if (runDir != null)
102  micPath = new File(runDir).toURI().relativize(new File(micPath).toURI()).getPath();
103 
104  String name = micrograph.getName();
105  autopickCommand = autopickCommand.replace("%(micrograph)", micPath);
106  autopickCommand = autopickCommand.replace("%(micrographName)", name);
107 
108  try
109  {
110  execute("Preprocess", preprocessCommand, runDir);
111  execute("Autopick", autopickCommand, runDir);
112  convert();
113  writeProperties();
114  }
115  catch (Exception e)
116  {
117  // TODO Auto-generated catch block
118  e.printStackTrace();
119  }
120  }
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xmipp.jni.Classifier.params
List< Classifier.Parameter > params
Definition: Classifier.java:7
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Definition at line 172 of file GenericClassifier.java.

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172  {
173  return properties.getProperty("doPickAll", "").equals("true");
174  }
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int xmipp.viewer.particlepicker.training.model.GenericClassifier.getTrainingParticlesMinimum ()
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Definition at line 123 of file GenericClassifier.java.

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124  {
125  // TODO Auto-generated method stub
126  return 0;
127  }
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169  return properties.getProperty("hasInitialCoordinates", "").equals("true");
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138  return false;
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164  super.setApplyChanges(applyChanges);
165  writeProperties();
166  }
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132  // TODO Auto-generated method stub
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142  {
143  try
144  {
145  for(Classifier.Parameter param: params)
146  properties.setProperty(param.name + ".value", param.value);
147  properties.setProperty("applyChanges", String.valueOf(applyChanges));
148  File file = new File(classifierProperties);
149  FileOutputStream fileOut;
150  fileOut = new FileOutputStream(file);
151  properties.store(fileOut, "Favorite Things");
152  fileOut.close();
153  }
154  catch (Exception e)
155  {
156  // TODO Auto-generated catch block
157  e.printStackTrace();
158  if(!e.getMessage().isEmpty())
159  XmippDialog.showError(null,e.getMessage());
160  }
161  }
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xmipp.viewer.particlepicker.training.model.ManualParticle Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.model.ManualParticle, including all inherited members.

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compareTo(Particle p)xmipp.jni.Particleinline
contains(int x2, int y2)xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.contains(int x2, int y2, int size)xmipp.jni.Particleinline
costxmipp.jni.Particleprotected
getCost()xmipp.jni.Particleinline
getImageGeneric()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getLastalign()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getMicrograph()xmipp.viewer.particlepicker.PickerParticleinline
getParticleCanvas(ParticlePickerJFrame frame)xmipp.viewer.particlepicker.PickerParticleinline
getParticlePicker()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getPosition()xmipp.jni.Particleinline
getSize()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateIndex()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplatePsi()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateRotation()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getTemplateTilt()xmipp.viewer.particlepicker.training.model.ManualParticleinline
getX()xmipp.jni.Particleinline
getX0()xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.getX0(int size)xmipp.viewer.particlepicker.PickerParticleinline
getY()xmipp.jni.Particleinline
getY0()xmipp.viewer.particlepicker.training.model.ManualParticleinline
xmipp::viewer::particlepicker::PickerParticle.getY0(int size)xmipp.viewer.particlepicker.PickerParticleinline
igxmipp.viewer.particlepicker.training.model.ManualParticleprotected
lastalignxmipp.viewer.particlepicker.training.model.ManualParticleprotected
loadImagePlus()xmipp.viewer.particlepicker.training.model.ManualParticleinlineprotected
ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph)xmipp.viewer.particlepicker.training.model.ManualParticleinline
ManualParticle(int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)xmipp.viewer.particlepicker.training.model.ManualParticleinline
micrographxmipp.viewer.particlepicker.PickerParticleprotected
Particle(int x, int y)xmipp.jni.Particleinline
Particle(int x, int y, double cost)xmipp.jni.Particleinline
pickerxmipp.viewer.particlepicker.training.model.ManualParticleprotected
PickerParticle(int x, int y, Micrograph m)xmipp.viewer.particlepicker.PickerParticleinline
PickerParticle(int x, int y, Micrograph m, double cost)xmipp.viewer.particlepicker.PickerParticleinline
resetImage()xmipp.viewer.particlepicker.training.model.ManualParticleinline
resetParticleCanvas()xmipp.viewer.particlepicker.PickerParticleinline
setCost(double cost)xmipp.jni.Particleinline
setLastalign(double[] lastalign)xmipp.viewer.particlepicker.training.model.ManualParticleinline
setMicrograph(Micrograph micrograph)xmipp.viewer.particlepicker.PickerParticleinline
setPosition(int x, int y)xmipp.viewer.particlepicker.training.model.ManualParticleinline
setX(int x)xmipp.jni.Particleinline
setY(int y)xmipp.jni.Particleinline
toString()xmipp.jni.Particleinline
xxmipp.jni.Particleprotected
yxmipp.jni.Particleprotected
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle.html deleted file mode 100644 index 60646cda..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle.html +++ /dev/null @@ -1,861 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.training.model.ManualParticle Class Reference - - - - - - - - - -
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xmipp.viewer.particlepicker.training.model.ManualParticle Class Reference
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-Public Member Functions

double [] getLastalign ()
 
void setLastalign (double[] lastalign)
 
 ManualParticle (int x, int y, ParticlePicker picker, Micrograph micrograph)
 
 ManualParticle (int x, int y, ParticlePicker picker, Micrograph micrograph, double cost)
 
ParticlePicker getParticlePicker ()
 
int getX0 ()
 
int getY0 ()
 
boolean contains (int x2, int y2)
 
void setPosition (int x, int y)
 
void resetImage ()
 
ImageGeneric getImageGeneric ()
 
double getTemplateRotation ()
 
double getTemplateTilt ()
 
double getTemplatePsi ()
 
int getTemplateIndex ()
 
int getSize ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.PickerParticle
 PickerParticle (int x, int y, Micrograph m)
 
 PickerParticle (int x, int y, Micrograph m, double cost)
 
int getX0 (int size)
 
int getY0 (int size)
 
ParticleCanvas getParticleCanvas (ParticlePickerJFrame frame)
 
void resetParticleCanvas ()
 
Micrograph getMicrograph ()
 
void setMicrograph (Micrograph micrograph)
 
- Public Member Functions inherited from xmipp.jni.Particle
 Particle (int x, int y)
 
 Particle (int x, int y, double cost)
 
int getX ()
 
void setX (int x)
 
int getY ()
 
void setY (int y)
 
double getCost ()
 
void setCost (double cost)
 
boolean contains (int x2, int y2, int size)
 
void setPosition (int x, int y)
 
Point getPosition ()
 
String toString ()
 
int compareTo (Particle p)
 
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void loadImagePlus ()
 
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ParticlePicker picker
 
ImageGeneric ig
 
double [] lastalign
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.PickerParticle
Micrograph micrograph
 
- Protected Attributes inherited from xmipp.jni.Particle
int x
 
int y
 
double cost
 
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Definition at line 17 of file ManualParticle.java.

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Definition at line 34 of file ManualParticle.java.

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35  {
36  this(x, y, picker, micrograph, 2);
37  }
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Definition at line 39 of file ManualParticle.java.

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40  {
41  super(x, y, micrograph, cost);
42  this.picker = picker;
43  }
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Definition at line 64 of file ManualParticle.java.

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65  {
66  return super.contains(x2, y2, picker.getSize());
67  }
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Definition at line 113 of file ManualParticle.java.

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113  {
114  loadImagePlus();//to ensure there is an image generic setted
115  return ig;
116  }
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Definition at line 24 of file ManualParticle.java.

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25  {
26  return lastalign;
27  }
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Definition at line 46 of file ManualParticle.java.

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47  {
48  return picker;
49  }
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Definition at line 148 of file ManualParticle.java.

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149  {
150  return picker.getSize();
151  }
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Definition at line 141 of file ManualParticle.java.

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142  {
143  if(lastalign == null)
144  return -1;
145  return (int)lastalign[0];
146  }
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Definition at line 134 of file ManualParticle.java.

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135  {
136  if(lastalign == null)
137  return -1;
138  return lastalign[3];
139  }
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Definition at line 118 of file ManualParticle.java.

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119  {
120  if(lastalign == null)
121  return -1;
122  return lastalign[1];
123  }
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Definition at line 125 of file ManualParticle.java.

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126  {
127  if(lastalign == null)
128  return -1;
129  return lastalign[2];
130  }
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Definition at line 52 of file ManualParticle.java.

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53  {
54  return getX() - picker.getRadius();
55  }
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Definition at line 57 of file ManualParticle.java.

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58  {
59  return getY() - picker.getRadius();
60  }
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Definition at line 70 of file ManualParticle.java.

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71  {
72  if(ig == null)
73  {
74  try {
75  int size = picker.getSize();
76  ImagePlus mimage = micrograph.getImagePlus();
77  int radius = size/2;
78  Rectangle r = new Rectangle(x - radius , y - radius, size, size);
79  Roi roi = mimage.getRoi();
80  mimage.setRoi(r);
81  ImageProcessor processor = mimage.getProcessor().crop();
82  ImagePlus img = new ImagePlus("", processor);
83  mimage.setRoi(roi);
84  ig = XmippImageConverter.convertToImageGeneric(img);
85  } catch (Exception ex) {
86  Logger.getLogger(ManualParticle.class.getName()).log(Level.SEVERE, null, ex);
87  throw new IllegalArgumentException(ex.getMessage());
88  }
89  }
90  }
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Definition: ManualParticle.java:34
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Definition at line 104 of file ManualParticle.java.

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105  {
106 // if(ig != null)
107 // ig.destroy();
108  lastalign = null;
109  ig = null;
110  }
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Definition at line 29 of file ManualParticle.java.

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30  {
31  this.lastalign = lastalign;
32  }
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Definition at line 93 of file ManualParticle.java.

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94  {
95  int radius = picker.getSize()/2;
96  if(!getMicrograph().fits(x, y, picker.getSize()))
97  throw new IllegalArgumentException(XmippMessage.getOutOfBoundsMsg(String.format("Particle centered at %s, %s with size %s", x, y, picker.getSize())));
98  super.setPosition(x, y);
99  ig = null;
100  }
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Definition at line 20 of file ManualParticle.java.

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Definition at line 22 of file ManualParticle.java.

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ParticlePicker xmipp.viewer.particlepicker.training.model.ManualParticle.picker
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Definition at line 19 of file ManualParticle.java.

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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__coll__graph.dot deleted file mode 100644 index bc04f415..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__coll__graph.dot +++ /dev/null @@ -1,33 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.ManualParticle" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node7 [label="xmipp.viewer.particlepicker.training.model.\lManualParticle",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node8 -> Node7 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node8 [label="xmipp.viewer.particlepicker.\lPickerParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1PickerParticle.html"]; - Node9 -> Node8 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node9 [label="xmipp.jni.Particle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1Particle.html"]; - Node10 -> Node9 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node10 [label="Comparable\< Particle \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node11 -> Node8 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" micrograph" ,fontname="Helvetica"]; - Node11 [label="xmipp.viewer.particlepicker.\lMicrograph",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1Micrograph.html"]; - Node12 -> Node7 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" picker" ,fontname="Helvetica"]; - Node12 [label="xmipp.viewer.particlepicker.\lParticlePicker",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePicker.html"]; - Node13 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" filters" ,fontname="Helvetica"]; - Node13 [label="List\< xmipp.ij.commons.IJCommand \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node14 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" emextensions" ,fontname="Helvetica"]; - Node14 [label="HashMap\< xmipp.viewer.particlepicker.\lFormat, String \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node15 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" color\ncolors" ,fontname="Helvetica"]; - Node15 [label="Color",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node12 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" picker" ,fontname="Helvetica"]; - Node16 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mode" ,fontname="Helvetica"]; - Node16 [label="xmipp.viewer.particlepicker.training.model.Mode",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$enumxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1Mode.html"]; - Node17 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" logger" ,fontname="Helvetica"]; - Node17 [label="Logger",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node18 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" params" ,fontname="Helvetica"]; - Node18 [label="xmipp.viewer.particlepicker.\lParticlePickerParams",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerParams.html"]; - Node16 -> Node18 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mode" ,fontname="Helvetica"]; - Node19 -> Node7 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ig" ,fontname="Helvetica"]; - Node19 [label="xmipp.jni.ImageGeneric",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1ImageGeneric.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__coll__graph.md5 deleted file mode 100644 index 4236db3f..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -9133667dcc9055e8a05b3ced6ecd4f58 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__inherit__graph.dot deleted file mode 100644 index 25ce2ed6..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__inherit__graph.dot +++ /dev/null @@ -1,19 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.ManualParticle" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node0 [label="xmipp.viewer.particlepicker.training.model.\lManualParticle",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lPickerParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1PickerParticle.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.jni.Particle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1Particle.html"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="Comparable\< Particle \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node0 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="xmipp.viewer.particlepicker.tiltpair.model.\lTiltedParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1TiltedParticle.html"]; - Node0 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="xmipp.viewer.particlepicker.tiltpair.model.\lUntiltedParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1tiltpair_1_1model_1_1UntiltedParticle.html"]; - Node0 -> Node6 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="xmipp.viewer.particlepicker.training.model.\lAutomaticParticle",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1AutomaticParticle.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__inherit__graph.md5 deleted file mode 100644 index 494e6961..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ManualParticle__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -6f934447eefceb99b1f964b6ee3cb9d9 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask-members.html deleted file mode 100644 index 8eedf951..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask-members.html +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask, including all inherited members.

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doInBackground()xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTaskinlineprotected
done()xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTaskinlineprotected
ParticleToTemplatesTask(ManualParticle particle)xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTaskinline
setTemplatesDialog(TemplatesJDialog d)xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTaskinlinestatic
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xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask:
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-Public Member Functions

 ParticleToTemplatesTask (ManualParticle particle)
 
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-Static Public Member Functions

static void setTemplatesDialog (TemplatesJDialog d)
 
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-Protected Member Functions

String doInBackground () throws Exception
 
void done ()
 
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Detailed Description

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Definition at line 6 of file ParticleToTemplatesTask.java.

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Constructor & Destructor Documentation

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◆ ParticleToTemplatesTask()

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xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask.ParticleToTemplatesTask (ManualParticle particle)
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Definition at line 13 of file ParticleToTemplatesTask.java.

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14  {
15  this.particle = particle;
16  }
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◆ doInBackground()

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String xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask.doInBackground () throws Exception
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Definition at line 24 of file ParticleToTemplatesTask.java.

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25  {
26  try
27  {
28 
29  SupervisedParticlePicker picker = (SupervisedParticlePicker)particle.getParticlePicker();
30  if (particle.getMicrograph().fits(particle.getX(), particle.getY(), picker.getSize()))
31  picker.addParticleToTemplates(particle);
32 
33  }
34  catch (Exception e)
35  {
36  throw new IllegalArgumentException(e);
37  }
38 
39  return "";
40  }
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ done()

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void xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask.done ()
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Definition at line 43 of file ParticleToTemplatesTask.java.

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43  {
44  if(dialog != null && dialog.isVisible())
45  dialog.loadTemplates(true);
46  }
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◆ setTemplatesDialog()

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static void xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask.setTemplatesDialog (TemplatesJDialog d)
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Definition at line 18 of file ParticleToTemplatesTask.java.

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19  {
20  dialog = d;
21  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__coll__graph.dot deleted file mode 100644 index d4142915..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.training.model.\lParticleToTemplatesTask",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="javax::swing::SwingWorker\l\< String, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__coll__graph.md5 deleted file mode 100644 index 781162bc..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -db4df0f288fd45753f448b461b4034a5 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__inherit__graph.dot deleted file mode 100644 index f3e1b492..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.ParticleToTemplatesTask" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.training.model.\lParticleToTemplatesTask",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="javax::swing::SwingWorker\l\< String, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__inherit__graph.md5 deleted file mode 100644 index c7a8700f..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1ParticleToTemplatesTask__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -c1819ee349680e21dc61dc5fd75a8c49 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker-members.html deleted file mode 100644 index a3ed4b57..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker-members.html +++ /dev/null @@ -1,231 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker Member List
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This is the complete list of members for xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker, including all inherited members.

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addFilter(String command, String options)xmipp.viewer.particlepicker.ParticlePickerinline
addParticleToTemplates(ManualParticle particle)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
applyAlignment(ManualParticle particle, ImageGeneric igp, double[] align)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
autopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph next)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
autopickpercentxmipp.viewer.particlepicker.training.model.SupervisedParticlePickerprotected
blockxmipp.viewer.particlepicker.ParticlePickerprotected
centerParticle(ManualParticle p)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
changedxmipp.viewer.particlepicker.ParticlePickerprotected
colorxmipp.viewer.particlepicker.ParticlePickerprotected
colorsxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
configfilexmipp.viewer.particlepicker.ParticlePickerprotected
containsPSD()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
convertAutomaticToManual()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinlineprotected
correct()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
correctAndAutopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph current, SupervisedPickerMicrograph next)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
detectFileFormat(String path)xmipp.viewer.particlepicker.ParticlePickerinline
detectFormat(String path, String preffix, StringBuffer suffix)xmipp.viewer.particlepicker.ParticlePickerinline
dtemplatesnumxmipp.viewer.particlepicker.training.model.SupervisedParticlePickerstatic
emextensionsxmipp.viewer.particlepicker.ParticlePicker
exportParticles(String file)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
fillParticlesMdFromEmanFile(String file, Micrograph m, MetaData md, float scale)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromRelionFile(String file, Micrograph m, MetaData md)xmipp.viewer.particlepicker.ParticlePickerinline
fillParticlesMdFromXmipp301File(String file, Micrograph m, MetaData md)xmipp.viewer.particlepicker.ParticlePickerinline
filtersxmipp.viewer.particlepicker.ParticlePickerprotected
getAutomaticColor()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getAutomaticParticlesNumber(double threshold)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getAutomaticParticlesNumber()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getAutopickpercent()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getClassifier()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getColor()xmipp.viewer.particlepicker.ParticlePickerinline
getColor(String name)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getCoordsFiles(String folder)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getDefaultSize()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getDeletedColor()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getExportFile(String path)xmipp.viewer.particlepicker.ParticlePickerinline
getFilters()xmipp.viewer.particlepicker.ParticlePickerinline
getLogger()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getManualParticlesNumber()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getMicrograph()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
xmipp::viewer::particlepicker::ParticlePicker.getMicrograph(String name)xmipp.viewer.particlepicker.ParticlePickerinline
getMicrographIndex()xmipp.viewer.particlepicker.ParticlePickerinline
getMicrographs()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getMicrographsSelFile()xmipp.viewer.particlepicker.ParticlePickerinline
getMode()xmipp.viewer.particlepicker.ParticlePickerinline
getNextColor()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getOutputDir()xmipp.viewer.particlepicker.ParticlePickerinline
getOutputPath(String file)xmipp.viewer.particlepicker.ParticlePickerinline
getParams()xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesAutoBlock(String file)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesAutoBlock(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesBlock(Format f, String file)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesBlock(String file)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesBlock(Micrograph m)xmipp.viewer.particlepicker.ParticlePickerinline
getParticlesBlockName(Format f)xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getParticlesCount()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getParticlesThreshold()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getPicker()xmipp.viewer.particlepicker.ParticlePickerinlinestatic
getPort()xmipp.viewer.particlepicker.ParticlePickerinline
getPosFileFromXmipp24Project(String projectdir, String mname)xmipp.viewer.particlepicker.ParticlePickerinline
getRadius()xmipp.viewer.particlepicker.ParticlePickerinline
getSize()xmipp.viewer.particlepicker.ParticlePickerinline
getTemplateIndex()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getTemplates()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getTemplatesFile()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
xmipp::viewer::particlepicker::ParticlePicker.getTemplatesFile(String name)xmipp.viewer.particlepicker.ParticlePickerinline
getTemplatesNumber()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getThreads()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
getZoom()xmipp.viewer.particlepicker.ParticlePickerinline
hasDefocusU()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
hasManualParticles()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
importAllParticles(String file)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
importAllParticles(String file, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
importParticlesFromFile(String path, Format f, SupervisedPickerMicrograph m, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
importParticlesFromFolder(String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
importParticlesFromMd(SupervisedPickerMicrograph m, MetaData md)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
importSize(String path, Format f, double scale)xmipp.viewer.particlepicker.ParticlePickerinline
initTemplates()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
initTemplates(int num)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
isAutopick()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
isChanged()xmipp.viewer.particlepicker.ParticlePickerinline
isCorrectPending()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
isFastMode()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
isFilterAdded(String filter)xmipp.viewer.particlepicker.ParticlePickerinline
isIncore()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
isReviewFile(String file)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
isSaved()xmipp.viewer.particlepicker.ParticlePickerinline
isScipionSave()xmipp.viewer.particlepicker.ParticlePickerinline
isShowDeleted()xmipp.viewer.particlepicker.ParticlePickerinline
isValidSize(JFrame parent, int size)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadAutomaticParticles(SupervisedPickerMicrograph m, MetaData md)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadAutomaticParticles(SupervisedPickerMicrograph m, String file)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadConfig()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadEmptyMicrographs()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadEmptyMicrographsFromMd()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadEmptyMicrographsFromSqlite()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadManualParticles(SupervisedPickerMicrograph m, String file)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadMicrographData(SupervisedPickerMicrograph m)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loadParticles(SupervisedPickerMicrograph micrograph, Particle[] autopickRows)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
loggerxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
macrosfilexmipp.viewer.particlepicker.ParticlePickerprotected
micrographsxmipp.viewer.particlepicker.training.model.SupervisedParticlePickerprotected
modexmipp.viewer.particlepicker.ParticlePickerprotected
nextcolorxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
outputdirxmipp.viewer.particlepicker.ParticlePickerprotected
paramsxmipp.viewer.particlepicker.ParticlePickerprotected
ParticlePicker(String selfile, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
ParticlePicker(String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
ParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.ParticlePickerinline
particlesAutoBlockxmipp.viewer.particlepicker.ParticlePickerstatic
pickerxmipp.viewer.particlepicker.ParticlePickerprotectedstatic
resetMicrograph(SupervisedPickerMicrograph micrograph)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
resetParticleImages()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
runXmippProgram(String program, String args)xmipp.viewer.particlepicker.ParticlePickerinline
saveAllData()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
saveConfig()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
saveConfig(MetaData md, long id)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinlineprotected
savedxmipp.viewer.particlepicker.ParticlePickerprotected
saveData()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
saveData(Micrograph m)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
saveTemplates()xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
selfilexmipp.viewer.particlepicker.ParticlePickerprotected
setAutopickpercent(int autopickpercent)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
setChanged(boolean changed)xmipp.viewer.particlepicker.ParticlePickerinline
setColor(Color color)xmipp.viewer.particlepicker.ParticlePickerinline
setFilterOptions(String command, String options)xmipp.viewer.particlepicker.ParticlePickerinline
setMicrograph(Micrograph m)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
setMode(Mode mode)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
setSaved(boolean saved)xmipp.viewer.particlepicker.ParticlePickerinline
setShowDeleted(boolean showDeleted)xmipp.viewer.particlepicker.ParticlePickerinline
setSize(int size)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
setTemplate(ImageGeneric ig)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
setTemplatesDialog(TemplatesJDialog d)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
setTemplatesNumber(int num)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
setZoom(double zoom)xmipp.viewer.particlepicker.ParticlePickerinline
sizexmipp.viewer.particlepicker.ParticlePickerprotected
sizemaxxmipp.viewer.particlepicker.ParticlePickerstatic
SupervisedParticlePicker(String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
SupervisedParticlePicker(String block, String selfile, String outputdir, ParticlePickerParams params)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
SupervisedParticlePicker(String selfile, String outputdir, Integer threads, boolean fastmode, boolean incore, ParticlePickerParams params)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
toggleShowDeleted()xmipp.viewer.particlepicker.ParticlePickerinline
trainAndAutopick(SupervisedPickerJFrame frame, SupervisedPickerMicrograph trainmic)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
updateFilters(String command)xmipp.viewer.particlepicker.ParticlePickerinline
updateTemplates(ImageGeneric templates, int templateindex)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
updateTemplatesStack(boolean resize)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
updateTemplatesStack(int num, boolean resize)xmipp.viewer.particlepicker.training.model.SupervisedParticlePickerinline
validateState(Mode state)xmipp.viewer.particlepicker.ParticlePickerinline
xmippsmoothfilterxmipp.viewer.particlepicker.ParticlePickerstatic
zoomxmipp.viewer.particlepicker.ParticlePickerprotected
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker Class Reference
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-Classes

class  UpdateTemplatesTask
 
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-Public Member Functions

 SupervisedParticlePicker (String selfile, String outputdir, ParticlePickerParams params)
 
 SupervisedParticlePicker (String block, String selfile, String outputdir, ParticlePickerParams params)
 
 SupervisedParticlePicker (String selfile, String outputdir, Integer threads, boolean fastmode, boolean incore, ParticlePickerParams params)
 
void saveData ()
 
void saveAllData ()
 
boolean isFastMode ()
 
boolean isIncore ()
 
int getThreads ()
 
int getTemplatesNumber ()
 
void setSize (int size)
 
synchronized void initTemplates ()
 
synchronized void initTemplates (int num)
 
synchronized void setTemplatesNumber (int num)
 
synchronized ImageGeneric getTemplates ()
 
synchronized void setTemplate (ImageGeneric ig)
 
synchronized void resetParticleImages ()
 
synchronized void updateTemplates (ImageGeneric templates, int templateindex)
 
synchronized void addParticleToTemplates (ManualParticle particle)
 
synchronized void centerParticle (ManualParticle p)
 
synchronized void applyAlignment (ManualParticle particle, ImageGeneric igp, double[] align)
 
String getTemplatesFile ()
 
void saveTemplates ()
 
boolean containsPSD ()
 
boolean hasDefocusU ()
 
void loadEmptyMicrographs ()
 
void loadEmptyMicrographsFromMd ()
 
void loadEmptyMicrographsFromSqlite ()
 
List< SupervisedPickerMicrograph > getMicrographs ()
 
synchronized void saveData (Micrograph m)
 
SupervisedPickerMicrograph getMicrograph ()
 
void setMicrograph (Micrograph m)
 
boolean isValidSize (JFrame parent, int size)
 
void loadConfig ()
 
boolean isAutopick ()
 
synchronized void saveConfig ()
 
void setAutopickpercent (int autopickpercent)
 
int getAutopickpercent ()
 
void setMode (Mode mode)
 
int getManualParticlesNumber ()
 
void exportParticles (String file)
 
int getAutomaticParticlesNumber (double threshold)
 
int getAutomaticParticlesNumber ()
 
void loadAutomaticParticles (SupervisedPickerMicrograph m, MetaData md)
 
void loadAutomaticParticles (SupervisedPickerMicrograph m, String file)
 
String importParticlesFromFolder (String path, Format f, String preffix, String suffix, float scale, boolean invertx, boolean inverty)
 
String importParticlesFromFile (String path, Format f, SupervisedPickerMicrograph m, float scale, boolean invertx, boolean inverty)
 
String importParticlesFromMd (SupervisedPickerMicrograph m, MetaData md)
 
boolean isReviewFile (String file)
 
void importAllParticles (String file)
 
String importAllParticles (String file, float scale, boolean invertx, boolean inverty)
 
boolean hasManualParticles ()
 
synchronized int getTemplateIndex ()
 
void loadMicrographData (SupervisedPickerMicrograph m)
 
void loadManualParticles (SupervisedPickerMicrograph m, String file)
 
void trainAndAutopick (SupervisedPickerJFrame frame, SupervisedPickerMicrograph trainmic)
 
int getParticlesCount ()
 
void loadParticles (SupervisedPickerMicrograph micrograph, Particle[] autopickRows)
 
void autopick (SupervisedPickerJFrame frame, SupervisedPickerMicrograph next)
 
Classifier getClassifier ()
 
void correctAndAutopick (SupervisedPickerJFrame frame, SupervisedPickerMicrograph current, SupervisedPickerMicrograph next)
 
void resetMicrograph (SupervisedPickerMicrograph micrograph)
 
void correct ()
 
int getParticlesThreshold ()
 
void updateTemplatesStack (boolean resize)
 
void updateTemplatesStack (int num, boolean resize)
 
void setTemplatesDialog (TemplatesJDialog d)
 
boolean isCorrectPending ()
 
Color getAutomaticColor ()
 
Color getDeletedColor ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
boolean isShowDeleted ()
 
void setShowDeleted (boolean showDeleted)
 
void toggleShowDeleted ()
 
double getZoom ()
 
void setZoom (double zoom)
 
ParticlePickerParams getParams ()
 
String getParticlesAutoBlock (String file)
 
String getParticlesBlock (Micrograph m)
 
String getParticlesAutoBlock (Micrograph m)
 
 ParticlePicker (String selfile, ParticlePickerParams params)
 
 ParticlePicker (String selfile, String outputdir, ParticlePickerParams params)
 
 ParticlePicker (String block, String selfile, String outputdir, ParticlePickerParams params)
 
void loadConfig ()
 
synchronized void saveConfig ()
 
Format detectFileFormat (String path)
 
Format detectFormat (String path, String preffix, StringBuffer suffix)
 
String getExportFile (String path)
 
String getPosFileFromXmipp24Project (String projectdir, String mname)
 
abstract void loadEmptyMicrographs ()
 
void updateFilters (String command)
 
boolean isFilterAdded (String filter)
 
String getMicrographsSelFile ()
 
void setFilterOptions (String command, String options)
 
void addFilter (String command, String options)
 
List< IJCommand > getFilters ()
 
void setChanged (boolean changed)
 
boolean isChanged ()
 
boolean isSaved ()
 
void setSaved (boolean saved)
 
Mode getMode ()
 
String getOutputPath (String file)
 
String getOutputDir ()
 
abstract List<? extends Micrograph > getMicrographs ()
 
int getMicrographIndex ()
 
String getTemplatesFile (String name)
 
Mode validateState (Mode state)
 
void saveData ()
 
abstract void saveData (Micrograph m)
 
Micrograph getMicrograph (String name)
 
void fillParticlesMdFromFile (String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
 
void fillParticlesMdFromXmipp301File (String file, Micrograph m, MetaData md)
 
void fillParticlesMdFromRelionFile (String file, Micrograph m, MetaData md)
 
void fillParticlesMdFromEmanFile (String file, Micrograph m, MetaData md, float scale)
 
void runXmippProgram (String program, String args)
 
abstract Micrograph getMicrograph ()
 
abstract void setMicrograph (Micrograph m)
 
abstract boolean isValidSize (JFrame parent, int size)
 
int getSize ()
 
void setSize (int size)
 
Color getColor ()
 
void setColor (Color color)
 
int getRadius ()
 
void importSize (String path, Format f, double scale)
 
boolean isScipionSave ()
 
abstract int getParticlesCount ()
 
Integer getPort ()
 
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-Static Public Attributes

static int dtemplatesnum = 1
 
- Static Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
static final String xmippsmoothfilter = "Xmipp Smooth Filter"
 
static final String particlesAutoBlock = "particles_auto"
 
static final int sizemax = 2000
 
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-Protected Member Functions

synchronized void saveConfig (MetaData md, long id)
 
void convertAutomaticToManual ()
 
- Protected Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
void saveConfig (MetaData md, long id)
 
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-Protected Attributes

List< SupervisedPickerMicrograph > micrographs
 
int autopickpercent
 
- Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
String macrosfile
 
String outputdir = "."
 
boolean changed
 
boolean saved
 
Mode mode
 
List< IJCommand > filters
 
String selfile
 
String configfile
 
Color color
 
int size
 
String block
 
ParticlePickerParams params
 
double zoom = -1.f
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.viewer.particlepicker.ParticlePicker
static Color getNextColor ()
 
static String getParticlesBlock (Format f, String file)
 
static String getParticlesBlockName (Format f)
 
static String getParticlesBlock (String file)
 
static Logger getLogger ()
 
static Color getColor (String name)
 
static int getDefaultSize ()
 
static File [] getCoordsFiles (String folder)
 
static ParticlePicker getPicker ()
 
- Public Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
final HashMap< Format, String > emextensions
 
- Static Protected Attributes inherited from xmipp.viewer.particlepicker.ParticlePicker
static Logger logger
 
static Color [] colors = new Color[]{Color.GREEN, Color.BLUE, Color.CYAN, Color.MAGENTA, Color.ORANGE, Color.PINK, Color.YELLOW}
 
static int nextcolor
 
static ParticlePicker picker
 
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Detailed Description

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Business object for Single Particle Picker GUI. Inherits from ParticlePicker

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Author
airen
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Definition at line 40 of file SupervisedParticlePicker.java.

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Constructor & Destructor Documentation

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◆ SupervisedParticlePicker() [1/3]

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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.SupervisedParticlePicker (String selfile,
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Definition at line 67 of file SupervisedParticlePicker.java.

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68  {
69  this(null, selfile, outputdir, params);
70 
71  }
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.SupervisedParticlePicker (String block,
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Definition at line 73 of file SupervisedParticlePicker.java.

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74  {
75 
76  super(block, selfile, outputdir, params);
77  try
78  {
79  templatesfile = getOutputPath("templates.stk");
80  if (!new File(templatesfile).exists())
81  initTemplates(dtemplatesnum);
82  else
83  {
84  this.templates = new ImageGeneric(templatesfile);
85  templates.read(templatesfile, false);
86  radialtemplates = new ImageGeneric(ImageGeneric.Float);
87  radialtemplates.resize(getSize(), getSize(), 1, getTemplatesNumber());
88  templateindex = (templates.getStatistics()[2] == 0)? 0: getTemplatesNumber();
89  }
90  templates.getRadialAvg(radialtemplates);
91  MDRow[] micsmd = new MDRow[micrographs.size()];
92  MDRow row; int index = 0;
93 
94  if(params.classifierProperties != null)
95  {
96  classifier = new GenericClassifier(params.classifierProperties);
97  for (SupervisedPickerMicrograph m : micrographs)
98  loadMicrographData(m);
99  }
100  else
101  {
102  for (SupervisedPickerMicrograph m : micrographs) {
103  loadMicrographData(m);
104  row = new MDRow();
105  row.setValueString(MDLabel.MDL_MICROGRAPH, m.getFile());
106  micsmd[index] = row;
107  index ++;
108  }
109  classifier = new PickingClassifier(getSize(), getOutputPath("model"), micsmd);
110  }
111  }
112  catch (Exception e)
113  {
114  e.printStackTrace();
115  throw new IllegalArgumentException(e.getMessage());
116  }
117  }
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xmipp.jni.ImageGeneric.getStatistics
native double [] getStatistics()
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static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
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xmipp.jni.ImageGeneric.read
void read(int slice)
Definition: ImageGeneric.java:126
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void resize(int w, int h)
Definition: ImageGeneric.java:90
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Definition: ImageGeneric.java:24
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.SupervisedParticlePicker (String selfile,
String outputdir,
Integer threads,
boolean fastmode,
boolean incore,
ParticlePickerParams params 
)
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Definition at line 120 of file SupervisedParticlePicker.java.

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121  {
122  this(selfile, outputdir, params);
123 
124  this.threads = threads;
125  this.fastmode = fastmode;
126  this.incore = incore;
127 
128  }
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◆ addParticleToTemplates()

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synchronized void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.addParticleToTemplates (ManualParticle particle)
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Definition at line 272 of file SupervisedParticlePicker.java.

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273  {
274  try
275  {
276  ImageGeneric igp = particle.getImageGeneric();
277  // will happen only in manual mode
278  if (getTemplateIndex() < getTemplatesNumber())
279  setTemplate(igp);
280  else
281  {
282  double[] align = getTemplates().alignImage(igp);
283  applyAlignment(particle, igp, align);
284  }
285  templates.getRadialAvg(radialtemplates);
286  }
287  catch (Exception e)
288  {
289  throw new IllegalArgumentException(e.getMessage());
290  }
291 
292  }
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.applyAlignment
synchronized void applyAlignment(ManualParticle particle, ImageGeneric igp, double[] align)
Definition: SupervisedParticlePicker.java:323
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synchronized void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.applyAlignment (ManualParticle particle,
ImageGeneric igp,
double [] align 
)
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Definition at line 323 of file SupervisedParticlePicker.java.

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324  {
325  try
326  {
327  particle.setLastalign(align);
328  templates.applyAlignment(igp, particle.getTemplateIndex(), particle.getTemplateRotation(), particle.getTemplateTilt(), particle
329  .getTemplatePsi());
330  }
331  catch (Exception e)
332  {
333  // TODO Auto-generated catch block
334  e.printStackTrace();
335  }
336 
337  }
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native void applyAlignment(ImageGeneric img, int index, double rot, double tilt, double psi)
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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.autopick (SupervisedPickerJFrame frame,
SupervisedPickerMicrograph next 
)
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Definition at line 1124 of file SupervisedParticlePicker.java.

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1125  {
1126  frame.getCanvas().setEnabled(false);
1127  XmippWindowUtil.blockGUI(frame, "Autopicking...");
1128 
1129  try {
1130  new Thread(new AutopickRunnable(frame, next), "Autopick").start();
1131  }catch (Exception e){
1132  this.logger.log(Level.SEVERE,"Autopick thread failed.");
1133  }
1134 
1135 
1136  }
xmipp.utils.XmippWindowUtil.blockGUI
static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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-
-
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◆ centerParticle()

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-
- - - - - -
- - - - - - - - -
synchronized void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.centerParticle (ManualParticle p)
- 		-inline
-
- -

Definition at line 294 of file SupervisedParticlePicker.java.

-
295  {
296 
297  if (getManualParticlesNumber() <= getTemplatesNumber())
298  return;// templates not ready
299  Particle shift = null;
300  try
301  {
302  ImageGeneric igp = p.getImageGeneric();
303 
304  shift = radialtemplates.bestShift(igp);
305  double distance = Math.sqrt(Math.pow(shift.getX(), 2) + Math.pow(shift.getY(), 2)) / getSize();
306  // System.out.printf("normalized distance:%.2f\n", distance);
307  if (distance < 0.25)
308  {
309  p.setX(p.getX() + shift.getX());
310  p.setY(p.getY() + shift.getY());
311 
312  }
313 
314  }
315  catch (Exception e)
316  {
317  // TODO Auto-generated catch block
318  e.printStackTrace();
319  }
320 
321  }
xmipp.jni.Particle.setX
void setX(int x)
Definition: Particle.java:30
- - - - - - - -
xmipp.jni.ImageGeneric.bestShift
native Particle bestShift(ImageGeneric img)
- -
xmipp.jni.Particle.setY
void setY(int y)
Definition: Particle.java:38
-
-
-
- -

◆ containsPSD()

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-
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- - - - - - - -
boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.containsPSD ()
- 		-inline
-
- -

Definition at line 357 of file SupervisedParticlePicker.java.

-
358  {
359  return existspsd;
360  }
-
-
- -

◆ convertAutomaticToManual()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.convertAutomaticToManual ()
- 		-inlineprotected
-
- -

Definition at line 641 of file SupervisedParticlePicker.java.

-
642  {
643  ManualParticle p;
644  for (SupervisedPickerMicrograph m : micrographs)
645  {
646  m.deleteBelowThreshold();
647  for (AutomaticParticle ap : m.getAutomaticParticles())
648  {
649  if (!ap.isDeleted())
650  {
651  p = new ManualParticle(ap.getX(), ap.getY(), this, m);
652  m.addManualParticle(p, this);
653  }
654  }
655 
656  m.getAutomaticParticles().clear();
657  if (m.hasManualParticles())
658  m.setState(MicrographState.Manual);
659  else
660  m.setState(MicrographState.Available);
661  }
662 
663  saveAllData();
664  updateTemplatesStack(false);
665 
666  }
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-
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◆ correct()

- -
-
- - - - - -
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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.correct ()
- 		-inline
-
- -

Definition at line 1226 of file SupervisedParticlePicker.java.

-
1227  {
1228  micrograph.setState(MicrographState.Corrected);
1229  saveData(micrograph);
1230  MDRow[] manualRows = getAddedRows(micrograph);
1231  MDRow[] autoRows = getAutomaticRows(micrograph);
1232  ((PickingClassifier)classifier).correct(manualRows, autoRows);
1233  }
- -
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- -

◆ correctAndAutopick()

- -
-
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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.correctAndAutopick (SupervisedPickerJFrame frame,
SupervisedPickerMicrograph current,
SupervisedPickerMicrograph next 
)
- 		-inline
-
- -

Definition at line 1144 of file SupervisedParticlePicker.java.

-
1145  {
1146  current.setState(MicrographState.Corrected);
1147  if (getMode() == Mode.Supervised && next.getState() == MicrographState.Available)
1148  next.setState(MicrographState.Supervised);
1149  saveData(current);
1150 
1151 
1152  MDRow[] autoRows = getAutomaticRows(current);
1153  MDRow[] addedRows = getAddedRows(current);
1154  frame.getCanvas().setEnabled(false);
1155 
1156  boolean isautopick = getMode() == Mode.Supervised && next.getState() == MicrographState.Available;
1157  // Show progress wheel
1158  if(isautopick)
1159  XmippWindowUtil.blockGUI(frame, "Correcting and Autopicking...");
1160  else
1161  XmippWindowUtil.blockGUI(frame, "Correcting ...");
1162 
1163  try {
1164  new Thread(new CorrectAndAutopickRunnable(frame, addedRows, autoRows, next), "CorrectAndAutopick").start();
1165  }catch (Exception e){
1166  this.logger.log(Level.SEVERE,"Correct and Autopick thread failed.");
1167  }
1168 
1169  }
-
xmipp.utils.XmippWindowUtil.blockGUI
static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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◆ exportParticles()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.exportParticles (String file)
- 		-inline
-
- -

Definition at line 676 of file SupervisedParticlePicker.java.

-
677  {
678 
679  try
680  {
681  MetaData md = new MetaData();
682  boolean append = false;
683  long id;
684  for (SupervisedPickerMicrograph m : micrographs)
685  {
686  if (m.isEmpty())
687  continue;
688  for (ManualParticle p : m.getParticles())
689  {
690  id = md.addObject();
691  md.setValueInt(MDLabel.MDL_XCOOR, p.getX(), id);
692  md.setValueInt(MDLabel.MDL_YCOOR, p.getY(), id);
693  md.setValueDouble(MDLabel.MDL_COST, p.getCost(), id);
694  }
695  if (!append)
696  md.write("mic_" + m.getName() + "@" + file);
697  else
698  md.writeBlock("mic_" + m.getName() + "@" + file);
699  append = true;
700  md.clear();
701  }
702  md.destroy();
703 
704  this.setSaved(false);
705  }
706  catch (Exception e)
707  {
708  getLogger().log(Level.SEVERE, e.getMessage(), e);
709  throw new IllegalArgumentException(e.getMessage());
710  }
711  }
- -
xmipp.jni.MetaData.addObject
native long addObject()
-
xmipp.jni.MetaData.write
native void write(String filename)
-
xmipp.jni.MetaData.clear
native void clear()
-
xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
-
xmipp.jni.MetaData.writeBlock
native void writeBlock(String filename)
-
xmipp.jni.MDLabel.MDL_COST
static final int MDL_COST
< Store a score for the coords. consensus (it will change the behavoir of the viewer) ...
Definition: MDLabel.java:46
- -
xmipp.jni.MetaData.destroy
synchronized native void destroy()
- -
xmipp.jni.MetaData.setValueDouble
native boolean setValueDouble(int label, double value, long objId)
- - - -
xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
-
xmipp.jni.MetaData.setValueInt
native boolean setValueInt(int label, int value, long objId)
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◆ getAutomaticColor()

- -
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Color xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getAutomaticColor ()
- 		-inline
-
- -

Definition at line 1349 of file SupervisedParticlePicker.java.

-
1349  {
1350  return getMode() == Mode.Automatic ? getColor() : moveColorHue(getColor(), 0.66f);
1351  }
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◆ getAutomaticParticlesNumber() [1/2]

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int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getAutomaticParticlesNumber (double threshold)
- 		-inline
-
- -

Definition at line 713 of file SupervisedParticlePicker.java.

-
714  {
715  int count = 0;
716  for (SupervisedPickerMicrograph m : micrographs)
717  count += m.getAutomaticParticlesNumber(threshold);
718  return count;
719  }
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◆ getAutomaticParticlesNumber() [2/2]

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int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getAutomaticParticlesNumber ()
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-
- -

Definition at line 721 of file SupervisedParticlePicker.java.

-
722  {
723  int count = 0;
724  for (SupervisedPickerMicrograph m : micrographs)
725  count += m.getAutomaticParticlesNumber(m.getThreshold());
726  return count;
727  }
- -
-
-
- -

◆ getAutopickpercent()

- -
-
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int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getAutopickpercent ()
- 		-inline
-
- -

Definition at line 620 of file SupervisedParticlePicker.java.

-
621  {
622  if(autopickpercent == 0)
623  autopickpercent = 50;
624  return autopickpercent;
625  }
-
-
-
- -

◆ getClassifier()

- -
-
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Classifier xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getClassifier ()
- 		-inline
-
- -

Definition at line 1138 of file SupervisedParticlePicker.java.

-
1138  {
1139  return classifier;
1140  }
-
-
- -

◆ getDeletedColor()

- -
-
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Color xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getDeletedColor ()
- 		-inline
-
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Definition at line 1353 of file SupervisedParticlePicker.java.

-
1353  {
1354 
1355  return moveColorHue(getColor(), 0.33f);
1356  }
-
-
-
- -

◆ getManualParticlesNumber()

- -
-
- - - - - -
- - - - - - - -
int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getManualParticlesNumber ()
- 		-inline
-
- -

Definition at line 668 of file SupervisedParticlePicker.java.

-
669  {
670  int count = 0;
671  for (SupervisedPickerMicrograph m : micrographs)
672  count += m.getManualParticles().size();
673  return count;
674  }
- -
-
-
- -

◆ getMicrograph()

- -
-
- - - - - -
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SupervisedPickerMicrograph xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getMicrograph ()
- 		-inline
-
- -

Definition at line 490 of file SupervisedParticlePicker.java.

-
491  {
492  return micrograph;
493  }
-
-
- -

◆ getMicrographs()

- -
-
- - - - - -
- - - - - - - -
List<SupervisedPickerMicrograph> xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getMicrographs ()
- 		-inline
-
- -

Definition at line 477 of file SupervisedParticlePicker.java.

-
478  {
479  return micrographs;
480  }
-
-
-
- -

◆ getParticlesCount()

- -
-
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- - - - - - - -
int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getParticlesCount ()
- 		-inline
-
- -

Definition at line 1098 of file SupervisedParticlePicker.java.

-
1098  {
1099  return getManualParticlesNumber() + getAutomaticParticlesNumber();
1100  }
- -
-
-
- -

◆ getParticlesThreshold()

- -
-
- - - - - -
- - - - - - - -
int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getParticlesThreshold ()
- 		-inline
-
- -

Definition at line 1235 of file SupervisedParticlePicker.java.

-
1235  {
1236  return classifier.getTrainingParticlesMinimum();
1237  }
xmipp.jni.Classifier.getTrainingParticlesMinimum
abstract int getTrainingParticlesMinimum()
-
-
-
- -

◆ getTemplateIndex()

- -
-
- - - - - -
- - - - - - - -
synchronized int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getTemplateIndex ()
- 		-inline
-
- -

Definition at line 985 of file SupervisedParticlePicker.java.

-
986  {
987  return templateindex;
988  }
-
-
- -

◆ getTemplates()

- -
-
- - - - - -
- - - - - - - -
synchronized ImageGeneric xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getTemplates ()
- 		-inline
-
- -

Definition at line 219 of file SupervisedParticlePicker.java.

-
220  {
221  return templates;
222  }
-
-
- -

◆ getTemplatesFile()

- -
-
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- - - - - - - -
String xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getTemplatesFile ()
- 		-inline
-
- -

Definition at line 339 of file SupervisedParticlePicker.java.

-
340  {
341  return templatesfile;
342  }
-
-
- -

◆ getTemplatesNumber()

- -
-
- - - - - -
- - - - - - - -
int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getTemplatesNumber ()
- 		-inline
-
- -

Definition at line 163 of file SupervisedParticlePicker.java.

-
164  {
165  if (templates == null)
166  return dtemplatesnum;
167  try
168  {
169  return (int) templates.getNDim();
170  }
171  catch (Exception e)
172  {
173  // TODO Auto-generated catch block
174  e.printStackTrace();
175  }
176  return dtemplatesnum;
177  }
xmipp.jni.ImageGeneric.getNDim
native long getNDim()
- -
-
-
- -

◆ getThreads()

- -
-
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- - - - - - - -
int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.getThreads ()
- 		-inline
-
- -

Definition at line 158 of file SupervisedParticlePicker.java.

-
159  {
160  return threads;
161  }
-
-
- -

◆ hasDefocusU()

- -
-
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- - - - - - - -
boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.hasDefocusU ()
- 		-inline
-
- -

Definition at line 362 of file SupervisedParticlePicker.java.

-
362  {
363  return hasDefocusU;
364  }
-
-
-
- -

◆ hasManualParticles()

- -
-
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- - - - - - - -
boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.hasManualParticles ()
- 		-inline
-
- -

Definition at line 975 of file SupervisedParticlePicker.java.

-
976  {
977  for (SupervisedPickerMicrograph m : micrographs)
978  {
979  if (m.hasManualParticles())
980  return true;
981  }
982  return false;
983  }
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◆ importAllParticles() [1/2]

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importAllParticles (String file)
- 		-inline
-
- -

Definition at line 900 of file SupervisedParticlePicker.java.

-
901  {// Expected a file for all
902  // micrographs
903  try
904  {
905  String[] blocksArray = MetaData.getBlocksInMetaDataFile(file);
906  List<String> blocks = Arrays.asList(blocksArray);
907  String block;
908  MetaData md = new MetaData();
909 
910  for (SupervisedPickerMicrograph m : micrographs)
911  {
912  resetMicrograph(m);
913  block = "mic_" + m.getName();
914  if (blocks.contains(block))
915  {
916  String blockName = block + "@" + file;
917  md.read(blockName);
918  importParticlesFromMd(m, md);
919  }
920  }
921  md.destroy();
922  }
923  catch (Exception e)
924  {
925  getLogger().log(Level.SEVERE, e.getMessage(), e);
926  throw new IllegalArgumentException(e.getMessage());
927  }
928 
929  }// function importAllParticles
-
xmipp.jni.MetaData.read
final void read(String filename)
Definition: MetaData.java:125
-
xmipp.jni.MetaData.getBlocksInMetaDataFile
static native String [] getBlocksInMetaDataFile(String filename)
- -
xmipp.jni.MetaData.destroy
synchronized native void destroy()
-
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromMd
String importParticlesFromMd(SupervisedPickerMicrograph m, MetaData md)
Definition: SupervisedParticlePicker.java:838
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◆ importAllParticles() [2/2]

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String xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importAllParticles (String file,
float scale,
boolean invertx,
boolean inverty 
)
- 		-inline
-
- -

Definition at line 931 of file SupervisedParticlePicker.java.

-
932  {// Expected a file for all
933  // micrographs
934  try
935  {
936 
937  String[] blocksArray = MetaData.getBlocksInMetaDataFile(file);
938  List<String> blocks = Arrays.asList(blocksArray);
939  String block;
940  MetaData md = new MetaData();
941  int width, height;
942 
943  for (SupervisedPickerMicrograph m : micrographs)
944  {
945  resetMicrograph(m);
946  block = "mic_" + m.getName();
947  if (blocks.contains(block))
948  {
949  String blockName = block + "@" + file;
950  md.read(blockName);
951  width = (int) (m.getWidth() / scale);// original width
952  height = (int) (m.getHeigth() / scale);// original height
953  if (invertx)
954  md.operate(String.format("xcoor=%d-xcoor", width));
955  if (inverty)
956  md.operate(String.format("ycoor=%d-ycoor", height));
957  if (scale != 1.f)
958  md.operate(String.format("xcoor=xcoor*%f,ycoor=ycoor*%f", scale, scale));
959  importParticlesFromMd(m, md);
960  }
961  }
962  md.destroy();
963  }
964  catch (Exception e)
965  {
966  getLogger().log(Level.SEVERE, e.getMessage(), e);
967  throw new IllegalArgumentException(e.getMessage());
968  }
969  return null;
970 
971  }// function importAllParticles
-
xmipp.jni.MetaData.read
final void read(String filename)
Definition: MetaData.java:125
-
xmipp.jni.MetaData.getBlocksInMetaDataFile
static native String [] getBlocksInMetaDataFile(String filename)
- -
xmipp.jni.MetaData.destroy
synchronized native void destroy()
-
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromMd
String importParticlesFromMd(SupervisedPickerMicrograph m, MetaData md)
Definition: SupervisedParticlePicker.java:838
- - -
xmipp.jni.MetaData.operate
native void operate(String operateStr)
- - -
-
-
- -

◆ importParticlesFromFile()

- -
-
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String xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFile (String path,
Format f,
SupervisedPickerMicrograph m,
float scale,
boolean invertx,
boolean inverty 
)
- 		-inline
-
-

Return the number of particles imported from a file

- -

Definition at line 817 of file SupervisedParticlePicker.java.

-
818  {
819  String result = "";
820  try
821  {
822  MetaData md = new MetaData();
823  fillParticlesMdFromFile(path, f, m, md, scale, invertx, inverty);
824  if (md.size() > 0)
825  {
826  //Be sure that width and height are loaded
827  result = importParticlesFromMd(m, md);
828  }
829  md.destroy();
830  }
831  catch (Exception ex)
832  {
833  XmippDialog.showInfo(null, ex.getMessage());
834  }
835  return result;
836  }// function importParticlesFromFile
xmipp.jni.MetaData.destroy
synchronized native void destroy()
-
xmipp.jni.MetaData.size
native int size()
-
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromMd
String importParticlesFromMd(SupervisedPickerMicrograph m, MetaData md)
Definition: SupervisedParticlePicker.java:838
-
xmipp.utils.XmippDialog.showInfo
boolean showInfo(String message)
Definition: XmippDialog.java:199
- - -
xmipp.viewer.particlepicker.ParticlePicker.fillParticlesMdFromFile
void fillParticlesMdFromFile(String path, Format f, Micrograph m, MetaData md, float scale, boolean invertx, boolean inverty)
Definition: ParticlePicker.java:497
-
-
-
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◆ importParticlesFromFolder()

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String xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFolder (String path,
Format f,
String preffix,
String suffix,
float scale,
boolean invertx,
boolean inverty 
)
- 		-inline
-
-

Return the number of particles imported

- -

Definition at line 777 of file SupervisedParticlePicker.java.

-
778  {
779 
780  if (f == Format.Auto)
781  {
782  StringBuffer suffixPtr = new StringBuffer(suffix);
783  f = detectFormat(path, preffix, suffixPtr);
784  suffix = suffixPtr.toString();
785  }
786  if (f == Format.None)
787  throw new IllegalArgumentException("Unable to detect format. You may try specifying format or renaming files");
788 
789  String result = "";
790 
791  String particlesfile = getExportFile(path);
792  if (particlesfile != null && f == Format.Xmipp30)
793  {
794  importAllParticles(particlesfile);
795  return "";
796  }
797 
798  importSize(path, f, scale);
799  String file;
800 
801  for (SupervisedPickerMicrograph m : micrographs)
802  {
803  resetMicrograph(m);
804  file = Filename.join(path, preffix + m.getName() + suffix);
805  if(new File(file).exists())
806  result += importParticlesFromFile(file, f, m, scale, invertx, inverty);
807  }
808 
809 
810 
811  return result;
812  }// function importParticlesFromFolder
xmipp.viewer.particlepicker.ParticlePicker.detectFormat
Format detectFormat(String path, String preffix, StringBuffer suffix)
Definition: ParticlePicker.java:295
-
xmipp.jni.Filename.join
static String join(String... paths)
Definition: Filename.java:473
- - - -
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromFile
String importParticlesFromFile(String path, Format f, SupervisedPickerMicrograph m, float scale, boolean invertx, boolean inverty)
Definition: SupervisedParticlePicker.java:817
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xmipp.viewer.particlepicker.ParticlePicker.importSize
void importSize(String path, Format f, double scale)
Definition: ParticlePicker.java:643
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◆ importParticlesFromMd()

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String xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.importParticlesFromMd (SupervisedPickerMicrograph m,
MetaData md 
)
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-
- -

Definition at line 838 of file SupervisedParticlePicker.java.

-
839  {
840  long[] ids = md.findObjects();
841  int x, y;
842  String result = "";
843  int size = getSize();
844 
845  for (long id : ids)
846  {
847  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
848  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
849  if ( !m.fits(x, y, size))// ignore out of bounds particles
850  {
851  result += XmippMessage.getOutOfBoundsMsg(String.format("Particle on x:%s y:%s\n", x, y)) + " dismissed\n";
852  continue;
853  }
854  m.addManualParticle(new ManualParticle(x, y, this, m, 2), this);
855 
856  }
857  saveData(m);
858 
859  return result;
860  }// function importParticlesFromMd
-
xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.addManualParticle
void addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:122
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xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
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xmipp.utils.XmippMessage.getOutOfBoundsMsg
static String getOutOfBoundsMsg(Object o)
Definition: XmippMessage.java:56
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xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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xmipp.viewer.particlepicker.Micrograph.fits
boolean fits(int x, int y, int size)
Definition: Micrograph.java:129
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◆ initTemplates() [1/2]

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synchronized void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.initTemplates ()
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Definition at line 186 of file SupervisedParticlePicker.java.

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187  {
188  initTemplates(getTemplatesNumber());
189  }
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synchronized void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.initTemplates (int num)
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Definition at line 191 of file SupervisedParticlePicker.java.

-
192  {
193  if (num == 0)
194  return;
195  try
196  {
197  this.templates = new ImageGeneric(ImageGeneric.Float);
198  templates.resize(getSize(), getSize(), 1, num);
199  templates.write(templatesfile);
200  templateindex = 0;
201  radialtemplates = new ImageGeneric(ImageGeneric.Float);
202  radialtemplates.resize(getSize(), getSize(), 1, num);
203  }
204  catch (Exception e)
205  {
206  throw new IllegalArgumentException(e.getMessage());
207  }
208  }
xmipp.jni.ImageGeneric.write
native void write(String filename)
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xmipp.jni.ImageGeneric.resize
void resize(int w, int h)
Definition: ImageGeneric.java:90
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static final int Float
Definition: ImageGeneric.java:24
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◆ isAutopick()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.isAutopick ()
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Definition at line 584 of file SupervisedParticlePicker.java.

-
585  {
586  return isautopick;
587  }
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◆ isCorrectPending()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.isCorrectPending ()
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- -

Definition at line 1344 of file SupervisedParticlePicker.java.

-
1345  {
1346  return getMode() == Mode.Supervised && getMicrograph().getState() == MicrographState.Supervised && isChanged();
1347  }
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◆ isFastMode()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.isFastMode ()
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-
- -

Definition at line 148 of file SupervisedParticlePicker.java.

-
149  {
150  return fastmode;
151  }
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◆ isIncore()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.isIncore ()
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Definition at line 153 of file SupervisedParticlePicker.java.

-
154  {
155  return incore;
156  }
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◆ isReviewFile()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.isReviewFile (String file)
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-
- -

Definition at line 862 of file SupervisedParticlePicker.java.

-
863  {
864  if (!file.endsWith("xmd"))
865  return false;
866  boolean result = false;
867  boolean nullMicrograph = false;
868  try
869  {
870  MetaData md = new MetaData(file);
871 
872  if (md.containsLabel(MDLabel.MDL_XCOOR) && md.containsLabel(MDLabel.MDL_YCOOR) && md.containsLabel(MDLabel.MDL_COST))
873  {
874  String[] blocksArray = MetaData.getBlocksInMetaDataFile(file);
875  List<String> blocks = Arrays.asList(blocksArray);
876 
877  String name;
878  for (String block : blocks)
879  {
880  name = block.replace("mic_", "");
881  if (getMicrograph(name) == null)
882  {
883  nullMicrograph = true;
884  break;
885  }
886  }
887  }
888  md.destroy();
889 
890  if (!nullMicrograph)
891  result = true;
892  }
893  catch (Exception e)
894  {
895  e.printStackTrace();
896  }
897  return result;
898  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
- -
xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
-
xmipp.jni.MDLabel.MDL_COST
static final int MDL_COST
< Store a score for the coords. consensus (it will change the behavoir of the viewer) ...
Definition: MDLabel.java:46
-
xmipp.jni.MetaData.getBlocksInMetaDataFile
static native String [] getBlocksInMetaDataFile(String filename)
-
xmipp.jni.MetaData.destroy
synchronized native void destroy()
- - - -
xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
-
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- -

◆ isValidSize()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.isValidSize (JFrame parent,
int size 
)
- 		-inline
-
- -

Definition at line 506 of file SupervisedParticlePicker.java.

-
507  {
508 
509 
510  if (size > ParticlePicker.sizemax) {
511  XmippDialog.showInfo(parent, String.format("Max size is %s, %s not allowed", ParticlePicker.sizemax, size));
512  return false;
513  }
514  String outmsg = "";
515  int count;
516  boolean valid = true;
517  List<ManualParticle> outlist = new ArrayList<ManualParticle>();
518  for (SupervisedPickerMicrograph m : micrographs)
519  {
520  count = 0;
521  for (ManualParticle p : m.getParticles())
522  if (!m.fits(p.getX(), p.getY(), size))
523  {
524  outlist.add(p);
525  count ++;
526  valid = false;
527  }
528  if(count > 0)
529  outmsg += String.format("%s %s from micrograph %s will be dismissed if size %s is set.", count, (count == 1)? "particle": "particles", m.getName(), size);
530  }
531  if(valid)
532  return true;
533  else
534  {
535  String msg = outmsg + " Are you sure you want to continue?";
536  valid = XmippDialog.showQuestion(parent, msg);
537  if(valid)
538  for(ManualParticle p: outlist)
539  ((SupervisedPickerMicrograph)p.getMicrograph()).removeParticle(p, this);
540  return valid;
541 
542  }
543  }
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xmipp.utils.XmippDialog.showQuestion
static boolean showQuestion(JFrame parent, String message)
Definition: XmippDialog.java:258
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boolean showInfo(String message)
Definition: XmippDialog.java:199
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◆ loadAutomaticParticles() [1/2]

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadAutomaticParticles (SupervisedPickerMicrograph m,
MetaData md 
)
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-
- -

Definition at line 729 of file SupervisedParticlePicker.java.

-
730  {
731 
732  int x, y;
733  AutomaticParticle particle;
734  Double cost;
735  boolean deleted;
736  try
737  {
738  boolean added = false;
739 
740  for (long id : md.findObjects())
741  {
742 
743  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
744  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
745  cost = md.getValueDouble(MDLabel.MDL_COST, id);
746  if (cost == null)
747  throw new IllegalArgumentException("Invalid format for " + md.getFilename());
748  deleted = (md.getValueInt(MDLabel.MDL_ENABLED, id) == 1) ? false : true;
749  particle = new AutomaticParticle(x, y, this, m, cost, deleted);
750  m.addAutomaticParticle(particle);
751  added = true;
752  }
753  // Change the state of the micrograph if some automatic particles
754  // were added
755  if (added && m.getState() == MicrographState.Available)
756  m.setState(MicrographState.Auto);
757 
758  }
759  catch (Exception e)
760  {
761  getLogger().log(Level.SEVERE, e.getMessage(), e);
762  throw new IllegalArgumentException(e.getMessage());
763  }
764  }
xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
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xmipp.jni.MDLabel.MDL_COST
static final int MDL_COST
< Store a score for the coords. consensus (it will change the behavoir of the viewer) ...
Definition: MDLabel.java:46
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xmipp.jni.MetaData.findObjects
native long [] findObjects()
-
xmipp.jni.MDLabel.MDL_ENABLED
static final int MDL_ENABLED
< Dose e/A^2 (double)
Definition: MDLabel.java:177
- -
xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
- -
xmipp.jni.MetaData.getFilename
String getFilename()
Definition: MetaData.java:418
- - - -
xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
-
xmipp.jni.MDLabel.MDL_XCOOR
static final int MDL_XCOOR
< X component (double)
Definition: MDLabel.java:426
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◆ loadAutomaticParticles() [2/2]

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadAutomaticParticles (SupervisedPickerMicrograph m,
String file 
)
- 		-inline
-
- -

Definition at line 766 of file SupervisedParticlePicker.java.

-
767  {
768  if (new File(file).exists() && MetaData.containsBlock(file, particlesAutoBlock))// todo: // exists
769  {
770  MetaData md = new MetaData(getParticlesAutoBlock(file));
771  loadAutomaticParticles(m, md);
772  md.destroy();
773  }
774  }
-
xmipp.jni.MetaData.containsBlock
static boolean containsBlock(String file, String block)
Definition: MetaData.java:230
-
xmipp.jni.MetaData.destroy
synchronized native void destroy()
- -
xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadAutomaticParticles
void loadAutomaticParticles(SupervisedPickerMicrograph m, MetaData md)
Definition: SupervisedParticlePicker.java:729
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◆ loadConfig()

- -
-
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- - - - - - - -
void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadConfig ()
- 		-inline
-
- -

Definition at line 546 of file SupervisedParticlePicker.java.

-
547  {
548  super.loadConfig();
549  String file = configfile;
550  if (!new File(file).exists())
551  return;
552 
553  try
554  {
555  MetaData md = new MetaData(file);
556  Mode configmode;
557  boolean hasautopercent = md.containsLabel(MDLabel.MDL_PICKING_AUTOPICKPERCENT);
558  long id = md.firstObject();
559 
560  if(hasautopercent)
561  autopickpercent = md.getValueInt(MDLabel.MDL_PICKING_AUTOPICKPERCENT, id);
562 
563  dtemplatesnum = md.getValueInt(MDLabel.MDL_PICKING_TEMPLATES, id);
564  if (dtemplatesnum == 0)
565  dtemplatesnum = 1;// for compatibility with previous projects
566  configmode = Mode.valueOf(md.getValueString(MDLabel.MDL_PICKING_STATE, id));
567  isautopick = configmode == Mode.Supervised || configmode == Mode.Review;
568 
569  if (mode == Mode.Review && configmode == Mode.Manual)//Review mode makes no sense if manual mode
570  throw new IllegalArgumentException("Cannot review picking in manual mode, use manual mode instead");
571 
572  if (mode != Mode.ReadOnly && mode != Mode.Review)
573  mode = configmode;
574 
575  md.destroy();
576  }
577  catch (Exception e)
578  {
579  getLogger().log(Level.SEVERE, e.getMessage(), e);
580  throw new IllegalArgumentException(e.getMessage());
581  }
582  }
- -
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
- -
xmipp.jni.MDLabel.MDL_PICKING_AUTOPICKPERCENT
static final int MDL_PICKING_AUTOPICKPERCENT
< Micrograph state for particle picking
Definition: MDLabel.java:286
- -
xmipp.jni.MDLabel.MDL_PICKING_TEMPLATES
static final int MDL_PICKING_TEMPLATES
< Color for particle picking
Definition: MDLabel.java:283
- -
xmipp.jni.MetaData.destroy
synchronized native void destroy()
- -
xmipp.jni.MetaData.getValueInt
native int getValueInt(int label, long objId)
-
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
- -
xmipp.jni.MetaData.firstObject
native long firstObject()
- -
xmipp.jni.MDLabel.MDL_PICKING_STATE
static final int MDL_PICKING_STATE
< Number of templates
Definition: MDLabel.java:284
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◆ loadEmptyMicrographs()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadEmptyMicrographs ()
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-
- -

Definition at line 367 of file SupervisedParticlePicker.java.

-
368  {
369  String selfile = getMicrographsSelFile();
370  if(selfile.endsWith(".sqlite"))
371  loadEmptyMicrographsFromSqlite();
372  else
373  loadEmptyMicrographsFromMd();
374  }
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◆ loadEmptyMicrographsFromMd()

- -
-
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- - - - - - - -
void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadEmptyMicrographsFromMd ()
- 		-inline
-
- -

Definition at line 376 of file SupervisedParticlePicker.java.

-
377  {
378  if (micrographs == null)
379  micrographs = new ArrayList<SupervisedPickerMicrograph>();
380  else
381  micrographs.clear();
382  SupervisedPickerMicrograph micrograph;
383  String psd = null, ctf = null, filename;
384  try
385  {
386  String selfile = getMicrographsSelFile();
387  MetaData md = new MetaData(selfile);
388 
389  //md.removeDisabled();
390 
391  int fileLabel;
392  if (md.containsLabel(MDLabel.MDL_MICROGRAPH))
393  fileLabel = MDLabel.MDL_MICROGRAPH;
394  else if (md.containsLabel(MDLabel.MDL_IMAGE))
395  fileLabel = MDLabel.MDL_IMAGE;
396  else
397  throw new IllegalArgumentException(String.format("Labels MDL_MICROGRAPH or MDL_IMAGE not found in metadata %s", selfile));
398  existspsd = md.containsLabel(MDLabel.MDL_PSD_ENHANCED);
399  boolean existsctf = md.containsLabel(MDLabel.MDL_CTF_MODEL);
400  hasDefocusU = md.containsLabel(MDLabel.MDL_CTF_DEFOCUSV);
401 
402  boolean hasctfinfo = existsctf || existspsd || hasDefocusU;
403 
404  long[] ids = md.findObjects();
405  CtfInfo ctfInfo;
406 
407  for (long id : ids)
408  {
409  ctfInfo = hasctfinfo ? new CtfInfo() : null;
410 
411  filename = md.getValueString(fileLabel, id);
412  if (existspsd)
413  ctfInfo.psd = md.getValueString(MDLabel.MDL_PSD_ENHANCED, id);
414  if (existsctf)
415  ctfInfo.ctf = md.getValueString(MDLabel.MDL_CTF_MODEL, id);
416  if (hasDefocusU)
417  ctfInfo.defocusU = new Float(md.getValueDouble(MDLabel.MDL_CTF_DEFOCUSV, id));
418 
419  micrograph = new SupervisedPickerMicrograph(filename, ctfInfo);
420 
421  micrographs.add(micrograph);
422  }
423  if (micrographs.isEmpty())
424  throw new IllegalArgumentException(String.format("No micrographs specified on %s", getMicrographsSelFile()));
425  md.destroy();
426  }
427  catch (Exception e)
428  {
429  getLogger().log(Level.SEVERE, e.getMessage(), e);
430  throw new IllegalArgumentException(e.getMessage());
431  }
432 
433  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
- - - -
xmipp.jni.MDLabel.MDL_CTF_MODEL
static final int MDL_CTF_MODEL
< Parameters file for the CTF Model (std::string)
Definition: MDLabel.java:80
- -
xmipp.jni.MetaData.findObjects
native long [] findObjects()
-
xmipp.jni.MetaData.destroy
synchronized native void destroy()
-
xmipp.jni.MDLabel.MDL_PSD_ENHANCED
static final int MDL_PSD_ENHANCED
< A Power Spectrum Density file name (std::string)
Definition: MDLabel.java:309
- -
xmipp.jni.MDLabel.MDL_CTF_DEFOCUSV
static final int MDL_CTF_DEFOCUSV
< Defocus U (Angstroms)
Definition: MDLabel.java:87
- -
xmipp.jni.MDLabel.MDL_MICROGRAPH
static final int MDL_MICROGRAPH
< Correlation from previous alignment
Definition: MDLabel.java:227
- - -
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
- -
xmipp.jni.MDLabel.MDL_IMAGE
static final int MDL_IMAGE
< Index within a list (size_t)
Definition: MDLabel.java:190
- - - -
xmipp.jni.MetaData.getValueDouble
native double getValueDouble(int label, long objId)
-
-
-
- -

◆ loadEmptyMicrographsFromSqlite()

- -
-
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- - - - - - - -
void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadEmptyMicrographsFromSqlite ()
- 		-inline
-
- -

Definition at line 435 of file SupervisedParticlePicker.java.

-
436  {
437  if (micrographs == null)
438  micrographs = new ArrayList<SupervisedPickerMicrograph>();
439  else
440  micrographs.clear();
441  SupervisedPickerMicrograph micrograph;
442  String filename;
443  try
444  {
445  String selfile = getMicrographsSelFile();
446  ScipionMetaData md = new ScipionMetaData(selfile);
447 
448  ColumnInfo ci;
449  if(md.getSelf().equals("Micrograph"))
450  {
451  ci = md.getColumnInfo("_filename");
452  long[] ids = md.findObjects();
453  for (long id : ids)
454  {
455 
456  filename = md.getValueString(ci.label, id);
457  micrograph = new SupervisedPickerMicrograph(filename, null);
458  micrographs.add(micrograph);
459  }
460  }
461  else
462  throw new IllegalArgumentException(String.format("Labels MDL_MICROGRAPH or MDL_IMAGE not found in metadata %s", selfile));
463 
464  if (micrographs.isEmpty())
465  throw new IllegalArgumentException(String.format("No micrographs specified on %s", getMicrographsSelFile()));
466  md.destroy();
467  }
468  catch (Exception e)
469  {
470  getLogger().log(Level.SEVERE, e.getMessage(), e);
471  throw new IllegalArgumentException(e.getMessage());
472  }
473  }
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◆ loadManualParticles()

- -
-
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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadManualParticles (SupervisedPickerMicrograph m,
String file 
)
- 		-inline
-
- -

Definition at line 1024 of file SupervisedParticlePicker.java.

-
1025  {
1026  if (new File(file).exists() && MetaData.containsBlock(file, getParticlesBlockName(Format.Xmipp301)))
1027  {
1028 
1029  int x, y;
1030  ManualParticle particle;
1031 
1032  try
1033  {
1034  MetaData md = new MetaData(getParticlesBlock(file));
1035 
1036  for (long id : md.findObjects())
1037  {
1038  x = md.getValueInt(MDLabel.MDL_XCOOR, id);
1039  y = md.getValueInt(MDLabel.MDL_YCOOR, id);
1040  particle = new ManualParticle(x, y, this, m);
1041  m.addManualParticle(particle, this);
1042  }
1043  md.destroy();
1044  }
1045  catch (Exception e)
1046  {
1047  getLogger().log(Level.SEVERE, e.getMessage(), e);
1048  throw new IllegalArgumentException(e.getMessage());
1049  }
1050  }
1051  }
- -
xmipp.viewer.particlepicker.ParticlePicker.getParticlesBlock
static String getParticlesBlock(Format f, String file)
Definition: ParticlePicker.java:97
-
xmipp.jni.MDLabel.MDL_YCOOR
static final int MDL_YCOOR
< Y component (double)
Definition: MDLabel.java:430
- -
xmipp.jni.MetaData.findObjects
native long [] findObjects()
-
xmipp.jni.MetaData.containsBlock
static boolean containsBlock(String file, String block)
Definition: MetaData.java:230
-
xmipp.jni.MetaData.destroy
synchronized native void destroy()
-
xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.addManualParticle
void addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:122
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xmipp.jni.MetaData.getValueInt
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Definition: MDLabel.java:426
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◆ loadMicrographData()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadMicrographData (SupervisedPickerMicrograph m)
- 		-inline
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- -

Definition at line 991 of file SupervisedParticlePicker.java.

-
992  {
993  try
994  {
995  String file = getOutputPath(m.getPosFile());
996  MicrographState state;
997  int micautopickpercent;
998  if (!new File(file).exists())
999  return;
1000  if (MetaData.containsBlock(file, "header"))
1001  {
1002  MetaData md = new MetaData("header@" + file);
1003  boolean hasautopercent = md.containsLabel(MDLabel.MDL_PICKING_AUTOPICKPERCENT);
1004  long id = md.firstObject();
1005  state = MicrographState.valueOf(md.getValueString(MDLabel.MDL_PICKING_MICROGRAPH_STATE, id));
1006  micautopickpercent = hasautopercent ? md.getValueInt(MDLabel.MDL_PICKING_AUTOPICKPERCENT, id) : getAutopickpercent();
1007  double threshold = md.getValueDouble(MDLabel.MDL_COST, id);
1008  m.setThreshold(threshold);
1009  m.setState(state);
1010  m.setAutopickpercent(micautopickpercent);
1011  md.destroy();
1012  }
1013  loadManualParticles(m, file);
1014  loadAutomaticParticles(m, file);
1015  }
1016  catch (Exception e)
1017  {
1018  getLogger().log(Level.SEVERE, e.getMessage(), e);
1019  throw new IllegalArgumentException(e.getMessage());
1020  }
1021 
1022  }
xmipp.jni.MetaData.containsLabel
native boolean containsLabel(int label)
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xmipp.jni.MDLabel.MDL_PICKING_AUTOPICKPERCENT
static final int MDL_PICKING_AUTOPICKPERCENT
< Micrograph state for particle picking
Definition: MDLabel.java:286
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xmipp.jni.MDLabel.MDL_PICKING_MICROGRAPH_STATE
static final int MDL_PICKING_MICROGRAPH_STATE
< State for particle picking
Definition: MDLabel.java:285
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static final int MDL_COST
< Store a score for the coords. consensus (it will change the behavoir of the viewer) ...
Definition: MDLabel.java:46
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xmipp.jni.MetaData.containsBlock
static boolean containsBlock(String file, String block)
Definition: MetaData.java:230
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadAutomaticParticles
void loadAutomaticParticles(SupervisedPickerMicrograph m, MetaData md)
Definition: SupervisedParticlePicker.java:729
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◆ loadParticles()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.loadParticles (SupervisedPickerMicrograph micrograph,
Particle [] autopickRows 
)
- 		-inline
-
- -

Definition at line 1102 of file SupervisedParticlePicker.java.

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1103  {
1104  Rectangle rectangle = micrograph.getRectangle();
1105  int x, y;
1106  double cost;
1107  AutomaticParticle ap;
1108  for (Particle row: autopickRows)
1109  {
1110  x = row.getX();
1111  y = row.getY();
1112  cost = row.getCost();
1113  ap = new AutomaticParticle(x, y, SupervisedParticlePicker.this, micrograph, cost, false);
1114  if (rectangle != null && rectangle.contains(new Point(x, y)))
1115  {
1116  ap.setDeleted(true);
1117  ap.setCost(-1);
1118  }
1119  micrograph.addAutomaticParticle(ap);
1120  }
1121  }
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◆ resetMicrograph()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.resetMicrograph (SupervisedPickerMicrograph micrograph)
- 		-inline
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- -

Definition at line 1214 of file SupervisedParticlePicker.java.

-
1215  {
1216  micrograph.getManualParticles().clear();
1217  micrograph.getAutomaticParticles().clear();
1218  micrograph.setState(MicrographState.Available);
1219  micrograph.setThreshold(0);
1220  micrograph.resetParticlesRectangle();
1221  new File(getOutputPath(micrograph.getPosFile())).delete();
1222 
1223  }
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◆ resetParticleImages()

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Definition at line 244 of file SupervisedParticlePicker.java.

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245  {
246  for (SupervisedPickerMicrograph m : micrographs)
247  {
248  for (ManualParticle p : m.getManualParticles())
249  p.resetImage();
250 
251  }
252  }
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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.saveAllData ()
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Definition at line 140 of file SupervisedParticlePicker.java.

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141  {
142  super.saveData();
143  for (Micrograph m : micrographs)
144  saveData(m);
145  setChanged(false);
146  }
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Definition at line 590 of file SupervisedParticlePicker.java.

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591  {
592  JMetaDataIO.saveConfig(this, configfile);
593  }
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long id 
)
- 		-inlineprotected
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Definition at line 596 of file SupervisedParticlePicker.java.

-
597  {
598  try
599  {
600  super.saveConfig(md, id);
601  md.setValueInt(MDLabel.MDL_PICKING_AUTOPICKPERCENT, getAutopickpercent(), id);
602  md.setValueInt(MDLabel.MDL_PICKING_TEMPLATES, getTemplatesNumber(), id);
603  md.setValueString(MDLabel.MDL_PICKING_STATE, mode.toString(), id);
604  md.setValueInt(MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE, getManualParticlesNumber(), id);
605  md.setValueInt(MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE, getAutomaticParticlesNumber(), id);
606 
607  }
608  catch (Exception e)
609  {
610  getLogger().log(Level.SEVERE, e.getMessage(), e);
611  throw new IllegalArgumentException(e.getMessage());
612  }
613  }
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xmipp.jni.MDLabel.MDL_PICKING_AUTOPICKPERCENT
static final int MDL_PICKING_AUTOPICKPERCENT
< Micrograph state for particle picking
Definition: MDLabel.java:286
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xmipp.jni.MDLabel.MDL_PICKING_TEMPLATES
static final int MDL_PICKING_TEMPLATES
< Color for particle picking
Definition: MDLabel.java:283
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xmipp.jni.MDLabel.MDL_PICKING_AUTOPARTICLES_SIZE
static final int MDL_PICKING_AUTOPARTICLES_SIZE
< Particle size for particle picking
Definition: MDLabel.java:288
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static final int MDL_PICKING_STATE
< Number of templates
Definition: MDLabel.java:284
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xmipp.jni.MDLabel.MDL_PICKING_MANUALPARTICLES_SIZE
static final int MDL_PICKING_MANUALPARTICLES_SIZE
< Number of automatic particles picked
Definition: MDLabel.java:289
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Definition at line 131 of file SupervisedParticlePicker.java.

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132  {
133  super.saveData();
134  saveData(micrograph);
135  setChanged(false);
136  setSaved(true);
137  }
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Definition at line 482 of file SupervisedParticlePicker.java.

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483  {
484 
485  JMetaDataIO.saveData((SupervisedPickerMicrograph) m, getOutputPath(m.getPosFile()));
486  saveTemplates();
487 
488  }
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◆ saveTemplates()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.saveTemplates ()
- 		-inline
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Definition at line 344 of file SupervisedParticlePicker.java.

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345  {
346  try
347  {
348  if(templateindex == getTemplatesNumber())
349  templates.write(getTemplatesFile());
350  }
351  catch (Exception e)
352  {
353  throw new IllegalArgumentException(e.getMessage());
354  }
355  }
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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.setAutopickpercent (int autopickpercent)
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Definition at line 615 of file SupervisedParticlePicker.java.

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616  {
617  this.autopickpercent = autopickpercent;
618  }
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◆ setMicrograph()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.setMicrograph (Micrograph m)
- 		-inline
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Definition at line 496 of file SupervisedParticlePicker.java.

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497  {
498  if (m == null)
499  return;
500  if (m.equals(micrograph))
501  return;
502  this.micrograph = (SupervisedPickerMicrograph) m;
503  }
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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.setMode (Mode mode)
- 		-inline
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Definition at line 627 of file SupervisedParticlePicker.java.

-
628  {
629  if (mode == Mode.Supervised && getManualParticlesNumber() < classifier.getTrainingParticlesMinimum())
630  throw new IllegalArgumentException(String.format("You should have at least %s particles to go to %s mode", classifier.getTrainingParticlesMinimum(), Mode.Supervised));
631  this.mode = mode;
632 
633  // If supervised
634  if(mode == Mode.Supervised)
635  isautopick = true;
636  if (mode == Mode.Manual)
637  convertAutomaticToManual();
638 
639  }
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Definition at line 179 of file SupervisedParticlePicker.java.

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180  {
181 
182  super.setSize(size);
183  classifier.setSize(size);
184  }
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Definition at line 224 of file SupervisedParticlePicker.java.

-
225  {
226  float[] matrix;
227  try
228  {
229  // TODO getArrayFloat and setArrayFloat must be call from C both in
230  // one function
231  matrix = ig.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE);
232  templates.setArrayFloat(matrix, ImageGeneric.FIRST_IMAGE + templateindex, ImageGeneric.FIRST_SLICE);
233  templateindex++;
234 
235  }
236  catch (Exception e)
237  {
238  e.printStackTrace();
239  throw new IllegalArgumentException(e.getMessage());
240  }
241  }
xmipp.jni.ImageGeneric.FIRST_SLICE
static final int FIRST_SLICE
Definition: ImageGeneric.java:9
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native void setArrayFloat(float data[], long select_image, int slice)
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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◆ setTemplatesDialog()

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- 		-inline
-
- -

Definition at line 1253 of file SupervisedParticlePicker.java.

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1254  {
1255  dialog = d;
1256  }
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◆ setTemplatesNumber()

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- 		-inline
-
- -

Definition at line 210 of file SupervisedParticlePicker.java.

-
211  {
212  if (num <= 0)
213  throw new IllegalArgumentException(
214  XmippMessage.getIllegalValueMsgWithInfo("Templates Number", Integer.valueOf(num), "Must have at least one template"));
215  updateTemplatesStack(num, false);
216  saveConfig();
217  }
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static String getIllegalValueMsgWithInfo(String field, Object value, String message)
Definition: XmippMessage.java:79
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◆ trainAndAutopick()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.trainAndAutopick (SupervisedPickerJFrame frame,
SupervisedPickerMicrograph trainmic 
)
- 		-inline
-
-

This function will be called when the user selects Autopick for the first time. In order to train the classifier a metadata will be create with a list of micrographs and the corresponding .pos file associated with the micrograph, but only for those micrographs containing manual particles.

-
Parameters
- - - -
frame
trainmic
-
-
- -

Definition at line 1062 of file SupervisedParticlePicker.java.

-
1063  {
1064  frame.getCanvas().setEnabled(false);
1065  XmippWindowUtil.blockGUI(frame, "Training and Autopicking...");
1066  // Change the state of the micrograph and save changes
1067  micrograph.setState(MicrographState.Supervised);
1068  saveData(micrograph);
1069  setChanged(false);
1070  // Create the metadata with each micrograph and its .pos file
1071  // Add all micrographs with manual particles except the train
1072  // micrograph
1073  ArrayList<MDRow> trainRows = new ArrayList<MDRow>();
1074  for (SupervisedPickerMicrograph m : micrographs)
1075  {
1076  if (m.hasManualParticles() && !m.equals(trainmic))
1077  addMicrographPos(trainRows, m);
1078  }
1079  // Add the train micrograph as the last one
1080 
1081  addMicrographPos(trainRows, trainmic);
1082 
1083  new Thread(new TrainRunnable(frame, trainRows.toArray(new MDRow[]{}), trainmic), "TrainAndAutopick").start();
1084  }
xmipp.utils.XmippWindowUtil.blockGUI
static void blockGUI(JFrame window, String status)
Definition: XmippWindowUtil.java:219
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)
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Definition at line 254 of file SupervisedParticlePicker.java.

-
255  {
256 
257  try
258  {
259  this.templates = templates;
260  radialtemplates = new ImageGeneric(ImageGeneric.Float);
261  radialtemplates.resize(getSize(), getSize(), 1, getTemplatesNumber());
262  templates.getRadialAvg(radialtemplates);
263  this.templateindex = templateindex;
264  saveTemplates();
265  }
266  catch (Exception e)
267  {
268  throw new IllegalArgumentException(e.getMessage());
269  }
270  }
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xmipp.jni.ImageGeneric.resize
void resize(int w, int h)
Definition: ImageGeneric.java:90
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synchronized native void getRadialAvg(ImageGeneric radialimg)
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Definition at line 1240 of file SupervisedParticlePicker.java.

-
1241  {
1242  updateTemplatesStack(getTemplatesNumber(), resize);
1243  }
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Definition at line 1245 of file SupervisedParticlePicker.java.

-
1246  {
1247  if(mode != Mode.Manual)
1248  return;
1249  initTemplates(num);//to avoid any error with templates while updating
1250  new UpdateTemplatesTask(resize).execute();
1251  }
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Member Data Documentation

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◆ autopickpercent

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int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.autopickpercent
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Definition at line 45 of file SupervisedParticlePicker.java.

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◆ dtemplatesnum

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int xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.dtemplatesnum = 1
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Definition at line 53 of file SupervisedParticlePicker.java.

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◆ micrographs

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Definition at line 43 of file SupervisedParticlePicker.java.

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doInBackground()xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.UpdateTemplatesTaskinlineprotected
done()xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.UpdateTemplatesTaskinlineprotected
UpdateTemplatesTask(boolean resize)xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.UpdateTemplatesTaskinline
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-Public Member Functions

 UpdateTemplatesTask (boolean resize)
 
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String doInBackground () throws Exception
 
void done ()
 
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Detailed Description

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Definition at line 1258 of file SupervisedParticlePicker.java.

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Constructor & Destructor Documentation

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◆ UpdateTemplatesTask()

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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.UpdateTemplatesTask.UpdateTemplatesTask (boolean resize)
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Definition at line 1261 of file SupervisedParticlePicker.java.

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1262  {
1263  this.resize = resize;
1264  }
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◆ doInBackground()

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Definition at line 1267 of file SupervisedParticlePicker.java.

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1268  {
1269  try
1270  {
1271  if(uttask != null)
1272  uttask.cancel(true);
1273  uttask = this;
1274 
1275 
1276  ImageGeneric templates = new ImageGeneric(ImageGeneric.Float);
1277  templates.resize(getSize(), getSize(), 1, getTemplatesNumber());
1278 
1279  ImageGeneric igp;
1280  List<ManualParticle> particles;
1281 
1282  ManualParticle particle;
1283  double[] align;
1284 
1285  //FIXME: the template update needs to be done in a
1286  // more efficient way, now we are using this maxcount
1287  // to limit the number of particles used in the update
1288  int count = 0;
1289  int maxcount = 50;
1290  //FIXME: This is a tweak to avoid losing time with big particles
1291  if (getSize() > 256)
1292  maxcount = 10;
1293  float[] matrix;
1294  int templateindex = 0;
1295  for (SupervisedPickerMicrograph m : getMicrographs())
1296  {
1297  particles = m.getManualParticles();
1298  for (int i = 0; i < particles.size(); i++)
1299  {
1300  if(isCancelled())
1301  return null;
1302  if(count < maxcount)
1303  {
1304  particle = particles.get(i);
1305  if(resize)
1306  particle.resetImage();
1307  igp = particle.getImageGeneric();
1308  if (templateindex < getTemplatesNumber())
1309  {
1310  matrix = igp.getArrayFloat(ImageGeneric.FIRST_IMAGE, ImageGeneric.FIRST_SLICE);
1311  templates.setArrayFloat(matrix, ImageGeneric.FIRST_IMAGE + templateindex, ImageGeneric.FIRST_SLICE);
1312  templateindex ++;
1313  }
1314  else
1315  {
1316  align = templates.alignImage(igp);
1317  particle.setLastalign(align);
1318  templates.applyAlignment(igp, particle.getTemplateIndex(), particle.getTemplateRotation(), particle.getTemplateTilt(), particle.getTemplatePsi());
1319  }
1320  count++;
1321  }
1322 
1323  }
1324  }
1325 
1326  updateTemplates(templates, templateindex);
1327  }
1328  catch (Exception e)
1329  {
1330  e.printStackTrace();
1331  throw new IllegalArgumentException(e);
1332  }
1333  return "";
1334  }
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xmipp.jni.ImageGeneric.FIRST_SLICE
static final int FIRST_SLICE
Definition: ImageGeneric.java:9
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xmipp.jni.ImageGeneric.setArrayFloat
native void setArrayFloat(float data[], long select_image, int slice)
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xmipp.jni.ImageGeneric.resize
void resize(int w, int h)
Definition: ImageGeneric.java:90
- -
xmipp.jni.ImageGeneric.applyAlignment
native void applyAlignment(ImageGeneric img, int index, double rot, double tilt, double psi)
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xmipp.jni.ImageGeneric.FIRST_IMAGE
static final long FIRST_IMAGE
Definition: ImageGeneric.java:8
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xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.updateTemplates
synchronized void updateTemplates(ImageGeneric templates, int templateindex)
Definition: SupervisedParticlePicker.java:254
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xmipp.jni.ImageGeneric.getArrayFloat
native float [] getArrayFloat(long select_image, int slice)
- -
xmipp.jni.ImageGeneric.alignImage
synchronized native double [] alignImage(ImageGeneric img)
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xmipp.jni.ImageGeneric.Float
static final int Float
Definition: ImageGeneric.java:24
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◆ done()

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void xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.UpdateTemplatesTask.done ()
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Definition at line 1337 of file SupervisedParticlePicker.java.

-
1337  {
1338  if(dialog != null && dialog.isVisible())
1339  dialog.loadTemplates(true);
1340  }
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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__coll__graph.dot deleted file mode 100644 index bb4a23df..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.UpdateTemplatesTask" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.particlepicker.training.model.\lSupervisedParticlePicker.UpdateTemplatesTask",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="javax::swing::SwingWorker\l\< String, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__coll__graph.md5 deleted file mode 100644 index b5150021..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -7e6323c83cab96e884a38dba3dbc4e6c \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__inherit__graph.dot deleted file mode 100644 index 33ba10dd..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker.UpdateTemplatesTask" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.training.model.\lSupervisedParticlePicker.UpdateTemplatesTask",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="javax::swing::SwingWorker\l\< String, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__inherit__graph.md5 deleted file mode 100644 index 3df2d9a1..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker_1_1UpdateTemplatesTask__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -cdce8f740c3a52741df013e714b70c0d \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__coll__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__coll__graph.dot deleted file mode 100644 index b5d811bc..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__coll__graph.dot +++ /dev/null @@ -1,25 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; 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- Node6 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" color\ncolors" ,fontname="Helvetica"]; - Node6 [label="Color",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" picker" ,fontname="Helvetica"]; - Node7 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mode" ,fontname="Helvetica"]; - Node7 [label="xmipp.viewer.particlepicker.training.model.Mode",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$enumxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1Mode.html"]; - Node8 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" logger" ,fontname="Helvetica"]; - Node8 [label="Logger",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" params" ,fontname="Helvetica"]; - Node9 [label="xmipp.viewer.particlepicker.\lParticlePickerParams",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePickerParams.html"]; - Node7 -> Node9 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mode" ,fontname="Helvetica"]; - Node10 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" micrographs" ,fontname="Helvetica"]; - Node10 [label="List\< xmipp.viewer.particlepicker.training.model.\lSupervisedPickerMicrograph \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__coll__graph.md5 deleted file mode 100644 index 25ed414f..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -8d1d4f2413b5052e497d0acc704d700b \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__inherit__graph.dot deleted file mode 100644 index e8c290a9..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.particlepicker.training.model.\lSupervisedParticlePicker",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.particlepicker.\lParticlePicker",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1particlepicker_1_1ParticlePicker.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__inherit__graph.md5 deleted file mode 100644 index 89ab1d79..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedParticlePicker__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -8e2485321a8a06e9567caf5aaa7a9ac8 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedPickerMicrograph-members.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedPickerMicrograph-members.html deleted file mode 100644 index 4054d313..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedPickerMicrograph-members.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph Member List
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- -

This is the complete list of members for xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph, including all inherited members.

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addAutomaticParticle(AutomaticParticle p)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
addManualParticle(ManualParticle p, SupervisedParticlePicker ppicker)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
deleteBelowThreshold()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
extxmipp.viewer.particlepicker.Micrographstatic
fits(int x, int y, int size)xmipp.viewer.particlepicker.Micrographinline
getAutomaticParticle(int x, int y, double threshold)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getAutomaticParticles()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getAutomaticParticlesDeleted()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getAutomaticParticlesDeleted(double threshold)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getAutomaticParticlesNumber(double threshold)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getAutomaticParticlesNumber()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getAutopickpercent()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getAvailableParticles(double threshold)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getCTF()xmipp.viewer.particlepicker.Micrographinline
getCTFIcon()xmipp.viewer.particlepicker.Micrographinline
getCtfInfo()xmipp.viewer.particlepicker.Micrographinline
getFile()xmipp.viewer.particlepicker.Micrographinline
getHeigth()xmipp.viewer.particlepicker.Micrographinline
getImagePlus()xmipp.viewer.particlepicker.Micrographinline
getImagePlus(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
getLastAvailableParticle(double threshold)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getManualParticles()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getName(String file)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinlinestatic
xmipp::viewer::particlepicker::Micrograph.getName(String file, int level)xmipp.viewer.particlepicker.Micrographinlinestatic
xmipp::viewer::particlepicker::Micrograph.getName()xmipp.viewer.particlepicker.Micrographinline
getNoImageIcon()xmipp.viewer.particlepicker.Micrographinlinestatic
getParticle(int x, int y)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getParticleList()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getParticles()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getPosFile()xmipp.viewer.particlepicker.Micrographinline
getPosFileFromXmipp24()xmipp.viewer.particlepicker.Micrographinline
getPSD()xmipp.viewer.particlepicker.Micrographinline
getPSDImage()xmipp.viewer.particlepicker.Micrographinline
getRectangle()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getState()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getStep()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getThreshold()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
getWidth()xmipp.viewer.particlepicker.Micrographinline
hasAutomaticParticles()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
hasData()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
hasManualParticles()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
initParticlesRectangle(SupervisedParticlePicker picker)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
isAutopicking()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
isEmpty()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
isValid(SupervisedParticlePicker picker)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
loadDimensions()xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
Micrograph(String file, String name, CtfInfo ctfInfo)xmipp.viewer.particlepicker.Micrographinline
releaseImage()xmipp.viewer.particlepicker.Micrographinline
removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
removeParticles(int x, int y, SupervisedParticlePicker ppicker)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
resetParticlesRectangle()xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
runImageJFilters(List< IJCommand > filters)xmipp.viewer.particlepicker.Micrographinline
setAutopicking(boolean autopicking)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
setAutopickpercent(int autopickpercent)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
setPosFileFromXmipp24(String posfile)xmipp.viewer.particlepicker.Micrographinline
setState(MicrographState state)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
setThreshold(double threshold)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
SupervisedPickerMicrograph(String file, CtfInfo ctfInfo)xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrographinline
toString()xmipp.viewer.particlepicker.Micrographinline
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedPickerMicrograph.html b/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedPickerMicrograph.html deleted file mode 100644 index 8de8d716..00000000 --- a/html/classxmipp_1_1viewer_1_1particlepicker_1_1training_1_1model_1_1SupervisedPickerMicrograph.html +++ /dev/null @@ -1,1325 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Static Public Member Functions | -List of all members
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph Class Reference
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-Inheritance diagram for xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph:
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[legend]
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-Collaboration diagram for xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph:
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-Public Member Functions

double getThreshold ()
 
void setThreshold (double threshold)
 
 SupervisedPickerMicrograph (String file, CtfInfo ctfInfo)
 
boolean isAutopicking ()
 
void setAutopicking (boolean autopicking)
 
ManualParticle getParticle (int x, int y)
 
AutomaticParticle getAutomaticParticle (int x, int y, double threshold)
 
boolean hasManualParticles ()
 
void removeParticles (int x, int y, SupervisedParticlePicker ppicker)
 
List< ManualParticle > getManualParticles ()
 
List< AutomaticParticle > getAutomaticParticles ()
 
void addManualParticle (ManualParticle p, SupervisedParticlePicker ppicker)
 
void removeParticle (PickerParticle p, SupervisedParticlePicker ppicker)
 
boolean hasAutomaticParticles ()
 
boolean isEmpty ()
 
int getAutomaticParticlesNumber (double threshold)
 
int getAutomaticParticlesNumber ()
 
synchronized void addAutomaticParticle (AutomaticParticle p)
 
MicrographState getState ()
 
void setState (MicrographState state)
 
Mode getStep ()
 
int getAutomaticParticlesDeleted ()
 
synchronized int getAutomaticParticlesDeleted (double threshold)
 
List< ManualParticle > getParticles ()
 
List< ManualParticle > getAvailableParticles (double threshold)
 
ManualParticle getLastAvailableParticle (double threshold)
 
boolean hasData ()
 
List<? extends PickerParticle > getParticleList ()
 
int getAutopickpercent ()
 
void setAutopickpercent (int autopickpercent)
 
void initParticlesRectangle (SupervisedParticlePicker picker)
 
void resetParticlesRectangle ()
 
boolean isValid (SupervisedParticlePicker picker)
 
void deleteBelowThreshold ()
 
Rectangle getRectangle ()
 
- Public Member Functions inherited from xmipp.viewer.particlepicker.Micrograph
void setPosFileFromXmipp24 (String posfile)
 
String getPosFileFromXmipp24 ()
 
 Micrograph (String file)
 
 Micrograph (String file, String name)
 
 Micrograph (String file, CtfInfo ctfInfo)
 
 Micrograph (String file, String name, CtfInfo ctfInfo)
 
String getPSD ()
 
ImagePlus getPSDImage ()
 
Icon getCTFIcon ()
 
String getCTF ()
 
CtfInfo getCtfInfo ()
 
boolean fits (int x, int y, int size)
 
String getPosFile ()
 
void loadDimensions ()
 
ImagePlus getImagePlus ()
 
ImagePlus getImagePlus (List< IJCommand > filters)
 
void runImageJFilters (List< IJCommand > filters)
 
String getFile ()
 
String getName ()
 
String toString ()
 
abstract boolean hasData ()
 
int getWidth ()
 
int getHeigth ()
 
void releaseImage ()
 
List<? extends PickerParticle > getParticleList ()
 
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-Static Public Member Functions

static String getName (String file)
 
- Static Public Member Functions inherited from xmipp.viewer.particlepicker.Micrograph
static Icon getNoImageIcon ()
 
static String getName (String file, int level)
 
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-Additional Inherited Members

- Static Public Attributes inherited from xmipp.viewer.particlepicker.Micrograph
static final String ext = ".pos"
 
-

Detailed Description

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Definition at line 13 of file SupervisedPickerMicrograph.java.

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Constructor & Destructor Documentation

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◆ SupervisedPickerMicrograph()

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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.SupervisedPickerMicrograph (String file,
CtfInfo ctfInfo 
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Definition at line 36 of file SupervisedPickerMicrograph.java.

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37  {
38  super(file, ctfInfo);
39 
40  this.manualparticles = new ArrayList<ManualParticle>();
41  this.autoparticles = new ArrayList<AutomaticParticle>();
42  state = MicrographState.Available;
43  }
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Member Function Documentation

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◆ addAutomaticParticle()

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synchronized void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.addAutomaticParticle (AutomaticParticle p)
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Definition at line 185 of file SupervisedPickerMicrograph.java.

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186  {
187  autoparticles.add(p);
188 
189  }
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◆ addManualParticle()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.addManualParticle (ManualParticle p,
SupervisedParticlePicker ppicker 
)
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Definition at line 122 of file SupervisedPickerMicrograph.java.

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123  {
124  manualparticles.add(p);
125 
126  if (state == MicrographState.Available || state == MicrographState.Auto)
127  {
128  if (ppicker.getMode() == Mode.Manual)
129  state = MicrographState.Manual;
130  else if (ppicker.getMode() == Mode.Review)
131  state = MicrographState.Review;
132  else
133  throw new IllegalArgumentException(
134  String.format("Micrograph %s could not update its state to %s and can't keep previous state %s and have particles", getName(), state, MicrographState.Available));
135  }
136 
137 
138  }
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◆ deleteBelowThreshold()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.deleteBelowThreshold ()
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Definition at line 334 of file SupervisedPickerMicrograph.java.

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334  {
335  // TODO Auto-generated method stub
336  for (AutomaticParticle p : autoparticles)
337  if(!p.isDeleted())
338  p.setDeleted(p.getCost() < getThreshold());
339  }
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◆ getAutomaticParticle()

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AutomaticParticle xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getAutomaticParticle (int x,
int y,
double threshold 
)
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Definition at line 76 of file SupervisedPickerMicrograph.java.

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77  {
78  for (AutomaticParticle p : getAutomaticParticles())
79  if (!p.isDeleted() && p.getCost() >= threshold && p.contains(x, y))
80  return p;
81  return null;
82  }
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◆ getAutomaticParticles()

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List<AutomaticParticle> xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getAutomaticParticles ()
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Definition at line 117 of file SupervisedPickerMicrograph.java.

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118  {
119  return autoparticles;
120  }
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◆ getAutomaticParticlesDeleted() [1/2]

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int xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getAutomaticParticlesDeleted ()
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Definition at line 214 of file SupervisedPickerMicrograph.java.

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215  {
216  int count = 0;
217  for (AutomaticParticle p : autoparticles)
218  if (p.isDeleted())
219  count++;
220  return count;
221  }
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◆ getAutomaticParticlesDeleted() [2/2]

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synchronized int xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getAutomaticParticlesDeleted (double threshold)
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Definition at line 225 of file SupervisedPickerMicrograph.java.

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226  {
227  int count = 0;
228  for (AutomaticParticle p : autoparticles)
229  if (p.isDeleted() || p.getCost() < threshold)
230  count++;
231  return count;
232  }
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◆ getAutomaticParticlesNumber() [1/2]

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int xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getAutomaticParticlesNumber (double threshold)
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Definition at line 171 of file SupervisedPickerMicrograph.java.

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172  {
173  if (autoparticles.isEmpty())
174  return 0;
175  return autoparticles.size() - getAutomaticParticlesDeleted(threshold);
176  }
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◆ getAutomaticParticlesNumber() [2/2]

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int xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getAutomaticParticlesNumber ()
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Definition at line 178 of file SupervisedPickerMicrograph.java.

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179  {
180  if (autoparticles.isEmpty())
181  return 0;
182  return autoparticles.size() - getAutomaticParticlesDeleted();
183  }
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◆ getAutopickpercent()

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int xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getAutopickpercent ()
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Definition at line 281 of file SupervisedPickerMicrograph.java.

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282  {
283  return autopickpercent;
284  }
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◆ getAvailableParticles()

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List<ManualParticle> xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getAvailableParticles (double threshold)
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Definition at line 243 of file SupervisedPickerMicrograph.java.

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244  {
245  ArrayList<ManualParticle> result = new ArrayList<ManualParticle>();
246  result.addAll(manualparticles);
247  for (AutomaticParticle ap : autoparticles)
248  if (!ap.isDeleted() && ap.getCost() >= threshold)
249  result.add(ap);
250  return result;
251  }
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◆ getLastAvailableParticle()

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ManualParticle xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getLastAvailableParticle (double threshold)
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Definition at line 253 of file SupervisedPickerMicrograph.java.

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254  {
255  AutomaticParticle ap;
256  for (int i = autoparticles.size() - 1; i >= 0; i--)
257  {
258  ap = autoparticles.get(i);
259  if (!ap.isDeleted() && ap.getCost() >= threshold)
260  return ap;
261  }
262  if (!manualparticles.isEmpty())
263  return manualparticles.get(manualparticles.size() - 1);
264  return null;
265 
266  }
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◆ getManualParticles()

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List<ManualParticle> xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getManualParticles ()
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Definition at line 112 of file SupervisedPickerMicrograph.java.

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113  {
114  return manualparticles;
115  }
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◆ getName()

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static String xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getName (String file)
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Definition at line 58 of file SupervisedPickerMicrograph.java.

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59  {
60  String[] tokens = file.split(File.separator);
61  if (tokens.length < 2)
62  throw new IllegalArgumentException("Name for micrograph" + "is taken from parent dir, invalid path " + file);
63  return tokens[tokens.length - 2];
64  }
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◆ getParticle()

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ManualParticle xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getParticle (int x,
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Definition at line 68 of file SupervisedPickerMicrograph.java.

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69  {
70  for (ManualParticle p : getManualParticles())
71  if (p.contains(x, y))
72  return p;
73  return null;
74  }
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◆ getParticleList()

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List<? extends PickerParticle> xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getParticleList ()
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Definition at line 277 of file SupervisedPickerMicrograph.java.

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277  {
278  return getParticles();
279  }
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◆ getParticles()

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List<ManualParticle> xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getParticles ()
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Definition at line 235 of file SupervisedPickerMicrograph.java.

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236  {
237  ArrayList<ManualParticle> result = new ArrayList<ManualParticle>();
238  result.addAll(manualparticles);
239  result.addAll(autoparticles);
240  return result;
241  }
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◆ getRectangle()

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Rectangle xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getRectangle ()
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Definition at line 341 of file SupervisedPickerMicrograph.java.

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341  {
342  return rectangle;
343  }
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◆ getState()

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MicrographState xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getState ()
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Definition at line 193 of file SupervisedPickerMicrograph.java.

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194  {
195  return state;
196  }
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◆ getStep()

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Mode xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getStep ()
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Definition at line 205 of file SupervisedPickerMicrograph.java.

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206  {
207  if (state == MicrographState.Manual)
208  return Mode.Manual;
209  if (state == MicrographState.Available)
210  return Mode.Available;
211  return Mode.Supervised;
212  }
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◆ getThreshold()

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double xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.getThreshold ()
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Definition at line 24 of file SupervisedPickerMicrograph.java.

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24  {
25  return threshold;
26  }
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◆ hasAutomaticParticles()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.hasAutomaticParticles ()
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Definition at line 161 of file SupervisedPickerMicrograph.java.

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162  {
163  return autoparticles.size() != 0;
164  }
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◆ hasData()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.hasData ()
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Definition at line 271 of file SupervisedPickerMicrograph.java.

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272  {
273  return !isEmpty();
274  }
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◆ hasManualParticles()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.hasManualParticles ()
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Definition at line 85 of file SupervisedPickerMicrograph.java.

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86  {
87  if (getManualParticles().size() > 0)
88  return true;
89  return false;
90 
91  }
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◆ initParticlesRectangle()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.initParticlesRectangle (SupervisedParticlePicker picker)
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Definition at line 291 of file SupervisedPickerMicrograph.java.

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292  {
293  double x1 = Double.POSITIVE_INFINITY, y1 = Double.POSITIVE_INFINITY, x2 = Double.NEGATIVE_INFINITY, y2 = Double.NEGATIVE_INFINITY;
294  List<ManualParticle> particles = getParticles();
295  if(particles.isEmpty())
296  return;
297  for(Particle p: getParticles())
298  {
299  if(p.getX() < x1)
300  x1 = p.getX();
301  if(p.getY() < y1)
302  y1 = p.getY();
303  if(p.getX() > x2)
304  x2 = p.getX();
305  if(p.getY() > y2)
306  y2 = p.getY();
307  }
308 
309  int radius = picker.getRadius();
310  radius = radius + radius/5;
311  int x = Math.max(0, (int)(x1 - radius));
312  int y = Math.max(0, (int)(y1 - radius));
313  int width = Math.min((int)(x2 - x + radius), this.getWidth() - 1);
314  int height = Math.min((int)(y2 - y + radius), this.getHeigth() - 1);
315  rectangle = new Rectangle(x, y, width, height);
316  return;
317 
318  }
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◆ isAutopicking()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.isAutopicking ()
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Definition at line 48 of file SupervisedPickerMicrograph.java.

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49  {
50  return autopicking;
51  }
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◆ isEmpty()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.isEmpty ()
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Definition at line 166 of file SupervisedPickerMicrograph.java.

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167  {
168  return manualparticles.isEmpty() && autoparticles.isEmpty();
169  }
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◆ isValid()

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boolean xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.isValid (SupervisedParticlePicker picker)
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Definition at line 325 of file SupervisedPickerMicrograph.java.

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326  {
327  int count = getParticles().size();
328  if(count <= 3)
329  return false;
330  return true;
331 
332  }
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◆ removeParticle()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.removeParticle (PickerParticle p,
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Definition at line 140 of file SupervisedPickerMicrograph.java.

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141  {
142  if (p == null)
143  throw new IllegalArgumentException(XmippMessage.getEmptyFieldMsg("particle"));
144  if (p instanceof AutomaticParticle)
145  {
146  if (ppicker.getMode() != Mode.Review)
147  ((AutomaticParticle) p).setDeleted(true);
148  else
149  autoparticles.remove(p);
150  // deleting could be the first thing to do after autopick, so I have
151  // to mark micrograph on this choice too
152  if (state == MicrographState.Auto && ppicker.getMode() == Mode.Review)
153  state = MicrographState.Review;
154  }
155  else
156  manualparticles.remove(p);
157 
158 
159  }
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◆ removeParticles()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.removeParticles (int x,
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Definition at line 93 of file SupervisedPickerMicrograph.java.

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94  {
95  List<ManualParticle> particles = new ArrayList<ManualParticle>();
96 
97  for (ManualParticle p : getManualParticles())
98  if (p.contains(x, y))
99  particles.add(p);
100  for (ManualParticle p : particles)
101  removeParticle(p, ppicker);
102  particles.clear();
103  for (AutomaticParticle p : getAutomaticParticles())
104  if (p.contains(x, y))
105  particles.add(p);
106 
107  for (ManualParticle p : particles)
108  removeParticle(p, ppicker);
109 
110  }
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xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.removeParticle
void removeParticle(PickerParticle p, SupervisedParticlePicker ppicker)
Definition: SupervisedPickerMicrograph.java:140
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◆ resetParticlesRectangle()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.resetParticlesRectangle ()
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Definition at line 320 of file SupervisedPickerMicrograph.java.

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321  {
322  rectangle = null;
323  }
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◆ setAutopicking()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.setAutopicking (boolean autopicking)
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Definition at line 53 of file SupervisedPickerMicrograph.java.

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54  {
55  this.autopicking = autopicking;
56  }
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◆ setAutopickpercent()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.setAutopickpercent (int autopickpercent)
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Definition at line 286 of file SupervisedPickerMicrograph.java.

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287  {
288  this.autopickpercent = autopickpercent;
289  }
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◆ setState()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.setState (MicrographState state)
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Definition at line 198 of file SupervisedPickerMicrograph.java.

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199  {
200  if (state == MicrographState.Available && !(manualparticles.isEmpty() || autoparticles.isEmpty()))
201  throw new IllegalArgumentException("Micrograph has data. Can not be " + MicrographState.Available);
202  this.state = state;
203  }
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◆ setThreshold()

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void xmipp.viewer.particlepicker.training.model.SupervisedPickerMicrograph.setThreshold (double threshold)
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Definition at line 30 of file SupervisedPickerMicrograph.java.

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30  {
31  this.threshold = threshold;
32  }
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The documentation for this class was generated from the following file: -
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xmipp.viewer.scipion.ScipionGalleryData Member List
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This is the complete list of members for xmipp.viewer.scipion.ScipionGalleryData, including all inherited members.

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addClass(ClassInfo ci)xmipp.viewer.scipion.ScipionGalleryDatainline
addObject()xmipp.viewer.models.GalleryDatainline
allowGallery()xmipp.viewer.models.GalleryDatainline
allowsVolumeMode()xmipp.viewer.models.GalleryDatainline
changeMode()xmipp.viewer.models.GalleryDatainline
checkifIsClassificationMd()xmipp.viewer.scipion.ScipionGalleryDatainline
ciFirstRenderxmipp.viewer.models.GalleryDataprotected
classesxmipp.viewer.models.GalleryDataprotected
classesArrayxmipp.viewer.models.GalleryDataprotected
containsBlock(String block)xmipp.viewer.models.GalleryDatainline
containsGeometryInfo()xmipp.viewer.models.GalleryDatainline
containsGeometryInfo(String type)xmipp.viewer.models.GalleryDatainline
createModel(boolean[] selection)xmipp.viewer.models.GalleryDatainline
createSortFile(String psdFile, int row)xmipp.viewer.scipion.ScipionGalleryDatainline
displaycisxmipp.viewer.models.GalleryDataprotected
displayLabelsxmipp.viewer.models.GalleryDataprotected
filenamexmipp.viewer.models.GalleryDataprotected
fillConstant(int label, String value)xmipp.viewer.models.GalleryDatainline
fillLinear(int label, Double start, Double step)xmipp.viewer.models.GalleryDatainline
fillRandom(int label, String mode, double op1, double op2)xmipp.viewer.models.GalleryDatainline
GalleryData(GalleryJFrame window, String fn, Params parameters)xmipp.viewer.models.GalleryDatainline
GalleryData(GalleryJFrame window, Params parameters, MetaData md)xmipp.viewer.models.GalleryDatainline
getBlock(int index)xmipp.viewer.models.GalleryDatainline
getBlocks()xmipp.viewer.models.GalleryDatainline
getChimeraProjectionCmd(int row)xmipp.viewer.scipion.ScipionGalleryDatainline
getClasses()xmipp.viewer.models.GalleryDatainline
getClassesImages()xmipp.viewer.scipion.ScipionGalleryDatainline
xmipp::viewer::models::GalleryData.getClassesImages(boolean[] selection)xmipp.viewer.models.GalleryDatainline
getClassesMd()xmipp.viewer.scipion.ScipionGalleryDatainline
getClassImages(int index)xmipp.viewer.scipion.ScipionGalleryDatainline
getClassInfo(int classNumber)xmipp.viewer.scipion.ScipionGalleryDatainline
getColumnInfo(String labelName)xmipp.viewer.models.GalleryDatainline
getColumnInfo(int col)xmipp.viewer.models.GalleryDatainline
getColumns()xmipp.viewer.models.GalleryDatainline
getDefaultZoom(int xdim)xmipp.viewer.models.GalleryDatainlinestatic
getDisplayLabel(long id)xmipp.viewer.models.GalleryDatainline
getEMObjects()xmipp.viewer.scipion.ScipionGalleryDatainline
getEnabledClassesImages()xmipp.viewer.models.GalleryDatainline
getEnabledCount()xmipp.viewer.scipion.ScipionGalleryDatainline
getExtraPath()xmipp.viewer.scipion.ScipionGalleryDatainline
getFileExtension()xmipp.viewer.models.GalleryDatainline
getFileInfo()xmipp.viewer.models.GalleryDatainline
getFileName()xmipp.viewer.models.GalleryDatainline
getGeoMatrixColumn(ColumnInfo ci)xmipp.viewer.scipion.ScipionGalleryDatainline
getGeometry(long id, ColumnInfo ci)xmipp.viewer.scipion.ScipionGalleryDatainline
getGeometry(long id, String type, ColumnInfo ci)xmipp.viewer.scipion.ScipionGalleryDatainline
getId(int i)xmipp.viewer.models.GalleryDatainline
getIds()xmipp.viewer.models.GalleryDatainline
getImages(MetaData md)xmipp.viewer.models.GalleryDatainline
getImagesMd(boolean[] selection, boolean selected)xmipp.viewer.scipion.ScipionGalleryDatainline
xmipp::viewer::models::GalleryData.getImagesMd()xmipp.viewer.models.GalleryDatainline
getItemClassInfo(int index)xmipp.viewer.scipion.ScipionGalleryDatainline
getLabel(long objId, int label)xmipp.viewer.scipion.ScipionGalleryDatainline
getLabelFromCol(int col)xmipp.viewer.models.GalleryDatainline
getLabels()xmipp.viewer.models.GalleryDatainline
getLabelsInfo()xmipp.viewer.models.GalleryDatainline
getMd(List< Long > ids)xmipp.viewer.models.GalleryDatainline
getMd()xmipp.viewer.models.GalleryDatainline
getMdFilename()xmipp.viewer.models.GalleryDatainline
getMdSaveFileName()xmipp.viewer.models.GalleryDatainline
getMetaData(String block)xmipp.viewer.scipion.ScipionGalleryDatainline
getMetaDataRow()xmipp.viewer.models.GalleryDatainline
getMode()xmipp.viewer.models.GalleryDatainline
getModelColumns()xmipp.viewer.models.GalleryDatainline
getModelRows()xmipp.viewer.models.GalleryDatainline
getNormalized()xmipp.viewer.models.GalleryDatainline
getNumberOfBlocks()xmipp.viewer.models.GalleryDatainline
getOrderLabels()xmipp.viewer.models.GalleryDatainline
getPreffix()xmipp.viewer.scipion.ScipionGalleryDatainline
getRenderColumn()xmipp.viewer.models.GalleryDatainline
getRenderLabel()xmipp.viewer.models.GalleryDatainline
getRenderLabels()xmipp.viewer.models.GalleryDatainline
getResliceView()xmipp.viewer.models.GalleryDatainline
getSampleImage(ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
getScipionMetaData()xmipp.viewer.scipion.ScipionGalleryDatainline
getSelectedBlock()xmipp.viewer.models.GalleryDatainline
getSelectionMd(boolean[] selection)xmipp.viewer.scipion.ScipionGalleryDatainline
getSelVolId()xmipp.viewer.models.GalleryDatainline
getSelVolumeFile()xmipp.viewer.models.GalleryDatainline
getSortBy()xmipp.viewer.models.GalleryDatainline
getTmpFile(String suffix)xmipp.viewer.models.GalleryDatainline
getValueFromCol(int index, ColumnInfo ci)xmipp.viewer.scipion.ScipionGalleryDatainline
xmipp::viewer::models::GalleryData.getValueFromCol(int index, int col)xmipp.viewer.models.GalleryDatainline
getValueFromLabel(int index, int label)xmipp.viewer.scipion.ScipionGalleryDatainline
getValueString(int label, long id)xmipp.viewer.models.GalleryDatainline
getVisibleColumnIndex(int col)xmipp.viewer.models.GalleryDatainline
getVisibleLabels()xmipp.viewer.models.GalleryDatainline
getVolumeAt(int index)xmipp.viewer.models.GalleryDatainline
getZoom()xmipp.viewer.models.GalleryDatainline
hasClasses()xmipp.viewer.scipion.ScipionGalleryDatainline
hasClassesChanges()xmipp.viewer.models.GalleryDatainline
hasDisabled()xmipp.viewer.models.GalleryDatainline
hasMdChanges()xmipp.viewer.scipion.ScipionGalleryDatainline
xmipp::viewer::models::GalleryData.hasMdChangesxmipp.viewer.models.GalleryDataprotected
hasMicrographParticles()xmipp.viewer.scipion.ScipionGalleryDatainline
hasRecalculateCTF()xmipp.viewer.models.GalleryDatainline
hasRenderLabel()xmipp.viewer.models.GalleryDatainline
idsxmipp.viewer.models.GalleryDataprotected
initColumnInfo(int label)xmipp.viewer.scipion.ScipionGalleryDatainline
invertyxmipp.viewer.models.GalleryDataprotected
isAutoAdjust()xmipp.viewer.models.GalleryDatainline
isChimeraClient()xmipp.viewer.models.GalleryDatainline
isClassificationxmipp.viewer.models.GalleryDataprotected
isClassificationMd()xmipp.viewer.models.GalleryDatainline
isColumnFormat()xmipp.viewer.models.GalleryDatainline
isCTFMd()xmipp.viewer.models.GalleryDatainline
isDisplayLabel()xmipp.viewer.models.GalleryDatainline
isEnabled(int index)xmipp.viewer.scipion.ScipionGalleryDatainline
isFile(ColumnInfo ci)xmipp.viewer.scipion.ScipionGalleryDatainline
xmipp::viewer::models::GalleryData.isFile(int col)xmipp.viewer.models.GalleryDatainline
isGalleryMode()xmipp.viewer.models.GalleryDatainline
isImageFile(ColumnInfo ci)xmipp.viewer.scipion.ScipionGalleryDatainline
xmipp::viewer::models::GalleryData.isImageFile(int col)xmipp.viewer.models.GalleryDatainline
isInvertY()xmipp.viewer.models.GalleryDatainline
isMicrographsMode()xmipp.viewer.models.GalleryDatainline
isObjectCmd(String cmd)xmipp.viewer.models.GalleryDatainline
isRecalculateCTF(int row)xmipp.viewer.models.GalleryDatainline
isRenderLabel(ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
isScipionInstance()xmipp.viewer.models.GalleryDatainline
isTableMode()xmipp.viewer.models.GalleryDatainline
isVisibleLabel(ColumnInfo ci)xmipp.viewer.models.GalleryDatainline
isVolumeMdxmipp.viewer.models.GalleryDataprotected
isVolumeMd()xmipp.viewer.models.GalleryDatainline
isVolumeMode()xmipp.viewer.models.GalleryDatainline
isWrap()xmipp.viewer.models.GalleryDatainline
labelsxmipp.viewer.models.GalleryDataprotected
loadClassesInfo()xmipp.viewer.scipion.ScipionGalleryDatainline
loadLabels()xmipp.viewer.models.GalleryDatainline
loadMd()xmipp.viewer.models.GalleryDatainline
loadSelection(String selectedPath)xmipp.viewer.scipion.ScipionGalleryDatainline
MAX_SIZExmipp.viewer.models.GalleryDatastatic
mdxmipp.viewer.models.GalleryDataprotected
mdBlocksxmipp.viewer.models.GalleryDataprotected
MIN_SIZExmipp.viewer.models.GalleryDatastatic
modexmipp.viewer.models.GalleryDataprotected
normalizexmipp.viewer.models.GalleryDataprotected
orderLabelsxmipp.viewer.models.GalleryDataprotected
orderLabels()xmipp.viewer.models.GalleryDatainline
overwrite(String path, boolean[] selection)xmipp.viewer.scipion.ScipionGalleryDatainline
parametersxmipp.viewer.models.GalleryData
readMd()xmipp.viewer.scipion.ScipionGalleryDatainline
readMdParameters()xmipp.viewer.models.GalleryDatainlineprotected
recalculateCTF(int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)xmipp.viewer.scipion.ScipionGalleryDatainline
refLabelxmipp.viewer.models.GalleryDataprotected
removeClass(int classNumber)xmipp.viewer.scipion.ScipionGalleryDatainline
removeCTF(int row)xmipp.viewer.scipion.ScipionGalleryDatainline
removeDisabled()xmipp.viewer.models.GalleryDatainline
removeLabel(int label)xmipp.viewer.models.GalleryDatainline
removeSelection(boolean[] selection)xmipp.viewer.models.GalleryDatainline
renderImagesxmipp.viewer.models.GalleryDataprotected
renderImages()xmipp.viewer.models.GalleryDatainline
renderLabelxmipp.viewer.models.GalleryDataprotected
renderLabelsxmipp.viewer.models.GalleryDataprotected
resliceViewxmipp.viewer.models.GalleryDataprotected
rowsxmipp.viewer.models.GalleryDataprotected
runObjectCommand(int index, String objectCommand)xmipp.viewer.scipion.ScipionGalleryDatainline
saveAll(String path, boolean overwrite)xmipp.viewer.models.GalleryDatainline
saveClassSelection(boolean[]selection, String path)xmipp.viewer.models.GalleryDatainline
saveMd(String path, boolean saveall, boolean isoverwrite)xmipp.viewer.models.GalleryDatainline
saveSelection(boolean[] selection)xmipp.viewer.models.GalleryDatainline
saveSelection(boolean[] selection, String path, boolean overwrite)xmipp.viewer.models.GalleryDatainline
ScipionGalleryData(ScipionGalleryJFrame window, String fn, Params parameters)xmipp.viewer.scipion.ScipionGalleryDatainline
ScipionGalleryData(ScipionGalleryJFrame window, Params parameters, ScipionMetaData md)xmipp.viewer.scipion.ScipionGalleryDatainline
selectBlock(String block)xmipp.viewer.models.GalleryDatainline
selectedBlockxmipp.viewer.models.GalleryDataprotected
selectedVolFnxmipp.viewer.models.GalleryDataprotected
selectVolumeAt(int selectedIndex)xmipp.viewer.models.GalleryDatainline
setDisplayLabel(String key, boolean selected)xmipp.viewer.models.GalleryDatainline
setEnabled(int index, boolean isenabled)xmipp.viewer.scipion.ScipionGalleryDatainline
setFileName(String file)xmipp.viewer.scipion.ScipionGalleryDatainline
setItemClass(int index, ClassInfo cli)xmipp.viewer.scipion.ScipionGalleryDatainline
setMdChanges(boolean value)xmipp.viewer.models.GalleryDatainline
setModelDim(Integer rows, Integer cols)xmipp.viewer.models.GalleryDatainline
setOrderLabels(String[] orderLabels)xmipp.viewer.models.GalleryDatainline
setRenderColumn(String key)xmipp.viewer.models.GalleryDatainline
setRenderLabel(String renderLabel)xmipp.viewer.models.GalleryDatainline
setRenderLabels(String[] renderLabels)xmipp.viewer.models.GalleryDatainline
setResliceView(int view)xmipp.viewer.models.GalleryDatainline
setRow(MDRow mdRow, long objId)xmipp.viewer.models.GalleryDatainline
setValueString(int label, String newValue, long l)xmipp.viewer.models.GalleryDatainline
setValueToCol(int index, ColumnInfo ci, String value)xmipp.viewer.scipion.ScipionGalleryDatainline
setVisibleLabels(String[] visibleLabels)xmipp.viewer.models.GalleryDatainline
setWindow(GalleryJFrame frame)xmipp.viewer.models.GalleryDatainline
setZoom(int zoom)xmipp.viewer.models.GalleryDatainline
showCTF(boolean profile, int row, boolean[] selection, TasksEngine ctfTasks)xmipp.viewer.models.GalleryDatainline
showLabelxmipp.viewer.models.GalleryDataprotected
size()xmipp.viewer.models.GalleryDatainline
sortbyxmipp.viewer.models.GalleryDataprotected
sortMd(ColumnInfo sortci, boolean asc)xmipp.viewer.models.GalleryDatainline
updateClassesInfo()xmipp.viewer.scipion.ScipionGalleryDatainline
useGeoxmipp.viewer.models.GalleryDataprotected
useGeo()xmipp.viewer.models.GalleryDatainline
visibleLabelsxmipp.viewer.models.GalleryDataprotected
windowxmipp.viewer.models.GalleryDataprotected
wrapxmipp.viewer.models.GalleryDataprotected
write(String path)xmipp.viewer.models.GalleryDatainline
zoomxmipp.viewer.models.GalleryDataprotected
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- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData.html b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData.html deleted file mode 100644 index 9a31950d..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData.html +++ /dev/null @@ -1,2104 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.scipion.ScipionGalleryData Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -List of all members
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xmipp.viewer.scipion.ScipionGalleryData Class Reference
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-Inheritance diagram for xmipp.viewer.scipion.ScipionGalleryData:
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-Collaboration diagram for xmipp.viewer.scipion.ScipionGalleryData:
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-Public Member Functions

 ScipionGalleryData (ScipionGalleryJFrame window, String fn, Params parameters)
 
 ScipionGalleryData (ScipionGalleryJFrame window, Params parameters, ScipionMetaData md)
 
void setFileName (String file)
 
ColumnInfo initColumnInfo (int label)
 
String getValueFromLabel (int index, int label)
 
ScipionMetaData getSelectionMd (boolean[] selection)
 
MetaData getClassesImages ()
 
MetaData getClassImages (int index)
 
String getLabel (long objId, int label)
 
void readMd ()
 
MetaData getMetaData (String block)
 
ScipionMetaData getScipionMetaData ()
 
ClassInfo getItemClassInfo (int index)
 
void setItemClass (int index, ClassInfo cli)
 
ClassInfo getClassInfo (int classNumber)
 
void updateClassesInfo ()
 
void loadClassesInfo ()
 
MetaData [] getClassesMd ()
 
void addClass (ClassInfo ci)
 
void removeClass (int classNumber)
 
boolean hasClasses ()
 
boolean hasMicrographParticles ()
 
List< ScipionMetaData.EMObject > getEMObjects ()
 
boolean isFile (ColumnInfo ci)
 
boolean isImageFile (ColumnInfo ci)
 
void overwrite (String path, boolean[] selection) throws SQLException
 
String getPreffix ()
 
void removeCTF (int row)
 
String createSortFile (String psdFile, int row)
 
void recalculateCTF (int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)
 
ColumnInfo getGeoMatrixColumn (ColumnInfo ci)
 
Geometry getGeometry (long id, ColumnInfo ci)
 
Geometry getGeometry (long id, String type, ColumnInfo ci)
 
int getEnabledCount ()
 
void setEnabled (int index, boolean isenabled)
 
boolean hasMdChanges ()
 
boolean isEnabled (int index)
 
String getValueFromCol (int index, ColumnInfo ci)
 
void setValueToCol (int index, ColumnInfo ci, String value)
 
void loadSelection (String selectedPath)
 
String getExtraPath ()
 
boolean checkifIsClassificationMd ()
 
void runObjectCommand (int index, String objectCommand)
 
MetaData getImagesMd (boolean[] selection, boolean selected)
 
String getChimeraProjectionCmd (int row)
 
- Public Member Functions inherited from xmipp.viewer.models.GalleryData
boolean isObjectCmd (String cmd)
 
boolean isVolumeMd ()
 
Integer getModelRows ()
 
Integer getModelColumns ()
 
void runObjectCommand (int index, String objectCommand)
 
String getTmpFile (String suffix)
 
void selectVolumeAt (int selectedIndex)
 
boolean isAutoAdjust ()
 
void setModelDim (Integer rows, Integer cols)
 
boolean isScipionInstance ()
 
boolean isInvertY ()
 
String getChimeraProjectionCmd (int row)
 
 GalleryData (GalleryJFrame window, String fn, Params parameters)
 
 GalleryData (GalleryJFrame window, Params parameters, MetaData md)
 
List< ColumnInfo > getColumns ()
 
void setRenderColumn (String key)
 
ColumnInfo getRenderColumn ()
 
String getMdFilename ()
 
String getMdSaveFileName ()
 
void setFileName (String file)
 
void setDisplayLabel (String key, boolean selected)
 
void loadMd () throws Exception
 
ColumnInfo getColumnInfo (String labelName)
 
boolean isDisplayLabel ()
 
String getDisplayLabel (long id)
 
void loadLabels ()
 
String getSampleImage (ColumnInfo ci)
 
ColumnInfo initColumnInfo (int label)
 
void sortMd (ColumnInfo sortci, boolean asc)
 
void readMd ()
 
void selectBlock (String block)
 
ImageGalleryTableModel createModel (boolean[] selection)
 
int getNumberOfBlocks ()
 
Mode getMode ()
 
boolean hasRenderLabel ()
 
int getRenderLabel ()
 
boolean allowGallery ()
 
boolean isGalleryMode ()
 
boolean isVolumeMode ()
 
boolean isTableMode ()
 
boolean isColumnFormat ()
 
boolean isMicrographsMode ()
 
void changeMode ()
 
String getVolumeAt (int index)
 
boolean containsGeometryInfo ()
 
boolean containsGeometryInfo (String type)
 
boolean isEnabled (int index)
 
void setEnabled (int index, boolean value)
 
void setRow (MDRow mdRow, long objId)
 
boolean isFile (ColumnInfo ci)
 
boolean isFile (int col)
 
boolean isImageFile (int col)
 
boolean isImageFile (ColumnInfo ci)
 
boolean isClassificationMd ()
 
boolean checkifIsClassificationMd ()
 
ClassInfo getItemClassInfo (int index)
 
void setItemClass (int index, ClassInfo cli)
 
ClassInfo getClassInfo (int classNumber)
 
void updateClassesInfo ()
 
void loadClassesInfo ()
 
MetaData getSelectionMd (boolean[] selection)
 
MetaData [] getClassesMd ()
 
MetaData getClassImages (int index)
 
MetaData getClassesImages (boolean[] selection)
 
MetaData getEnabledClassesImages ()
 
boolean containsBlock (String block)
 
int getVisibleColumnIndex (int col)
 
int getLabelFromCol (int col)
 
ColumnInfo getColumnInfo (int col)
 
String getValueFromCol (int index, int col)
 
String getValueFromCol (int index, ColumnInfo ci)
 
String getValueFromLabel (int index, int label)
 
void setValueToCol (int index, ColumnInfo ci, String value)
 
void removeSelection (boolean[] selection) throws Exception
 
void addClass (ClassInfo ci)
 
void removeClass (int classNumber)
 
boolean hasMdChanges ()
 
void setMdChanges (boolean value)
 
boolean hasClassesChanges ()
 
boolean hasMicrographParticles ()
 
String getFileName ()
 
String getBlock (int index)
 
MDRow [] getImages (MetaData md)
 
String getFileInfo ()
 
void saveClassSelection (boolean[]selection, String path)
 
boolean isCTFMd ()
 
void saveSelection (boolean[] selection) throws Exception
 
void saveSelection (boolean[] selection, String path, boolean overwrite) throws Exception
 
int size ()
 
Integer getZoom ()
 
boolean useGeo ()
 
void fillConstant (int label, String value)
 
void fillLinear (int label, Double start, Double step)
 
void fillRandom (int label, String mode, double op1, double op2)
 
void removeDisabled ()
 
void removeLabel (int label)
 
long [] getIds ()
 
int [] getLabels ()
 
String getValueString (int label, long id)
 
boolean setValueString (int label, String newValue, long l)
 
Object getSelectedBlock ()
 
String getSelVolumeFile ()
 
void setResliceView (int view)
 
boolean isWrap ()
 
boolean renderImages ()
 
int getResliceView ()
 
boolean addObject ()
 
String [] getBlocks ()
 
long getId (int i)
 
String createSortFile (String psdFile, int row)
 
ArrayList< ClassInfo > getClasses ()
 
List< ColumnInfo > getLabelsInfo ()
 
MetaData getMetaDataRow ()
 
String getLabel (long objId, int label)
 
String getFileExtension ()
 
void saveAll (String path, boolean overwrite) throws Exception
 
void saveMd (String path, boolean saveall, boolean isoverwrite) throws Exception
 
MetaData getMetaData (String block)
 
boolean hasClasses ()
 
boolean getNormalized ()
 
MetaData getMd (List< Long > ids)
 
void setWindow (GalleryJFrame frame)
 
void write (String path)
 
MetaData getMd ()
 
boolean isRenderLabel (ColumnInfo ci)
 
boolean isVisibleLabel (ColumnInfo ci)
 
void orderLabels ()
 
void removeCTF (int row)
 
boolean isRecalculateCTF (int row)
 
boolean hasRecalculateCTF ()
 
void recalculateCTF (int row, boolean[] selection, EllipseCTF ellipseCTF, String sortFn)
 
void showCTF (boolean profile, int row, boolean[] selection, TasksEngine ctfTasks)
 
Geometry getGeometry (long id, ColumnInfo ci)
 
Geometry getGeometry (long id, String type, ColumnInfo ci)
 
void setRenderLabels (String[] renderLabels)
 
void setVisibleLabels (String[] visibleLabels)
 
void setOrderLabels (String[] orderLabels)
 
void setRenderLabel (String renderLabel)
 
String [] getRenderLabels ()
 
String [] getVisibleLabels ()
 
String [] getOrderLabels ()
 
Long getSelVolId ()
 
MetaData getImagesMd ()
 
MetaData getImagesMd (boolean[] selection, boolean selected)
 
String [] getSortBy ()
 
boolean isChimeraClient ()
 
boolean hasDisabled ()
 
int getEnabledCount ()
 
String getPreffix ()
 
void setZoom (int zoom)
 
boolean allowsVolumeMode ()
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.viewer.models.GalleryData
static int getDefaultZoom (int xdim)
 
- Public Attributes inherited from xmipp.viewer.models.GalleryData
final Params parameters
 
- Static Public Attributes inherited from xmipp.viewer.models.GalleryData
static int MIN_SIZE = 16
 
static int MAX_SIZE = 256
 
- Protected Member Functions inherited from xmipp.viewer.models.GalleryData
void readMdParameters ()
 
- Protected Attributes inherited from xmipp.viewer.models.GalleryData
HashMap< String, ColumnInfo > displaycis
 
MetaData md
 
long [] ids
 
String [] mdBlocks = null
 
String selectedBlock
 
String selectedVolFn = ""
 
List< ColumnInfo > labels = null
 
ColumnInfo ciFirstRender = null
 
Integer zoom
 
String filename
 
int resliceView
 
Mode mode
 
boolean showLabel = false
 
boolean renderImages
 
boolean normalize = false
 
boolean useGeo
 
boolean wrap
 
boolean isClassification = false
 
int refLabel
 
ArrayList< ClassInfo > classesArray
 
ClassInfo [] classes
 
boolean hasMdChanges
 
GalleryJFrame window
 
String [] displayLabels
 
String [] sortby
 
boolean isVolumeMd
 
Integer rows
 
String [] renderLabels
 
String renderLabel = "first"
 
String [] visibleLabels
 
String [] orderLabels
 
boolean inverty
 
-

Detailed Description

-
Author
airen
- -

Definition at line 33 of file ScipionGalleryData.java.

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Constructor & Destructor Documentation

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◆ ScipionGalleryData() [1/2]

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xmipp.viewer.scipion.ScipionGalleryData.ScipionGalleryData (ScipionGalleryJFrame window,
String fn,
Params parameters 
)
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Definition at line 35 of file ScipionGalleryData.java.

-
35  {
36  this(window, parameters, new ScipionMetaData(fn));
37  }
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◆ ScipionGalleryData() [2/2]

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xmipp.viewer.scipion.ScipionGalleryData.ScipionGalleryData (ScipionGalleryJFrame window,
Params parameters,
ScipionMetaData md 
)
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Definition at line 39 of file ScipionGalleryData.java.

-
39  {
40  super(window, parameters, md);
41  }
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Member Function Documentation

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◆ addClass()

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void xmipp.viewer.scipion.ScipionGalleryData.addClass (ClassInfo ci)
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-

Add a new class

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Definition at line 188 of file ScipionGalleryData.java.

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188  {
189 
190  }
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◆ checkifIsClassificationMd()

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boolean xmipp.viewer.scipion.ScipionGalleryData.checkifIsClassificationMd ()
- 		-inline
-
-

Return true if current metadata comes from 2d classification

- -

Definition at line 368 of file ScipionGalleryData.java.

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368  {
369  return ((ScipionMetaData)md).isClassificationMd();
370  }
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◆ createSortFile()

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String xmipp.viewer.scipion.ScipionGalleryData.createSortFile (String psdFile,
int row 
)
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Definition at line 243 of file ScipionGalleryData.java.

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243  {
244  return null;
245  }
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◆ getChimeraProjectionCmd()

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String xmipp.viewer.scipion.ScipionGalleryData.getChimeraProjectionCmd (int row)
- 		-inline
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Definition at line 416 of file ScipionGalleryData.java.

-
416  {
417  int label = getRenderLabel();
418  ColumnInfo ci = getColumnInfo(label);
419  Geometry geo = getGeometry(ids[row], "3D", ci);
420  if(geo == null)
421  geo = getGeometry(ids[row], "Projection", ci);
422  String command = String.format("rotate_matrix '%s'", geo.getMatrix());
423  return command;
424  }
- -
xmipp.viewer.models.GalleryData.getColumnInfo
ColumnInfo getColumnInfo(String labelName)
Definition: GalleryData.java:477
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xmipp.viewer.scipion.ScipionGalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: ScipionGalleryData.java:273
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◆ getClassesImages()

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MetaData xmipp.viewer.scipion.ScipionGalleryData.getClassesImages ()
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-
-

Get all the images assigned to all selected classes

- -

Definition at line 80 of file ScipionGalleryData.java.

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80  {
81  return null;
82  }
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◆ getClassesMd()

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MetaData [] xmipp.viewer.scipion.ScipionGalleryData.getClassesMd ()
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-
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Definition at line 181 of file ScipionGalleryData.java.

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181  {
182  return null;
183  }
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◆ getClassImages()

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MetaData xmipp.viewer.scipion.ScipionGalleryData.getClassImages (int index)
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-
-

Get the metadata with assigned images to this classes

- -

Definition at line 89 of file ScipionGalleryData.java.

-
89  {
90  try {
91  long id = ids[index];
92  ScipionMetaData childmd = ((ScipionMetaData) md).getEMObject(id).childmd;
93  return childmd;
94  } catch (Exception e) {
95  e.printStackTrace();
96  }
97  return null;
98  }
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◆ getClassInfo()

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ClassInfo xmipp.viewer.scipion.ScipionGalleryData.getClassInfo (int classNumber)
- 		-inline
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Definition at line 162 of file ScipionGalleryData.java.

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162  {
163  return null;
164  }
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◆ getEMObjects()

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List<ScipionMetaData.EMObject> xmipp.viewer.scipion.ScipionGalleryData.getEMObjects ()
- 		-inline
-
- -

Definition at line 208 of file ScipionGalleryData.java.

-
208  {
209  return ((ScipionMetaData)md).getEMObjects();
210  }
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◆ getEnabledCount()

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int xmipp.viewer.scipion.ScipionGalleryData.getEnabledCount ()
- 		-inline
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Definition at line 289 of file ScipionGalleryData.java.

-
289  {
290  return ((ScipionMetaData)md).getEnabledCount();
291  }
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◆ getExtraPath()

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String xmipp.viewer.scipion.ScipionGalleryData.getExtraPath ()
- 		-inline
-
- -

Definition at line 355 of file ScipionGalleryData.java.

-
356  {
357  if(filename == null)
358  return null;
359  String dir = new File(filename).getParent();
360  if(dir == null)
361  return null;
362  return Filename.join(dir, "extra");
363  }
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◆ getGeoMatrixColumn()

- -
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ColumnInfo xmipp.viewer.scipion.ScipionGalleryData.getGeoMatrixColumn (ColumnInfo ci)
- 		-inline
-
- -

Definition at line 268 of file ScipionGalleryData.java.

-
269  {
270  return ((ScipionMetaData)md).getGeoMatrixColumn(ci);
271  }
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◆ getGeometry() [1/2]

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Geometry xmipp.viewer.scipion.ScipionGalleryData.getGeometry (long id,
ColumnInfo ci 
)
- 		-inline
-
- -

Definition at line 273 of file ScipionGalleryData.java.

-
274  {
275  return getGeometry(id, "2D", ci);
276  }
xmipp.viewer.scipion.ScipionGalleryData.getGeometry
Geometry getGeometry(long id, ColumnInfo ci)
Definition: ScipionGalleryData.java:273
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◆ getGeometry() [2/2]

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Geometry xmipp.viewer.scipion.ScipionGalleryData.getGeometry (long id,
String type,
ColumnInfo ci 
)
- 		-inline
-
- -

Definition at line 278 of file ScipionGalleryData.java.

-
279  {
280  if (!containsGeometryInfo(type))
281  return null;
282  ScipionMetaData.EMObject emo = ((ScipionMetaData)md).getEMObject(id);
283  ColumnInfo column = getGeoMatrixColumn(ci);
284 
285  String matrix = (String)emo.getValue(column);
286  return new Geometry(matrix);
287  }
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◆ getImagesMd()

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MetaData xmipp.viewer.scipion.ScipionGalleryData.getImagesMd (boolean [] selection,
boolean selected 
)
- 		-inline
-
- -

Definition at line 386 of file ScipionGalleryData.java.

-
386  {
387 
388  MetaData imagesmd = new MetaData();
389  int index = 0;
390  String imagepath;
391  EMObject emo;
392  long imageid;
393  String matrix;
394 
395  for (long id : md.findObjects()) {
396  if (isEnabled(index) && (!selected ||selection[index])) {
397 
398  imagepath = md.getValueString(getRenderLabel(), id, true);
399  if (imagepath != null && ImageGeneric.exists(imagepath)) {
400  imageid = imagesmd.addObject();
401  imagesmd.setValueString(MDLabel.MDL_IMAGE, imagepath, imageid);
402  if (useGeo())
403  {
404  emo = ((ScipionMetaData)md).getEMObject(id);
405  matrix = String.format("'%s'", emo.getValueString(getGeoMatrixColumn(ciFirstRender)));
406  imagesmd.setValueString(MDLabel.MDL_TRANSFORM_MATRIX, matrix, imageid);//copy geo info in mdRow
407  }
408 
409  }
410  }
411  index++;
412  }
413  return imagesmd;
414  }
- - - -
xmipp.jni.MetaData.findObjects
native long [] findObjects()
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xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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◆ getItemClassInfo()

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ClassInfo xmipp.viewer.scipion.ScipionGalleryData.getItemClassInfo (int index)
- 		-inline
-
-

Get the assigned class of some element

- -

Definition at line 144 of file ScipionGalleryData.java.

-
144  {
145  return null;
146  }
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◆ getLabel()

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String xmipp.viewer.scipion.ScipionGalleryData.getLabel (long objId,
int label 
)
- 		-inline
-
- -

Definition at line 100 of file ScipionGalleryData.java.

-
100  {
101  try {
102  if (isClassification) {
103  ScipionMetaData.EMObject emo = ((ScipionMetaData) md).getEMObject(objId);
104  return String.format("Class %s (%d images)", emo.getId(), emo.childmd.size());
105  } else {
106  return md.getValueString(label, objId);
107  }
108  } catch (Exception e) {
109  e.printStackTrace();
110  }
111  return null;
112  }
- -
xmipp.jni.MetaData.getValueString
native String getValueString(int label, long objId)
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◆ getMetaData()

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MetaData xmipp.viewer.scipion.ScipionGalleryData.getMetaData (String block)
- 		-inline
-
- -

Definition at line 120 of file ScipionGalleryData.java.

-
120  {
121  if (md.getBlock().equals(block)) {
122  return md;
123  }
124  ScipionMetaData child = ((ScipionMetaData) md).getChild(block);
125  if (child != null) {
126  return child;
127  }
128  ScipionMetaData parent = ((ScipionMetaData) md).getParent();
129  if (parent.getBlock().equals(selectedBlock))// from child to parent
130  {
131  return parent;
132  }
133  return parent.getChild(selectedBlock);
134 
135  }
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◆ getPreffix()

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String xmipp.viewer.scipion.ScipionGalleryData.getPreffix ()
- 		-inline
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Definition at line 230 of file ScipionGalleryData.java.

-
230  {
231  return ((ScipionMetaData) md).getPreffix();
232  }
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◆ getScipionMetaData()

- -
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ScipionMetaData xmipp.viewer.scipion.ScipionGalleryData.getScipionMetaData ()
- 		-inline
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Definition at line 137 of file ScipionGalleryData.java.

-
137  {
138  return (ScipionMetaData) md;
139  }
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◆ getSelectionMd()

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ScipionMetaData xmipp.viewer.scipion.ScipionGalleryData.getSelectionMd (boolean [] selection)
- 		-inline
-
-

Create a metadata just with selected items

- -

Definition at line 73 of file ScipionGalleryData.java.

-
73  {
74  return null;//metadata operations are not used in scipion
75  }
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◆ getValueFromCol()

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String xmipp.viewer.scipion.ScipionGalleryData.getValueFromCol (int index,
ColumnInfo ci 
)
- 		-inline
-
- -

Definition at line 330 of file ScipionGalleryData.java.

-
330  {
331  try {
332  return getEMObjects().get(index).getValueString(ci);
333  } catch (Exception e) {
334  e.printStackTrace();
335  }
336  return null;
337  }
xmipp.viewer.scipion.ScipionGalleryData.getEMObjects
List< ScipionMetaData.EMObject > getEMObjects()
Definition: ScipionGalleryData.java:208
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◆ getValueFromLabel()

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String xmipp.viewer.scipion.ScipionGalleryData.getValueFromLabel (int index,
int label 
)
- 		-inline
-
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Definition at line 62 of file ScipionGalleryData.java.

-
62  {
63  return ((ScipionMetaData) md).getValueFromLabel(index, label);
64  }
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◆ hasClasses()

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boolean xmipp.viewer.scipion.ScipionGalleryData.hasClasses ()
- 		-inline
-
- -

Definition at line 199 of file ScipionGalleryData.java.

-
200  {
201  return mdBlocks.length > 1 && ((ScipionMetaData) md).getSetType().contains("SetOfClasses");
202  }
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◆ hasMdChanges()

- -
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boolean xmipp.viewer.scipion.ScipionGalleryData.hasMdChanges ()
- 		-inline
-
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Definition at line 310 of file ScipionGalleryData.java.

-
311  {
312  return ((ScipionMetaData)md).isChanged();
313  }
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◆ hasMicrographParticles()

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boolean xmipp.viewer.scipion.ScipionGalleryData.hasMicrographParticles ()
- 		-inline
-
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Definition at line 204 of file ScipionGalleryData.java.

-
204  {
205  return false;//fixme?? cannot open picker from sqlite
206  }
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◆ initColumnInfo()

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ColumnInfo xmipp.viewer.scipion.ScipionGalleryData.initColumnInfo (int label)
- 		-inline
-
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Definition at line 57 of file ScipionGalleryData.java.

-
58  {
59  return ((ScipionMetaData)md).getColumnInfo(label);
60  }
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◆ isEnabled()

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boolean xmipp.viewer.scipion.ScipionGalleryData.isEnabled (int index)
- 		-inline
-
-

Check if an item is enabled or not

- -

Definition at line 318 of file ScipionGalleryData.java.

-
318  {
319  try {
320  if (isVolumeMode()) {
321  return true;
322  }
323  return getEMObjects().get(index).isEnabled();
324  } catch (Exception e) {
325  e.printStackTrace();
326  }
327  return true;
328  }
-
xmipp.viewer.scipion.ScipionGalleryData.getEMObjects
List< ScipionMetaData.EMObject > getEMObjects()
Definition: ScipionGalleryData.java:208
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◆ isFile()

- -
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boolean xmipp.viewer.scipion.ScipionGalleryData.isFile (ColumnInfo ci)
- 		-inline
-
-

This is only needed for metadata table galleries

- -

Definition at line 215 of file ScipionGalleryData.java.

-
215  {
216  return ci.labelName.contains("filename") || ci.labelName.equals("_psdFile");
217  }
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◆ isImageFile()

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boolean xmipp.viewer.scipion.ScipionGalleryData.isImageFile (ColumnInfo ci)
- 		-inline
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Definition at line 219 of file ScipionGalleryData.java.

-
219  {
220  return ci.allowRender;
221  }
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◆ loadClassesInfo()

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void xmipp.viewer.scipion.ScipionGalleryData.loadClassesInfo ()
- 		-inline
-
-

Load classes structure if previously stored

- -

Definition at line 177 of file ScipionGalleryData.java.

-
177  {
178 
179  }// function loadClassesInfo
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◆ loadSelection()

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void xmipp.viewer.scipion.ScipionGalleryData.loadSelection (String selectedPath)
- 		-inline
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Definition at line 349 of file ScipionGalleryData.java.

-
349  {
350  ((ScipionMetaData)md).loadSelection(selectedPath);
351 
352  }
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◆ overwrite()

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void xmipp.viewer.scipion.ScipionGalleryData.overwrite (String path,
boolean [] selection 
) throws SQLException
- 		-inline
-
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Definition at line 224 of file ScipionGalleryData.java.

-
224  {
225  ((ScipionMetaData) md).overwrite(filename, path, selection);
226  }
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◆ readMd()

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void xmipp.viewer.scipion.ScipionGalleryData.readMd ()
- 		-inline
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Definition at line 114 of file ScipionGalleryData.java.

-
114  {
115  hasMdChanges = false;
116  hasClassesChanges = false;
117  md = getMetaData(selectedBlock);
118  }
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◆ recalculateCTF()

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void xmipp.viewer.scipion.ScipionGalleryData.recalculateCTF (int row,
boolean [] selection,
EllipseCTF ellipseCTF,
String sortFn 
)
- 		-inline
-
- -

Definition at line 248 of file ScipionGalleryData.java.

-
248  {
249 
250  ScipionMetaData.EMObject emo;
251  long id;
252  if(isEnabled(row))
253  {
254  for(int i = 0; i <selection.length; i ++ )
255  if(selection[i] && isEnabled(i))
256  {
257  id = ids[i];
258  emo = ((ScipionMetaData) md).getEMObject(id);
259  md.putCTF(id, ellipseCTF);
260  emo.setLabel("(recalculate ctf)");
261  emo.setComment(ellipseCTF.toString());
262  window.fireTableRowsUpdated(i, i);
263  }
264  }
265 
266  }
xmipp.viewer.windows.GalleryJFrame.fireTableRowsUpdated
void fireTableRowsUpdated(int from, int to)
Definition: GalleryJFrame.java:502
- - - -
xmipp.jni.MetaData.putCTF
void putCTF(long id, EllipseCTF ellipseCTF)
Definition: MetaData.java:694
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◆ removeClass()

- -
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void xmipp.viewer.scipion.ScipionGalleryData.removeClass (int classNumber)
- 		-inline
-
-

Remove a class from the selection

- -

Definition at line 195 of file ScipionGalleryData.java.

-
195  {
196 
197  }
-
-
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◆ removeCTF()

- -
-
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void xmipp.viewer.scipion.ScipionGalleryData.removeCTF (int row)
- 		-inline
-
- -

Definition at line 235 of file ScipionGalleryData.java.

-
235  {
236  ScipionMetaData.EMObject emo = ((ScipionMetaData) md).getEMObjects().get(row);
237  emo.setLabel("");
238  emo.setComment("");
239  super.removeCTF(row);
240  window.fireTableRowsUpdated(row, row);
241  }
xmipp.viewer.windows.GalleryJFrame.fireTableRowsUpdated
void fireTableRowsUpdated(int from, int to)
Definition: GalleryJFrame.java:502
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◆ runObjectCommand()

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void xmipp.viewer.scipion.ScipionGalleryData.runObjectCommand (int index,
String objectCommand 
)
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-
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Definition at line 372 of file ScipionGalleryData.java.

-
372  {
373  try {
374  ScipionParams params = (ScipionParams)parameters;
375  String command = String.format("run function runObjectCommand '%s' %s %s", objectCommand, params.inputid, getId(index));
376  XmippWindowUtil.runCommand(command, params.port);
377 // String[] cmd = new String[]{params.python, params.getObjectCmdScript(), String.format("'%s'", objectCommand), params.projectid, params.other, String.valueOf(getId(index))};
378 // XmippWindowUtil.executeCommand(cmd, false);
379  } catch (Exception ex) {
380  Logger.getLogger(GalleryData.class.getName()).log(Level.SEVERE, null, ex);
381  }
382  }
-
xmipp.viewer.models.GalleryData.GalleryData
GalleryData(GalleryJFrame window, String fn, Params parameters)
Definition: GalleryData.java:220
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◆ setEnabled()

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void xmipp.viewer.scipion.ScipionGalleryData.setEnabled (int index,
boolean isenabled 
)
- 		-inline
-
-

Set enabled state

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Definition at line 297 of file ScipionGalleryData.java.

-
297  {
298  try {
299  if (!isVolumeMode()) { // slices in a volume are always enabled
300  getEMObjects().get(index).setEnabled(isenabled);
301  hasMdChanges = true;
302  if(!isenabled && isRecalculateCTF(index))
303  removeCTF(index);
304  }
305  } catch (Exception e) {
306  e.printStackTrace();
307  }
308  }
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xmipp.viewer.scipion.ScipionGalleryData.getEMObjects
List< ScipionMetaData.EMObject > getEMObjects()
Definition: ScipionGalleryData.java:208
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◆ setFileName()

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void xmipp.viewer.scipion.ScipionGalleryData.setFileName (String file)
- 		-inline
-
- -

Definition at line 43 of file ScipionGalleryData.java.

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43  {
44  if (file.contains("@")) {
45  int sep = file.lastIndexOf("@");
46  selectedBlock = file.substring(0, sep);
47  filename = file.substring(sep + 1);
48  }
49  filename = file;
50  mdBlocks = ((ScipionMetaData)md).getBlocks();
51  selectedBlock = mdBlocks[0];
52 
53  }
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◆ setItemClass()

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void xmipp.viewer.scipion.ScipionGalleryData.setItemClass (int index,
ClassInfo cli 
)
- 		-inline
-
-

Set the class of an element

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Definition at line 158 of file ScipionGalleryData.java.

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158  {
159 
160  }
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◆ setValueToCol()

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void xmipp.viewer.scipion.ScipionGalleryData.setValueToCol (int index,
ColumnInfo ci,
String value 
)
- 		-inline
-
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Definition at line 339 of file ScipionGalleryData.java.

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339  {
340  try {
341  getEMObjects().get(index).setValue(ci, value);
342  setMdChanges(true);
343 
344  } catch (Exception e) {
345  e.printStackTrace();
346  }
347  }
xmipp.viewer.models.GalleryData.setMdChanges
void setMdChanges(boolean value)
Definition: GalleryData.java:1246
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xmipp.viewer.scipion.ScipionGalleryData.getEMObjects
List< ScipionMetaData.EMObject > getEMObjects()
Definition: ScipionGalleryData.java:208
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◆ updateClassesInfo()

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void xmipp.viewer.scipion.ScipionGalleryData.updateClassesInfo ()
- 		-inline
-
-

Compute and update the number of classes and images assigned to this superclass

- -

Definition at line 170 of file ScipionGalleryData.java.

-
170  {
171 
172  }// function upateClassesInfo
-
-
-
The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__coll__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__coll__graph.dot deleted file mode 100644 index dab53ff6..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__coll__graph.dot +++ /dev/null @@ -1,112 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionGalleryData" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node2 [label="xmipp.viewer.scipion.Scipion\lGalleryData",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.models.GalleryData",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1GalleryData.html"]; - Node4 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" displaycis" ,fontname="Helvetica"]; - Node4 [label="HashMap\< String, xmipp.viewer.models.\lColumnInfo \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" window" ,fontname="Helvetica"]; - Node5 [label="xmipp.viewer.windows.Gallery\lJFrame",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame.html"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="xmipp.viewer.ctf.iCTFGUI",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$interfacexmipp_1_1viewer_1_1ctf_1_1iCTFGUI.html"]; - Node8 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" plotbt\nchimerabt\nsearchbt" ,fontname="Helvetica"]; - Node8 [label="JButton",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" jsRows\njsGoToImage\njsZoom\njsColumns" ,fontname="Helvetica"]; - Node9 [label="JSpinner",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" fc" ,fontname="Helvetica"]; - Node10 [label="xmipp.utils.XmippFileChooser",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippFileChooser.html"]; - Node11 -> Node10 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node11 [label="JFileChooser",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node12 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" gallery" ,fontname="Helvetica"]; - Node12 [label="xmipp.viewer.models.Image\lGalleryTableModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel.html"]; - Node13 -> Node12 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node13 [label="AbstractTableModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node14 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" columnModel" ,fontname="Helvetica"]; - Node14 [label="xmipp.viewer.models.Gallery\lColumnModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1GalleryColumnModel.html"]; - Node15 -> Node14 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node15 [label="DefaultTableColumnModel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node16 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cache" ,fontname="Helvetica"]; - Node16 [label="xmipp.utils.Cache\<\l String, xmipp.viewer.models.\lImageGalleryTableModel.ImageItem \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1Cache.html"]; - Node17 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" dimension" ,fontname="Helvetica"]; - Node17 [label="xmipp.viewer.ImageDimension",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1ImageDimension.html"]; - Node18 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" renderer" ,fontname="Helvetica"]; - Node18 [label="xmipp.viewer.ImageItemRenderer",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1ImageItemRenderer.html"]; - Node19 -> Node18 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node19 [label="DefaultTableCellRenderer",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node20 -> Node18 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" BORDER_SELECTED\nBORDER_FOCUSED" ,fontname="Helvetica"]; - Node20 [label="Border",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node21 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" busyRows" ,fontname="Helvetica"]; - Node21 [label="ArrayList\< Integer \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node22 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cellDim" ,fontname="Helvetica"]; - Node22 [label="Dimension",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" data" ,fontname="Helvetica"]; - Node22 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" screenSize" ,fontname="Helvetica"]; - Node23 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ctfTasks" ,fontname="Helvetica"]; - Node23 [label="xmipp.viewer.ctf.TasksEngine",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1ctf_1_1TasksEngine.html"]; - Node24 -> Node23 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node24 [label="xmipp.viewer.ctf.iTaskCompletion\lListener",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$interfacexmipp_1_1viewer_1_1ctf_1_1iTaskCompletionListener.html"]; - Node25 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" jcbBlocks\njcbVolumes" ,fontname="Helvetica"]; - Node25 [label="JComboBox",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node26 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" jlBlocks\njlVolumes" ,fontname="Helvetica"]; - Node26 [label="JLabel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node27 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cbPanel\nbuttonspn\njpBottom" ,fontname="Helvetica"]; - Node27 [label="JPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" data" ,fontname="Helvetica"]; - Node28 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" menu" ,fontname="Helvetica"]; - Node28 [label="xmipp.viewer.windows.Gallery\lJFrame.GalleryMenu",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu.html"]; - Node29 -> Node28 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node29 [label="xmipp.utils.XmippMenuBar\lCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuBarCreator.html"]; - Node30 -> Node29 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node30 [label="xmipp.utils.XmippMenuCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuCreator.html"]; - Node31 -> Node30 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node31 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node32 -> Node30 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" groups" ,fontname="Helvetica"]; - Node32 [label="Map\< String, ButtonGroup \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node33 -> Node30 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" menu" ,fontname="Helvetica"]; - Node33 [label="JComponent",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node34 -> Node30 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" items" ,fontname="Helvetica"]; - Node34 [label="Map\< String, JMenuItem \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node35 -> Node28 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" quickhelpdlg" ,fontname="Helvetica"]; - Node35 [label="xmipp.utils.QuickHelpJDialog",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1QuickHelpJDialog.html"]; - Node36 -> Node35 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node36 [label="JDialog",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node35 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" okbt" ,fontname="Helvetica"]; - Node37 -> Node35 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helppn" ,fontname="Helvetica"]; - Node37 [label="xmipp.utils.QuickHelpPane",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1QuickHelpPane.html"]; - Node27 -> Node37 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node38 -> Node37 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helptb" ,fontname="Helvetica"]; - Node38 [label="JTable",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node27 -> Node37 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" buttonspn" ,fontname="Helvetica"]; - Node39 -> Node37 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helpmap" ,fontname="Helvetica"]; - Node39 [label="Map\< Object, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node39 -> Node35 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helpmap" ,fontname="Helvetica"]; - Node40 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ciFirstRender" ,fontname="Helvetica"]; - Node40 [label="xmipp.viewer.models.ColumnInfo",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1ColumnInfo.html"]; - Node41 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" labels" ,fontname="Helvetica"]; - Node41 [label="List\< xmipp.viewer.models.\lColumnInfo \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node42 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" md" ,fontname="Helvetica"]; - Node42 [label="xmipp.jni.MetaData",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1MetaData.html"]; - Node43 -> Node42 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ctfs" ,fontname="Helvetica"]; - Node43 [label="HashMap\< Long, xmipp.jni.\lEllipseCTF \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node44 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" classes" ,fontname="Helvetica"]; - Node44 [label="xmipp.viewer.models.ClassInfo",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1ClassInfo.html"]; - Node45 -> Node44 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" icon" ,fontname="Helvetica"]; - Node45 [label="xmipp.utils.ColorIcon",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1ColorIcon.html"]; - Node46 -> Node45 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node46 [label="Icon",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node47 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" classesArray" ,fontname="Helvetica"]; - Node47 [label="ArrayList\< xmipp.viewer.models.\lClassInfo \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node48 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" mode" ,fontname="Helvetica"]; - Node48 [label="xmipp.viewer.models.Gallery\lData.Mode",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$enumxmipp_1_1viewer_1_1models_1_1GalleryData_1_1Mode.html"]; - Node49 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" parameters" ,fontname="Helvetica"]; - Node49 [label="xmipp.utils.Params",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1Params.html"]; - Node50 -> Node49 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" options" ,fontname="Helvetica"]; - Node50 [label="Options",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node51 -> Node49 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cmdLine" ,fontname="Helvetica"]; - Node51 [label="CommandLine",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__coll__graph.md5 deleted file mode 100644 index b1ac15ae..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -f6d98381f7a00f5f65d9a88d907cb2a4 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__inherit__graph.dot deleted file mode 100644 index a01ee4e2..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionGalleryData" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.scipion.Scipion\lGalleryData",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.models.GalleryData",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1GalleryData.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__inherit__graph.md5 deleted file mode 100644 index 2eaf0891..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryData__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -c91f6ed2a1d6911137133b3c320bc165 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame-members.html b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame-members.html deleted file mode 100644 index a20e95cc..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame-members.html +++ /dev/null @@ -1,174 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.viewer.scipion.ScipionGalleryJFrame Member List
-
-
- -

This is the complete list of members for xmipp.viewer.scipion.ScipionGalleryJFrame, including all inherited members.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
buttonspnxmipp.viewer.windows.GalleryJFrameprotected
cbPanelxmipp.viewer.windows.GalleryJFrameprotected
changeView()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
CHIMERA_LAUNCHERxmipp.viewer.windows.GalleryJFramestatic
chimerabtxmipp.viewer.windows.GalleryJFrameprotected
close()xmipp.viewer.windows.GalleryJFrameinline
close(boolean ask)xmipp.viewer.windows.GalleryJFrameinline
confirmCreate(String output)xmipp.viewer.scipion.ScipionGalleryJFrameinline
confirmCreate(String output, int size)xmipp.viewer.scipion.ScipionGalleryJFrameinline
createCombos()xmipp.viewer.windows.GalleryJFrameinlineprotected
createCoordSubsetFromImages()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
createGUI()xmipp.viewer.windows.GalleryJFrameinlineprotected
createModel()xmipp.viewer.windows.GalleryJFrameinlineprotected
createModel(boolean[] selection)xmipp.viewer.windows.GalleryJFrameinlineprotected
createRepresentativesSubset()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
createSimpleSubset()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
createSubsetFromClasses()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
createToolbar()xmipp.viewer.windows.GalleryJFrameinlineprotected
createVolume()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
ctfTasksxmipp.viewer.windows.GalleryJFrameprotected
dataxmipp.viewer.windows.GalleryJFrameprotected
DIM_RATExmipp.viewer.windows.GalleryJFrameprotectedstatic
done()xmipp.viewer.windows.GalleryJFrameinline
enableActions()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
enableToolBarActions()xmipp.viewer.windows.GalleryJFrameinlineprotected
fcxmipp.viewer.windows.GalleryJFrameprotected
fillLabel(int label, String mode, String... values)xmipp.viewer.windows.GalleryJFrameinline
findReplace()xmipp.viewer.windows.GalleryJFrameinline
fireTableRowsUpdated(int from, int to)xmipp.viewer.windows.GalleryJFrameinline
galleryxmipp.viewer.windows.GalleryJFrameprotected
GalleryJFrame(String filename, Params parameters)xmipp.viewer.windows.GalleryJFrameinline
GalleryJFrame(MetaData md, Params parameters)xmipp.viewer.windows.GalleryJFrameinline
GalleryJFrame(GalleryData data)xmipp.viewer.windows.GalleryJFrameinline
getBlock()xmipp.viewer.windows.GalleryJFrameinline
getData()xmipp.viewer.windows.GalleryJFrameinline
getDBPreffix()xmipp.viewer.scipion.ScipionGalleryJFrameinline
getFilename()xmipp.viewer.windows.GalleryJFrameinline
getKeyAssist()xmipp.viewer.windows.GalleryJFrameinline
getRunLabel()xmipp.viewer.scipion.ScipionGalleryJFrameinline
getTasksEngine()xmipp.viewer.windows.GalleryJFrameinline
initComponents()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
initGalleryMenu()xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
initResliceButtonMenu()xmipp.viewer.windows.GalleryJFrameinlineprotected
jcbBlocksxmipp.viewer.windows.GalleryJFrameprotected
jcbVolumesxmipp.viewer.windows.GalleryJFrameprotected
jlBlocksxmipp.viewer.windows.GalleryJFrameprotected
jlVolumesxmipp.viewer.windows.GalleryJFrameprotected
jpBottomxmipp.viewer.windows.GalleryJFrameprotected
jsColumnsxmipp.viewer.windows.GalleryJFrameprotected
jsGoToImagexmipp.viewer.windows.GalleryJFrameprotected
jsRowsxmipp.viewer.windows.GalleryJFrameprotected
jsZoomxmipp.viewer.windows.GalleryJFrameprotected
MAX_HEIGHTxmipp.viewer.windows.GalleryJFrameprotectedstatic
MAX_HEIGHT_RATExmipp.viewer.windows.GalleryJFrameprotectedstatic
MAX_WIDTHxmipp.viewer.windows.GalleryJFrameprotectedstatic
menuxmipp.viewer.windows.GalleryJFrameprotected
MIN_HEIGHTxmipp.viewer.windows.GalleryJFrameprotectedstatic
MIN_WIDTHxmipp.viewer.windows.GalleryJFrameprotectedstatic
openChimera(String file, boolean link)xmipp.viewer.windows.GalleryJFrameinlineprotected
openMetadata(final MetaData md)xmipp.viewer.scipion.ScipionGalleryJFrameinline
openMicrographs()xmipp.viewer.windows.GalleryJFrameinline
openWithChimera()xmipp.viewer.windows.GalleryJFrameinlineprotected
plotbtxmipp.viewer.windows.GalleryJFrameprotected
plotColumns()xmipp.viewer.windows.GalleryJFrameinlineprotected
proceedWithChanges()xmipp.viewer.scipion.ScipionGalleryJFrameinline
readScipionParams(ScipionParams parameters)xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
refreshActive(long id, boolean enabled)xmipp.viewer.windows.GalleryJFrameinline
reloadFile(String file, boolean changed)xmipp.viewer.windows.GalleryJFrameinline
reloadTableData(boolean changed)xmipp.viewer.scipion.ScipionGalleryJFrameinline
xmipp::viewer::windows::GalleryJFrame.reloadTableData()xmipp.viewer.windows.GalleryJFrameinline
xmipp::viewer::windows::GalleryJFrame.reloadTableData(boolean[] selection)xmipp.viewer.windows.GalleryJFrameinline
xmipp::viewer::windows::GalleryJFrame.reloadTableData(boolean changed, boolean[] selection)xmipp.viewer.windows.GalleryJFrameinline
removeLabel(int label)xmipp.viewer.windows.GalleryJFrameinline
removeObjects(boolean selected)xmipp.viewer.windows.GalleryJFrameinline
runCommand(final String command, String msg)xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
runCommand(final String command, String msg, boolean useSelection)xmipp.viewer.scipion.ScipionGalleryJFrameinlineprotected
runInBackground(int operation)xmipp.viewer.windows.GalleryJFrameinline
saveMd()xmipp.viewer.windows.GalleryJFrameinlineprotected
saveMd(String path, boolean saveall, boolean isoverwrite, boolean reload)xmipp.viewer.windows.GalleryJFrameinlineprotected
ScipionGalleryJFrame(ScipionGalleryData data)xmipp.viewer.scipion.ScipionGalleryJFrameinline
screenSizexmipp.viewer.windows.GalleryJFrameprotectedstatic
searchbtxmipp.viewer.windows.GalleryJFrameprotected
selectBlock(String block)xmipp.viewer.windows.GalleryJFrameinline
selectItem(int row, int col)xmipp.viewer.windows.GalleryJFrameinline
setAutoAdjustColumns(boolean autoAdjustColumns)xmipp.viewer.windows.GalleryJFrameinline
setRowBusy(int row)xmipp.viewer.windows.GalleryJFrameinline
setRowIdle(int row)xmipp.viewer.windows.GalleryJFrameinline
setRunning(boolean running)xmipp.viewer.windows.GalleryJFrameinline
setupButton(AbstractButton btn, String icon, String text, ActionListener listener)xmipp.viewer.windows.GalleryJFrameinlineprotected
showException(Exception e)xmipp.viewer.windows.GalleryJFrameinline
tableMouseClicked(MouseEvent evt)xmipp.viewer.windows.GalleryJFrameinlineprotected
updateVisibleCombos()xmipp.viewer.windows.GalleryJFrameinlineprotected
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-Classes | -Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.scipion.ScipionGalleryJFrame Class Reference
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-Classes

class  ScipionGalleryMenu
 
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-Public Member Functions

 ScipionGalleryJFrame (ScipionGalleryData data)
 
String getRunLabel ()
 
String getDBPreffix ()
 
boolean confirmCreate (String output)
 
boolean confirmCreate (String output, int size)
 
void reloadTableData (boolean changed)
 
boolean proceedWithChanges ()
 
void openMetadata (final MetaData md)
 
- Public Member Functions inherited from xmipp.viewer.windows.GalleryJFrame
 GalleryJFrame (String filename, Params parameters)
 
 GalleryJFrame (MetaData md, Params parameters)
 
 GalleryJFrame (GalleryData data)
 
void openMetadata (final MetaData md)
 
GalleryData getData ()
 
void close ()
 
void close (boolean ask)
 
boolean proceedWithChanges ()
 
void fireTableRowsUpdated (int from, int to)
 
void setAutoAdjustColumns (boolean autoAdjustColumns)
 
void runInBackground (int operation)
 
void reloadTableData ()
 
void reloadTableData (boolean[] selection)
 
void reloadTableData (boolean changed, boolean[] selection)
 
void fillLabel (int label, String mode, String... values) throws Exception
 
void removeObjects (boolean selected)
 
void findReplace ()
 
void removeLabel (int label) throws Exception
 
void selectBlock (String block)
 
void selectItem (int row, int col)
 
void showException (Exception e)
 
void setRunning (boolean running)
 
void setRowBusy (int row)
 
void setRowIdle (int row)
 
void done ()
 
String getFilename ()
 
void openMicrographs ()
 
void refreshActive (long id, boolean enabled)
 
String getBlock ()
 
void reloadFile (String file, boolean changed) throws Exception
 
Map< Object, Object > getKeyAssist ()
 
TasksEngine getTasksEngine ()
 
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-Protected Member Functions

void readScipionParams (ScipionParams parameters)
 
void initComponents ()
 
void createVolume ()
 
void createSimpleSubset ()
 
void createCoordSubsetFromImages ()
 
void createSubsetFromClasses ()
 
void createRepresentativesSubset ()
 
void enableActions ()
 
void changeView ()
 
void runCommand (final String command, String msg)
 
void runCommand (final String command, String msg, boolean useSelection)
 
void initGalleryMenu ()
 
- Protected Member Functions inherited from xmipp.viewer.windows.GalleryJFrame
void createModel () throws Exception
 
void createModel (boolean[] selection)
 
void createGUI ()
 
void initGalleryMenu ()
 
void setupButton (AbstractButton btn, String icon, String text, ActionListener listener)
 
void changeView ()
 
void createToolbar ()
 
void createCombos ()
 
void enableToolBarActions ()
 
void updateVisibleCombos ()
 
void tableMouseClicked (MouseEvent evt)
 
void plotColumns ()
 
void saveMd () throws Exception
 
void saveMd (String path, boolean saveall, boolean isoverwrite, boolean reload)
 
void initResliceButtonMenu ()
 
void openChimera (String file, boolean link)
 
void openWithChimera ()
 
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-Additional Inherited Members

- Static Public Attributes inherited from xmipp.viewer.windows.GalleryJFrame
static final String CHIMERA_LAUNCHER = "CHIMERA_LAUNCHER"
 
- Protected Attributes inherited from xmipp.viewer.windows.GalleryJFrame
ImageGalleryTableModel gallery
 
GalleryMenu menu
 
XmippFileChooser fc
 
JPanel jpBottom
 
JSpinner jsColumns
 
JSpinner jsGoToImage
 
JSpinner jsRows
 
JSpinner jsZoom
 
JPanel cbPanel
 
JComboBox jcbBlocks
 
JComboBox jcbVolumes
 
JLabel jlBlocks
 
JLabel jlVolumes
 
TasksEngine ctfTasks
 
GalleryData data
 
JPanel buttonspn
 
JButton searchbt
 
JButton plotbt
 
JButton chimerabt
 
- Static Protected Attributes inherited from xmipp.viewer.windows.GalleryJFrame
static final float MAX_HEIGHT_RATE = 2.0f / 3.0f
 
static final float DIM_RATE = 4.0f / 3.0f
 
static final int MIN_WIDTH = 800
 
static int MIN_HEIGHT
 
static int MAX_HEIGHT
 
static int MAX_WIDTH
 
static Dimension screenSize
 
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Detailed Description

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Author
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Definition at line 35 of file ScipionGalleryJFrame.java.

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Constructor & Destructor Documentation

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◆ ScipionGalleryJFrame()

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xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryJFrame (ScipionGalleryData data)
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Definition at line 57 of file ScipionGalleryJFrame.java.

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57  {
58  super(data);
59  readScipionParams((ScipionParams)data.parameters);
60 
61  }
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xmipp.viewer.scipion.ScipionGalleryJFrame.readScipionParams
void readScipionParams(ScipionParams parameters)
Definition: ScipionGalleryJFrame.java:65
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◆ changeView()

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void xmipp.viewer.scipion.ScipionGalleryJFrame.changeView ()
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Definition at line 388 of file ScipionGalleryJFrame.java.

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389  {
390  super.changeView();
391 
392  if(setType.equals("SetOfVolumes") || setType.equals("SetOfClasses3D"))
393  {
394 
395  // It will be null when invoked as a stand alone viewer.
396  if (cmdbutton != null){
397  cmdbutton.setVisible(data.isTableMode());
398  createvolbt.setVisible(!data.isTableMode());
399  }
400  }
401  }
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boolean xmipp.viewer.scipion.ScipionGalleryJFrame.confirmCreate (String output)
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Definition at line 338 of file ScipionGalleryJFrame.java.

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339  {
340  int size;
341  if(!data.hasDisabled())
342  {
343  size = gallery.hasSelection()? gallery.getSelectionCount(): data.size();
344  }
345  else
346  size = data.getEnabledCount();
347  return confirmCreate(output, size);
348  }
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boolean xmipp.viewer.scipion.ScipionGalleryJFrame.confirmCreate (String output,
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Definition at line 350 of file ScipionGalleryJFrame.java.

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351  {
352  String msg = String.format("<html>Are you sure you want to create a new set of %s with <font color=red>%s</font> %s?", output, size, (size == 1)?"element":"elements");
353  dlg = new InputFieldsMessageDialog(ScipionGalleryJFrame.this, "Question", msg, msgfields);
354  return dlg.action == InputFieldsMessageDialog.OK_OPTION;
355  }
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void xmipp.viewer.scipion.ScipionGalleryJFrame.createCoordSubsetFromImages ()
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Definition at line 287 of file ScipionGalleryJFrame.java.

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288  {
289  int size = 0;
290 
291  if(data.hasClasses())
292  {
293  boolean[] selection = gallery.getSelection();
294  for(ScipionMetaData.EMObject emo: ((ScipionGalleryData)data).getEMObjects())
295  {
296  if(gallery.hasSelection() && !data.hasDisabled())
297  {
298  if(selection[emo.index] && emo.childmd != null)
299  size += emo.childmd.getEnabledCount();
300  }
301  else if(emo.isEnabled() && emo.childmd != null)
302  size += emo.childmd.getEnabledCount();
303  }
304  }
305  else if (gallery.hasSelection() && !data.hasDisabled())
306  size = gallery.getSelectionCount();
307  else
308  size = data.getEnabledCount();
309 
310  if (confirmCreate("Coordinates", size))
311  {
312  String runProtDeepConsSubset = "run protocol XmippProtDeepConsSubSet inputObject=%s sqliteFile='%s','%s' outputClassName=%s other='%s' label='%s'";
313  String command = String.format(runProtDeepConsSubset,
314  inputid, sqlitefile, data.getPreffix(),
315  String.format("SetOfCoordinates"), other, getRunLabel());
316  runCommand(command, "Creating set ...");
317  }
318  }
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xmipp.viewer.scipion.ScipionGalleryJFrame.runCommand
void runCommand(final String command, String msg)
Definition: ScipionGalleryJFrame.java:408
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void xmipp.viewer.scipion.ScipionGalleryJFrame.createRepresentativesSubset ()
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Definition at line 329 of file ScipionGalleryJFrame.java.

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330  {
331  if (confirmCreate("Representatives")) {
332  String output = setType.equals("SetOfClasses2D")? "SetOfAverages,Representatives":"SetOfVolumes,Representatives";
333  String command = String.format(runProtCreateSubset, inputid, sqlitefile, "", output , other, getRunLabel());
334  runCommand(command, "Creating set ...");
335  }
336  }
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void runCommand(final String command, String msg)
Definition: ScipionGalleryJFrame.java:408
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Definition at line 256 of file ScipionGalleryJFrame.java.

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257  {
258  int size = 0;
259 
260  if(data.hasClasses())
261  {
262  boolean[] selection = gallery.getSelection();
263  for(ScipionMetaData.EMObject emo: ((ScipionGalleryData)data).getEMObjects())
264  {
265  if(gallery.hasSelection() && !data.hasDisabled())
266  {
267  if(selection[emo.index] && emo.childmd != null)
268  size += emo.childmd.getEnabledCount();
269  }
270  else if(emo.isEnabled() && emo.childmd != null)
271  size += emo.childmd.getEnabledCount();
272  }
273  }
274  else if (gallery.hasSelection() && !data.hasDisabled())
275  size = gallery.getSelectionCount();
276  else
277  size = data.getEnabledCount();
278 
279  if (confirmCreate(type, size))
280  {
281  String command = String.format(runProtCreateSubset,
282  inputid, sqlitefile, data.getPreffix(), String.format("SetOf%s", type), other, getRunLabel());
283  runCommand(command, "Creating set ...");
284  }
285  }
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Definition: ScipionGalleryJFrame.java:408
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void xmipp.viewer.scipion.ScipionGalleryJFrame.createSubsetFromClasses ()
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Definition at line 320 of file ScipionGalleryJFrame.java.

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321  {
322  if (confirmCreate("Classes")) {
323  String command = String.format(runProtCreateSubset,
324  inputid, sqlitefile, "", setType , other, getRunLabel());
325  runCommand(command, "Creating set ...");
326  }
327  }
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void runCommand(final String command, String msg)
Definition: ScipionGalleryJFrame.java:408
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Definition at line 233 of file ScipionGalleryJFrame.java.

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234  {
235  msgfields.put(runNameKey, "ProtRegisterVolume");
236  dlg = new InputFieldsMessageDialog(ScipionGalleryJFrame.this, "Question", "Are you sure you want to register volume in scipion?", msgfields);
237  int create = dlg.action;
238  if (create == InputFieldsMessageDialog.OK_OPTION);
239  {
240  String command = String.format(runProtCreateSubset,
241  inputid, sqlitefile, "", setType, data.getSelVolId().toString() + ",Volume", getRunLabel());
242  runCommand(command, "Creating volume ...");
243  }
244  }
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Definition: ScipionGalleryJFrame.java:408
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Definition at line 363 of file ScipionGalleryJFrame.java.

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363  {
364  boolean isenabled = !data.isVolumeMode();
365  Color color = isenabled ? XmippWindowUtil.firebrick : XmippWindowUtil.lightgrey;
366  Color forecolor = isenabled ? Color.WHITE : Color.GRAY;
367  if(cmdbutton != null)
368  {
369  cmdbutton.setVisible(isenabled);
370  cmdbutton.setBackground(color);
371  cmdbutton.setForeground(forecolor);
372  }
373  if(classcmdbutton != null)
374  {
375  isenabled = data.hasClasses() && !data.isVolumeMode();
376  color = isenabled? XmippWindowUtil.firebrick: XmippWindowUtil.lightgrey;
377  forecolor = isenabled? Color.WHITE: Color.GRAY;
378  classcmdbutton.setVisible( isenabled);
379  classcmdbutton.setBackground(color);
380  classcmdbutton.setForeground(forecolor);
381  representativesbt.setVisible( isenabled);
382  representativesbt.setBackground(color);
383  representativesbt.setForeground(forecolor);
384  }
385  }
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Definition at line 251 of file ScipionGalleryJFrame.java.

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252  {
253  return ((ScipionGalleryData)data).getPreffix();
254  }
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Definition at line 246 of file ScipionGalleryJFrame.java.

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247  {
248  return dlg.getFieldValue(runNameKey);
249  }
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Definition at line 84 of file ScipionGalleryJFrame.java.

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84  {
85  Icon icon = XmippResource.getIcon("fa-times.png");
86  JButton closebt = new JButton("Close", icon);
87  closebt.addActionListener(new ActionListener() {
88 
89  @Override
90  public void actionPerformed(ActionEvent ae) {
91  close();
92  }
93  });
94 
95  buttonspn.add(closebt);
96  if(!XmippApplication.isScipion())
97  return;
98 
99  if (type != null) {
100  if(!data.isCTFMd()) {
101  if (other.equals("deepCons")) {
102  cmdbutton = XmippWindowUtil.getScipionIconButton("Create Coordinates");
103  cmdbutton.addActionListener(new ActionListener() {
104  @Override
105  public void actionPerformed(ActionEvent ae) {
106  createCoordSubsetFromImages();
107  }
108  });
109  }
110  else
111  {
112  cmdbutton = XmippWindowUtil.getScipionIconButton("Create " + type);
113  cmdbutton.addActionListener(new ActionListener() {
114  @Override
115  public void actionPerformed(ActionEvent ae) {
116  createSimpleSubset();
117  }
118  });
119  }
120  buttonspn.add(cmdbutton);
121  }
122  if(data.hasClasses())
123  {
124  classcmdbutton = XmippWindowUtil.getScipionIconButton("Create Classes");
125  classcmdbutton.addActionListener(new ActionListener() {
126 
127  @Override
128  public void actionPerformed(ActionEvent ae) {
129  createSubsetFromClasses();
130 
131  }
132  });
133 
134  String repText = setType.equals("SetOfClasses2D") ? "Create Averages": "Create Volumes";
135  representativesbt = XmippWindowUtil.getScipionIconButton(repText);
136  representativesbt.addActionListener(new ActionListener() {
137 
138  @Override
139  public void actionPerformed(ActionEvent ae) {
140  createRepresentativesSubset();
141 
142  }
143  });
144 
145  buttonspn.add(representativesbt);
146  buttonspn.add(classcmdbutton);
147  }
148 
149 
150  if(data.isCTFMd())
151  {
152  if (recalculateCTF) {
153  icon = XmippResource.getIcon("fa-cogs.png");
154  JButton recalculatectfbt = XmippWindowUtil.getScipionIconButton("Recalculate CTFs");
155  recalculatectfbt.addActionListener(new ActionListener() {
156 
157  @Override
158  public void actionPerformed(ActionEvent ae) {
159  if (!data.hasRecalculateCTF()) {
160  XmippDialog.showError(ScipionGalleryJFrame.this, "There are no ctfs to recalculate");
161  return;
162  }
163  String command = String.format("run function recalculateCTF %s %s", inputid, sqlitefile);
164  runCommand(command, "Recalculating CTF", false);
165  }
166  });
167  recalculatectfbt.setIcon(icon);
168  buttonspn.add(recalculatectfbt);
169  }
170 
171  JButton ctfsubsetbt = XmippWindowUtil.getScipionIconButton("Create Micrographs");
172  ctfsubsetbt.addActionListener(new ActionListener() {
173 
174  @Override
175  public void actionPerformed(ActionEvent ae) {
176  if (confirmCreate("Micrographs"))
177  {
178  String command = String.format(runProtCreateSubset,
179  inputid, sqlitefile, "", "SetOfMicrographs", other, getRunLabel());
180  runCommand(command, "Creating set ...");
181  }
182  }
183  });
184  buttonspn.add(ctfsubsetbt);
185 
186  }
187  if(setType.equals("SetOfVolumes") || setType.equals("SetOfClasses3D"))
188  {
189  createvolbt = XmippWindowUtil.getScipionIconButton("Create Volume");
190  createvolbt.addActionListener(new ActionListener() {
191 
192  @Override
193  public void actionPerformed(ActionEvent ae) {
194  createVolume();
195  }
196  });
197  buttonspn.add(createvolbt);
198  createvolbt.setVisible(!data.isTableMode());
199  }
200 
201 
202  if (!SwingUtilities.isEventDispatchThread()) {
203 
204  Runnable pack = new Runnable() {
205  @Override
206  public void run() {
207  ScipionGalleryJFrame.this.pack();
208  }
209  };
210 
211  try {
212  SwingUtilities.invokeAndWait(pack);
213  } catch (Exception e) {
214 
215  logger.log(Level.WARNING, "ScipionGalleryJFrame.pack threw an exception: " + e.getMessage());
216  }
217  } else {
218  pack();
219  }
220 
221  enableActions();
222  jcbBlocks.addActionListener(new ActionListener() {
223 
224  @Override
225  public void actionPerformed(ActionEvent ae) {
226  enableActions();
227  }
228  });
229  }
230  }
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xmipp.viewer.scipion.ScipionGalleryJFrame.runCommand
void runCommand(final String command, String msg)
Definition: ScipionGalleryJFrame.java:408
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Definition at line 450 of file ScipionGalleryJFrame.java.

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450  {
451  menu = new ScipionGalleryMenu();
452 
453  }
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void xmipp.viewer.scipion.ScipionGalleryJFrame.openMetadata (final MetaData md)
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Open another metadata separataly *

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Definition at line 431 of file ScipionGalleryJFrame.java.

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432  {
433  try
434  {
435  SwingUtilities.invokeLater(new Runnable() {
436 
437  @Override
438  public void run() {
439  new ScipionGalleryJFrame(new ScipionGalleryData(ScipionGalleryJFrame.this, ((ScipionParams)data.parameters).getScipionParams(), (ScipionMetaData)md));
440  }
441  });
442 
443  }
444  catch(Exception e)
445  {
446  XmippDialog.showError(this, e.getMessage());
447  }
448  }
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404  {
405  return true;
406  }
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Definition at line 65 of file ScipionGalleryJFrame.java.

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66  {
67  try {
68  setType = ((ScipionMetaData)data.getMd()).getSetType();
69  type = data.hasClasses()? "Particles": setType.replace("SetOf", "");
70  port = parameters.port;
71  inputid = parameters.inputid;
72  sqlitefile = data.getTmpFile("_state");
73  msgfields = new HashMap<String, String>();
74  msgfields.put(runNameKey, "create subset");
75  other = parameters.other;
76  recalculateCTF = parameters.recalculateCTF;
77  initComponents();
78  } catch (Exception ex) {
79  logger.log(Level.SEVERE, null, ex);
80  throw new IllegalArgumentException(ex.getMessage());
81  }
82  }
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xmipp.viewer.models.GalleryData.getTmpFile
String getTmpFile(String suffix)
Definition: GalleryData.java:158
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MetaData getMd(List< Long > ids)
Definition: GalleryData.java:1626
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Definition at line 357 of file ScipionGalleryJFrame.java.

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358  {
359  super.reloadTableData(changed, gallery.getSelection());
360  enableActions();
361  }
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void xmipp.viewer.scipion.ScipionGalleryJFrame.runCommand (final String command,
String msg 
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Definition at line 408 of file ScipionGalleryJFrame.java.

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409  {
410  runCommand(command, msg, gallery.hasSelection() && !data.hasDisabled());
411  }
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Definition: ScipionGalleryJFrame.java:408
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void xmipp.viewer.scipion.ScipionGalleryJFrame.runCommand (final String command,
String msg,
boolean useSelection 
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Definition at line 413 of file ScipionGalleryJFrame.java.

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414  {
415  try {
416  boolean[] selection = null;
417 
418  if(useSelection)
419  selection = gallery.getSelection();
420  ((ScipionGalleryData)data).overwrite(sqlitefile, selection);
421  XmippWindowUtil.runCommand(command, port);
422  //close(false);
423  } catch (SQLException ex) {
424  logger.log(Level.SEVERE, null, ex);
425  }
426  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu-members.html b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu-members.html deleted file mode 100644 index b1d43f7e..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu-members.html +++ /dev/null @@ -1,163 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenu Member List
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This is the complete list of members for xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenu, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippMenuCreatorinline
addDisplayLabelItems()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinlineprotected
addExtraMenuItems()xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenuinline
addItem(String key, String text, String... values)xmipp.utils.XmippMenuCreatorinline
addRenderImageColumnItems()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinlineprotected
addSeparator(String key)xmipp.utils.XmippMenuBarCreatorinline
createItems()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinlineprotected
CTF_PROFILExmipp.utils.XmippMenuCreatorstatic
CTF_RECALCULATExmipp.utils.XmippMenuCreatorstatic
DISABLEDxmipp.utils.XmippMenuCreatorstatic
DISPLAYxmipp.utils.XmippMenuCreator
DISPLAY_APPLYGEOxmipp.utils.XmippMenuCreator
DISPLAY_COLUMNSxmipp.utils.XmippMenuCreator
DISPLAY_INVERTYxmipp.utils.XmippMenuCreator
DISPLAY_NORMALIZExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGESxmipp.utils.XmippMenuCreator
DISPLAY_RESLICExmipp.utils.XmippMenuCreator
DISPLAY_RESLICE_VIEWSxmipp.utils.XmippMenuCreator
DISPLAY_SHOWLABELSxmipp.utils.XmippMenuCreator
DISPLAY_WRAPxmipp.utils.XmippMenuCreator
ENABLEDxmipp.utils.XmippMenuCreatorstatic
FILExmipp.utils.XmippMenuCreator
FILE_EXITxmipp.utils.XmippMenuCreator
FILE_EXPORTIMAGESxmipp.utils.XmippMenuCreator
FILE_INFOxmipp.utils.XmippMenuCreator
FILE_LINK_CHIMERAxmipp.utils.XmippMenuCreator
FILE_LOAD_SELxmipp.utils.XmippMenuCreator
FILE_OPENxmipp.utils.XmippMenuCreator
FILE_OPENMICROGRAPHSxmipp.utils.XmippMenuCreator
FILE_OPENWITH_CHIMERAxmipp.utils.XmippMenuCreator
FILE_OPENWITH_IJxmipp.utils.XmippMenuCreator
FILE_REFRESHxmipp.utils.XmippMenuCreator
FILE_SAVExmipp.utils.XmippMenuCreator
FILE_SAVE_SELxmipp.utils.XmippMenuCreator
FILE_SAVEASxmipp.utils.XmippMenuCreator
getItem(String key)xmipp.utils.XmippMenuCreatorinline
getItemEnabled(String key)xmipp.utils.XmippMenuCreatorinline
getItemSelected(String key)xmipp.utils.XmippMenuCreatorinline
getMenuBar()xmipp.utils.XmippMenuBarCreatorinline
groupsxmipp.utils.XmippMenuCreatorprotected
handleActionPerformed(ActionEvent evt)xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenuinlineprotected
HELPxmipp.utils.XmippMenuCreator
HELP_ONLINExmipp.utils.XmippMenuCreator
initItems()xmipp.utils.XmippMenuCreatorinline
INVERT_SELECTxmipp.utils.XmippMenuCreatorstatic
itemsxmipp.utils.XmippMenuCreatorprotected
KEY_ASSISTxmipp.utils.XmippMenuCreator
loadSelection(String path)xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenuinlineprotected
MD_ADD_OBJECTxmipp.utils.XmippMenuCreator
MD_CLASSESxmipp.utils.XmippMenuCreator
MD_EDIT_COLSxmipp.utils.XmippMenuCreator
MD_FIND_REPLACExmipp.utils.XmippMenuCreator
MD_REMOVE_DISABLEDxmipp.utils.XmippMenuCreator
MD_REMOVE_SELECTIONxmipp.utils.XmippMenuCreator
MD_SAVE_SELECTIONxmipp.utils.XmippMenuCreator
menuxmipp.utils.XmippMenuCreatorprotected
METADATAxmipp.utils.XmippMenuCreator
OPENxmipp.utils.XmippMenuCreatorstatic
OPEN_ASTEXTxmipp.utils.XmippMenuCreatorstatic
OPEN_IMAGESxmipp.utils.XmippMenuCreatorstatic
quickhelpdlgxmipp.viewer.windows.GalleryJFrame.GalleryMenuprotected
REFRESHxmipp.utils.XmippMenuCreatorstatic
SAVE_IMAGESxmipp.utils.XmippMenuCreatorstatic
saveSelection(String path)xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenuinlineprotected
SELECTxmipp.utils.XmippMenuCreatorstatic
SELECT_ALLxmipp.utils.XmippMenuCreatorstatic
SELECT_FROMHERExmipp.utils.XmippMenuCreatorstatic
SELECT_TOHERExmipp.utils.XmippMenuCreatorstatic
SET_CLASSxmipp.utils.XmippMenuCreatorstatic
setItemEnabled(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemSelected(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemVisible(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
TOOLSxmipp.utils.XmippMenuCreator
TOOLS_AVGSTDxmipp.utils.XmippMenuCreator
TOOLS_FSCxmipp.utils.XmippMenuCreator
TOOLS_PCAxmipp.utils.XmippMenuCreator
TOOLS_PLOTxmipp.utils.XmippMenuCreator
update()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinline
XmippMenuBarCreator()xmipp.utils.XmippMenuBarCreatorinline
XmippMenuCreator(JComponent menu)xmipp.utils.XmippMenuCreatorinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu.html b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu.html deleted file mode 100644 index 4db6cede..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu.html +++ /dev/null @@ -1,419 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenu Class Reference - - - - - - - - - -
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-Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenu Class Reference
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-Public Member Functions

void addExtraMenuItems ()
 
- Public Member Functions inherited from xmipp.viewer.windows.GalleryJFrame.GalleryMenu
void addExtraMenuItems ()
 
void update ()
 
- Public Member Functions inherited from xmipp.utils.XmippMenuBarCreator
 XmippMenuBarCreator ()
 
JMenuBar getMenuBar ()
 
void addSeparator (String key)
 
- Public Member Functions inherited from xmipp.utils.XmippMenuCreator
 XmippMenuCreator (JComponent menu)
 
JMenuItem addItem (String key, String text, String... values)
 
JMenuItem getItem (String key)
 
boolean getItemEnabled (String key)
 
void setItemEnabled (String key, boolean value)
 
boolean getItemSelected (String key)
 
void setItemSelected (String key, boolean value)
 
void setItemVisible (String key, boolean value)
 
void actionPerformed (ActionEvent evt)
 
void initItems ()
 
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-Protected Member Functions

void handleActionPerformed (ActionEvent evt)
 
void loadSelection (String path)
 
void saveSelection (String path)
 
- Protected Member Functions inherited from xmipp.viewer.windows.GalleryJFrame.GalleryMenu
void createItems () throws Exception
 
void handleActionPerformed (ActionEvent evt)
 
void addRenderImageColumnItems ()
 
void addDisplayLabelItems ()
 
- Protected Member Functions inherited from xmipp.utils.XmippMenuCreator
abstract void handleActionPerformed (ActionEvent evt)
 
abstract void createItems () throws Exception
 
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-Additional Inherited Members

- Public Attributes inherited from xmipp.utils.XmippMenuCreator
final String FILE = "File"
 
final String FILE_OPEN = "File.Open_mi"
 
final String FILE_OPENWITH_IJ = "File.OpenWithIJ_mi"
 
final String FILE_OPENMICROGRAPHS = "File.OpenMicrographs_mi"
 
final String FILE_OPENWITH_CHIMERA = "File.OpenWithChimera_mi"
 
final String FILE_INFO = "File.FileInfo_mi"
 
final String FILE_SAVE = "File.Save_mi"
 
final String FILE_SAVEAS = "File.SaveAs_mi"
 
final String FILE_LOAD_SEL = "File.LoadSel_mi"
 
final String FILE_SAVE_SEL = "File.SaveSel_mi"
 
final String FILE_EXPORTIMAGES = "File.ExportImages_mi"
 
final String FILE_REFRESH = "File.Refresh_mi"
 
final String FILE_EXIT = "File.Exit_mi"
 
final String FILE_LINK_CHIMERA = "File.LinkWithChimera_mi"
 
final String DISPLAY = "Display"
 
final String DISPLAY_SHOWLABELS = "Display.ShowLabel"
 
final String DISPLAY_RENDERIMAGES = "Display.RenderImages_cb"
 
final String DISPLAY_RENDERIMAGE = "Display.RenderImage"
 
final String DISPLAY_INVERTY = "Display.InvertY_cb"
 
final String DISPLAY_APPLYGEO = "Display.ApplyGeo_cb"
 
final String DISPLAY_WRAP = "Display.Wrap_cb"
 
final String DISPLAY_NORMALIZE = "Display.Normalize_cb"
 
final String DISPLAY_COLUMNS = "Display.Columns_mi"
 
final String DISPLAY_RESLICE = "Display.Reslice"
 
final String DISPLAY_RESLICE_VIEWS []
 
final String METADATA = "Metadata"
 
final String MD_CLASSES = "Metadata.Classes_mi"
 
final String MD_EDIT_COLS = "Metadata.EditCols_mi"
 
final String MD_ADD_OBJECT = "Metadata.AddObject_mi"
 
final String MD_REMOVE_SELECTION = "Metadata.RemoveSelection_mi"
 
final String MD_SAVE_SELECTION = "Metadata.SaveSelection_mi"
 
final String MD_REMOVE_DISABLED = "Metadata.RemoveDisabled_mi"
 
final String TOOLS = "Tools"
 
final String TOOLS_AVGSTD = "Tools.AvgStd_mi"
 
final String TOOLS_PCA = "Tools.Pca_mi"
 
final String TOOLS_FSC = "Tools.Fsc_mi"
 
final String TOOLS_PLOT = "Tools.Plot_mi"
 
final String MD_FIND_REPLACE = "Tools.FindReplace_mi"
 
final String HELP = "Help"
 
final String HELP_ONLINE = "Help.Online_mi"
 
final String KEY_ASSIST = "Help.Key_mi"
 
- Static Public Attributes inherited from xmipp.utils.XmippMenuCreator
static final String ENABLED = "Enabled_mi"
 
static final String DISABLED = "Disabled_mi"
 
static final String REFRESH = "Refresh_mi"
 
static final String OPEN = "Open_mi"
 
static final String OPEN_ASTEXT = "OpenAsText_mi"
 
static final String CTF_PROFILE = "CTFProfile_mi"
 
static final String CTF_RECALCULATE = "CTFRecalculate_cb"
 
static final String SELECT = "Select"
 
static final String SELECT_ALL = "Select.All_mi"
 
static final String SELECT_TOHERE = "Select.ToHere_mi"
 
static final String SELECT_FROMHERE = "Select.FromHere_mi"
 
static final String INVERT_SELECT = "Select.InvertSelection_mi"
 
static final String SET_CLASS = "SetClass_mi"
 
static final String OPEN_IMAGES = "OpenImages_mi"
 
static final String SAVE_IMAGES = "SaveImages_mi"
 
- Protected Attributes inherited from xmipp.viewer.windows.GalleryJFrame.GalleryMenu
QuickHelpJDialog quickhelpdlg
 
- Protected Attributes inherited from xmipp.utils.XmippMenuCreator
Map< String, JMenuItem > items
 
Map< String, ButtonGroup > groups
 
JComponent menu
 
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Detailed Description

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Definition at line 455 of file ScipionGalleryJFrame.java.

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Member Function Documentation

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◆ addExtraMenuItems()

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void xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenu.addExtraMenuItems ()
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Definition at line 517 of file ScipionGalleryJFrame.java.

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518  {
519  addItem(FILE_LOAD_SEL, "Load state ...");
520  addItem(FILE_SAVE_SEL, "Save state ...", "save_as.gif");
521 
522  }
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Definition: XmippMenuCreator.java:56
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◆ handleActionPerformed()

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void xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenu.handleActionPerformed (ActionEvent evt)
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Definition at line 459 of file ScipionGalleryJFrame.java.

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460  {
461  super.handleActionPerformed(evt);
462  String cmd = evt.getActionCommand();
463  try
464  {
465  if (cmd.equals(FILE_LOAD_SEL))
466  {
467  fc.setApproveButtonText("Open");
468  fc.setDialogTitle("Load a status file");
469  fc.setApproveButtonToolTipText("Choose a file with state data");
470 
471  if (fc.showOpenDialog(ScipionGalleryJFrame.this) != XmippFileChooser.CANCEL_OPTION)
472  loadSelection(fc.getSelectedPath());
473  }
474  if (cmd.equals(FILE_SAVE_SEL))
475  {
476  fc.setSelectedFile(new File(sqlitefile));
477  fc.setDialogTitle("Save state");
478  fc.setApproveButtonToolTipText("Choose where to save the status");
479  fc.setApproveButtonText("Save");
480  if (fc.showOpenDialog(ScipionGalleryJFrame.this) != XmippFileChooser.CANCEL_OPTION)
481  saveSelection(fc.getSelectedPath());
482  }
483  }
484  catch (Exception e)
485  {
486  showException(e);
487  }
488  }
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Definition at line 490 of file ScipionGalleryJFrame.java.

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490  {
491 
492  ((ScipionGalleryData)data).loadSelection(path);
493  reloadTableData();
494 
495  }
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Definition at line 497 of file ScipionGalleryJFrame.java.

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497  {
498  try {
499 // boolean[] selection = null;
500 // if(gallery.hasSelection() && !data.hasDisabled())
501 // selection = gallery.getSelection();
502 // ((ScipionGalleryData)data).overwrite(path, selection);
503 
504  ScipionGalleryData sgData = (ScipionGalleryData)data;
505 
506  if (sgData.getScipionMetaData().getParent() != null) {
507  sgData.getScipionMetaData().getParent().overwrite(getFilename(), path, null);
508  } else {
509  sgData.overwrite(path, null);
510  }
511  } catch (SQLException ex) {
512  logger.log(Level.SEVERE, null, ex);
513  }
514  }
- -
-
-
-
The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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- Node16 -> Node13 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helppn" ,fontname="Helvetica"]; - Node16 [label="xmipp.utils.QuickHelpPane",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1QuickHelpPane.html"]; - Node17 -> Node16 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node17 [label="JPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node18 -> Node16 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helptb" ,fontname="Helvetica"]; - Node18 [label="JTable",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node17 -> Node16 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" buttonspn" ,fontname="Helvetica"]; - Node19 -> Node16 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helpmap" ,fontname="Helvetica"]; - Node19 [label="Map\< Object, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node19 -> Node13 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helpmap" ,fontname="Helvetica"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__coll__graph.md5 deleted file mode 100644 index 64f1ae98..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -2dc6067ac3c834e6b55298ab88c70cb4 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__inherit__graph.dot deleted file mode 100644 index 9110568a..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__inherit__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionGalleryJFrame.ScipionGalleryMenu" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.scipion.Scipion\lGalleryJFrame.ScipionGalleryMenu",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.windows.Gallery\lJFrame.GalleryMenu",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.utils.XmippMenuBar\lCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuBarCreator.html"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.utils.XmippMenuCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuCreator.html"]; - Node4 -> Node3 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__inherit__graph.md5 deleted file mode 100644 index 66f80596..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -71cf1bb23af389bc02ef06e73addeb97 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame__coll__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame__coll__graph.dot deleted file mode 100644 index dc79286b..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame__coll__graph.dot +++ /dev/null @@ -1,112 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionGalleryJFrame" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node4 [label="xmipp.viewer.scipion.Scipion\lGalleryJFrame",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node5 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="xmipp.viewer.windows.Gallery\lJFrame",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame.html"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="xmipp.viewer.ctf.iCTFGUI",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$interfacexmipp_1_1viewer_1_1ctf_1_1iCTFGUI.html"]; - Node8 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" plotbt\nchimerabt\nsearchbt" ,fontname="Helvetica"]; - Node8 [label="JButton",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" jsRows\njsGoToImage\njsZoom\njsColumns" ,fontname="Helvetica"]; - Node9 [label="JSpinner",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" fc" ,fontname="Helvetica"]; - Node10 [label="xmipp.utils.XmippFileChooser",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippFileChooser.html"]; - Node11 -> Node10 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node11 [label="JFileChooser",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node12 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" gallery" ,fontname="Helvetica"]; - Node12 [label="xmipp.viewer.models.Image\lGalleryTableModel",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1ImageGalleryTableModel.html"]; 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xmipp.viewer.scipion.ScipionMetaData Member List
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This is the complete list of members for xmipp.viewer.scipion.ScipionMetaData, including all inherited members.

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add(EMObject emo)xmipp.viewer.scipion.ScipionMetaDatainline
addLabel(int label)xmipp.jni.MetaData
addObject()xmipp.jni.MetaData
blocksxmipp.viewer.scipion.ScipionMetaDataprotected
checkTmpxmipp.viewer.scipion.ScipionMetaDataprotected
clear()xmipp.jni.MetaData
columnsxmipp.viewer.scipion.ScipionMetaDataprotected
computeFourierStatistics(MetaData mdIn, int label)xmipp.jni.MetaData
containsBlock(String file, String block)xmipp.jni.MetaDatainlinestatic
containsCTF(long id)xmipp.jni.MetaDatainline
containsGeometryInfo(String type)xmipp.viewer.scipion.ScipionMetaDatainline
containsLabel(int label)xmipp.viewer.scipion.ScipionMetaDatainline
xmipp::jni::MetaData.containsLabel(int[] labels)xmipp.jni.MetaDatainline
containsMicrographParticles()xmipp.jni.MetaDatainline
containsMicrographsInfo()xmipp.viewer.scipion.ScipionMetaDatainline
ctfsxmipp.jni.MetaDataprotected
destroy()xmipp.viewer.scipion.ScipionMetaDatainline
emobjectsxmipp.viewer.scipion.ScipionMetaDataprotected
enableDebug()xmipp.jni.MetaData
enabledsxmipp.viewer.scipion.ScipionMetaDataprotected
filenamexmipp.jni.MetaDataprotected
FILL_CONSTANTxmipp.jni.MetaDatastatic
FILL_LINEARxmipp.jni.MetaDatastatic
FILL_RAND_GAUSSIANxmipp.jni.MetaDatastatic
FILL_RAND_UNIFORMxmipp.jni.MetaDatastatic
fillConstant(int label, String value)xmipp.jni.MetaData
fillLinear(int label, double start, double step)xmipp.jni.MetaData
fillRandom(int label, String mode, double op1, double op2)xmipp.jni.MetaData
finalize()xmipp.jni.MetaDatainlineprotected
findObjects()xmipp.viewer.scipion.ScipionMetaDatainline
firstObject()xmipp.jni.MetaData
fixPath(String value)xmipp.jni.MetaDatainline
fixPath(String value, String baseDir)xmipp.jni.MetaDatainline
GEOMETRY_LABELSxmipp.jni.MetaDatastatic
GEOMETRY_RELION_LABELSxmipp.jni.MetaDatastatic
getActiveLabels()xmipp.viewer.scipion.ScipionMetaDatainline
getBaseDir()xmipp.jni.MetaDatainline
getBlock()xmipp.viewer.scipion.ScipionMetaDatainline
getBlocks()xmipp.viewer.scipion.ScipionMetaDatainline
getBlocksInMetaDataFile(String filename)xmipp.jni.MetaDatastatic
getChild(String block)xmipp.viewer.scipion.ScipionMetaDatainline
getClassForType(int type)xmipp.jni.MetaDatainlinestatic
getColumnInfo(int label)xmipp.viewer.scipion.ScipionMetaDatainline
getColumnInfo(String labelName)xmipp.viewer.scipion.ScipionMetaDatainline
getColumnMax(int column)xmipp.jni.MetaData
getColumnMin(int column)xmipp.jni.MetaData
getColumnsInfo()xmipp.viewer.scipion.ScipionMetaDatainline
getColumnValues(int label)xmipp.jni.MetaData
getConnection(String filename)xmipp.viewer.scipion.ScipionMetaDatainlinestatic
getConnectionReadOnly(String filename)xmipp.viewer.scipion.ScipionMetaDatainlinestatic
getCTFDescription(long id)xmipp.viewer.scipion.ScipionMetaDatainline
getCTFFile(long id)xmipp.viewer.scipion.ScipionMetaDatainline
getEllipseCTF(long id, int D)xmipp.viewer.scipion.ScipionMetaDatainline
xmipp::jni::MetaData.getEllipseCTF(long id)xmipp.jni.MetaDatainline
getEMObject(long id)xmipp.viewer.scipion.ScipionMetaDatainline
getEMObjects()xmipp.viewer.scipion.ScipionMetaDatainline
getEnabled(long id)xmipp.viewer.scipion.ScipionMetaDatainline
getEnabledCount()xmipp.viewer.scipion.ScipionMetaDatainline
getFilename()xmipp.jni.MetaDatainline
getGeoMatrixColumn(ColumnInfo ci)xmipp.viewer.scipion.ScipionMetaDatainline
getLabelClass(int label)xmipp.jni.MetaDatainlinestatic
getLabelComment(int label)xmipp.jni.MetaDatastatic
getLabelName(int label)xmipp.jni.MetaDatainlinestatic
getLabelType(int label)xmipp.jni.MetaDatastatic
getLabelTypeString(int labelType)xmipp.jni.MetaDatainlinestatic
getMetaDataRow()xmipp.jni.MetaDatainline
getParent()xmipp.viewer.scipion.ScipionMetaDatainline
getPath()xmipp.jni.MetaDatainline
getPCAbasis(ImageGeneric basis, int label)xmipp.jni.MetaData
getPreffix()xmipp.viewer.scipion.ScipionMetaDatainline
getPSDEnhanced(long id)xmipp.viewer.scipion.ScipionMetaDatainline
getPSDFile(long id)xmipp.viewer.scipion.ScipionMetaDatainline
getRow(MDRow mdRow, long objId)xmipp.jni.MetaData
getRowValues(long objId)xmipp.jni.MetaDatainline
getSelf()xmipp.viewer.scipion.ScipionMetaDatainline
getSetType()xmipp.viewer.scipion.ScipionMetaDatainline
getStatistics(boolean applyGeo)xmipp.viewer.scipion.ScipionMetaDatainline
getStatistics(boolean applyGeo, int label)xmipp.viewer.scipion.ScipionMetaDatainline
getStatsImages(ImageGeneric imageAvg, ImageGeneric imageStd, boolean applyGeo, boolean wrap, int label)xmipp.jni.MetaData
getTypeMapping(int type)xmipp.viewer.scipion.ScipionMetaDatainlinestatic
getTypeMapping(String type)xmipp.viewer.scipion.ScipionMetaDatainlinestatic
getValueBoolean(int label, long objId)xmipp.jni.MetaData
getValueDouble(int label, long id)xmipp.viewer.scipion.ScipionMetaDatainline
getValueFromLabel(int index, int label)xmipp.viewer.scipion.ScipionMetaDatainline
getValueInt(int label, long id)xmipp.viewer.scipion.ScipionMetaDatainline
getValueLong(int label, long objId)xmipp.jni.MetaData
getValueObject(int label, long id)xmipp.viewer.scipion.ScipionMetaDatainline
getValueString(int label, long id)xmipp.viewer.scipion.ScipionMetaDatainline
xmipp::jni::MetaData.getValueString(int label, long objId, boolean fixPaths)xmipp.jni.MetaDatainline
haschildsxmipp.viewer.scipion.ScipionMetaDataprotected
hasIndex(String self)xmipp.viewer.scipion.ScipionMetaDatainlinestatic
hasRecalculateCTF()xmipp.jni.MetaDatainline
idcixmipp.viewer.scipion.ScipionMetaDataprotected
idsmapxmipp.viewer.scipion.ScipionMetaDataprotected
importObjects(MetaData md, long[] ids)xmipp.viewer.scipion.ScipionMetaDatainline
xmipp::jni::MetaData.importObjects(MetaData from, long ids[])xmipp.jni.MetaData
isChanged()xmipp.viewer.scipion.ScipionMetaDatainline
isColumnFormat()xmipp.viewer.scipion.ScipionMetaDatainline
isCTFMd()xmipp.viewer.scipion.ScipionMetaDatainline
isCtfParam(int label)xmipp.jni.MetaDatastatic
isImage(String label)xmipp.viewer.scipion.ScipionMetaDatainline
xmipp::jni::MetaData.isImage(int label)xmipp.jni.MetaDatastatic
isMetadata(int label)xmipp.jni.MetaDatastatic
isMetadataFile()xmipp.jni.MetaData
isMicrograph(int label)xmipp.jni.MetaDatastatic
isPathField(int label)xmipp.jni.MetaDatainlinestatic
isPlainPos(String file)xmipp.jni.MetaDatainlinestatic
isPSD(int label)xmipp.jni.MetaDatastatic
isScipionMetaData(String filename)xmipp.viewer.scipion.ScipionMetaDatainlinestatic
isStack(int label)xmipp.jni.MetaDatastatic
isTextFile(int label)xmipp.jni.MetaDatastatic
label2Str(int label)xmipp.jni.MetaDatastatic
LABEL_BOOLxmipp.jni.MetaDatastatic
LABEL_DOUBLExmipp.jni.MetaDatastatic
LABEL_INTxmipp.jni.MetaDatastatic
LABEL_NOTYPExmipp.jni.MetaDatastatic
LABEL_SIZETxmipp.jni.MetaDatastatic
LABEL_STRINGxmipp.jni.MetaDatastatic
LABEL_VECTOR_DOUBLExmipp.jni.MetaDatastatic
LABEL_VECTOR_SIZETxmipp.jni.MetaDatastatic
labelscountxmipp.viewer.scipion.ScipionMetaDataprotected
loadData()xmipp.viewer.scipion.ScipionMetaDatainline
loadValues(Connection c)xmipp.viewer.scipion.ScipionMetaDatainlineprotected
makeAbsPath(int label)xmipp.jni.MetaData
MD_APPENDxmipp.jni.MetaDatastatic
MD_OVERWRITExmipp.jni.MetaDatastatic
MetaData()xmipp.jni.MetaDatainline
MetaData(String filename)xmipp.jni.MetaDatainline
MICROGRAPH_BASIC_LABELSxmipp.jni.MetaDatastatic
operate(String operateStr)xmipp.jni.MetaData
overwrite(String src, String path, boolean[] selection)xmipp.viewer.scipion.ScipionMetaDatainline
overwriteBlock(String path, boolean[] selection)xmipp.viewer.scipion.ScipionMetaDatainline
parentxmipp.viewer.scipion.ScipionMetaDataprotected
preffixxmipp.viewer.scipion.ScipionMetaDataprotected
print()xmipp.viewer.scipion.ScipionMetaDatainline
propertiesxmipp.viewer.scipion.ScipionMetaDataprotected
putCTF(long id, EllipseCTF ellipseCTF)xmipp.jni.MetaDatainline
read(String filename)xmipp.jni.MetaDatainline
read_(String filename)xmipp.jni.MetaData
readPlain(String file, String columns)xmipp.jni.MetaData
removeCTF(long id)xmipp.jni.MetaDatainline
removeDisabled()xmipp.jni.MetaData
removeLabel(int label)xmipp.jni.MetaData
removeObject(long objId)xmipp.jni.MetaData
renameColumn(int oldLabel, int newLabel)xmipp.jni.MetaData
ScipionMetaData(String dbfile)xmipp.viewer.scipion.ScipionMetaDatainline
ScipionMetaData(String dbfile, String preffix)xmipp.viewer.scipion.ScipionMetaDatainline
selfxmipp.viewer.scipion.ScipionMetaDataprotected
setColumnFormat(boolean format)xmipp.jni.MetaData
setEnabled(boolean isenabled, long id)xmipp.viewer.scipion.ScipionMetaDatainline
setParent(ScipionMetaData md)xmipp.viewer.scipion.ScipionMetaDatainline
setRow(MDRow mdRow, long objId)xmipp.jni.MetaData
setValueBoolean(int label, boolean value, long objId)xmipp.jni.MetaData
setValueDouble(int label, double value, long id)xmipp.viewer.scipion.ScipionMetaDatainline
setValueInt(int label, int value, long id)xmipp.viewer.scipion.ScipionMetaDatainline
setValueLong(int label, long value, long objId)xmipp.jni.MetaData
setValueObject(int label, Object value, long id)xmipp.viewer.scipion.ScipionMetaDatainline
setValueString(int label, String value, long id)xmipp.viewer.scipion.ScipionMetaDatainline
size()xmipp.viewer.scipion.ScipionMetaDatainline
sort(int sortLabel, boolean ascending)xmipp.viewer.scipion.ScipionMetaDatainline
str2Label(String labelName)xmipp.jni.MetaDatastatic
unionAll(MetaData md)xmipp.viewer.scipion.ScipionMetaDatainline
write(String path)xmipp.viewer.scipion.ScipionMetaDatainline
writeBlock(String path)xmipp.viewer.scipion.ScipionMetaDatainline
writeMdToStack(String filename, boolean applyGeo, boolean wrap, int label)xmipp.jni.MetaData
writeWithException(String xmippFilename)xmipp.jni.MetaDatainline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData.html b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData.html deleted file mode 100644 index 7fe363eb..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData.html +++ /dev/null @@ -1,2913 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.scipion.ScipionMetaData Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Classes | -Public Member Functions | -Static Public Member Functions | -Protected Member Functions | -Protected Attributes | -List of all members
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xmipp.viewer.scipion.ScipionMetaData Class Reference
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-Inheritance diagram for xmipp.viewer.scipion.ScipionMetaData:
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-Collaboration diagram for xmipp.viewer.scipion.ScipionMetaData:
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-Classes

class  EMObject
 
class  EMObjectComparator
 
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-Public Member Functions

 ScipionMetaData (String dbfile)
 
 ScipionMetaData (String dbfile, String preffix)
 
void loadData ()
 
void setParent (ScipionMetaData md)
 
String [] getBlocks ()
 
String getBlock ()
 
List< EMObject > getEMObjects ()
 
EMObject getEMObject (long id)
 
synchronized String getValueFromLabel (int index, int label)
 
ColumnInfo getColumnInfo (int label)
 
ColumnInfo getColumnInfo (String labelName)
 
void add (EMObject emo)
 
long [] findObjects ()
 
int [] getActiveLabels ()
 
boolean containsLabel (int label)
 
boolean setEnabled (boolean isenabled, long id)
 
boolean getEnabled (long id)
 
List< ColumnInfo > getColumnsInfo ()
 
boolean isImage (String label)
 
boolean isColumnFormat ()
 
synchronized Object getValueObject (int label, long id)
 
int getValueInt (int label, long id)
 
double getValueDouble (int label, long id)
 
String getValueString (int label, long id)
 
int size ()
 
boolean setValueString (int label, String value, long id)
 
boolean setValueDouble (int label, double value, long id)
 
boolean setValueInt (int label, int value, long id)
 
boolean setValueObject (int label, Object value, long id)
 
void importObjects (MetaData md, long[] ids)
 
void unionAll (MetaData md)
 
void destroy ()
 
ScipionMetaData getParent ()
 
ScipionMetaData getChild (String block)
 
void write (String path)
 
void writeBlock (String path)
 
String getPreffix ()
 
void print ()
 
double [] getStatistics (boolean applyGeo)
 
void sort (int sortLabel, boolean ascending)
 
void overwrite (String src, String path, boolean[] selection) throws SQLException
 
void overwriteBlock (String path, boolean[] selection) throws SQLException
 
boolean isCTFMd ()
 
EllipseCTF getEllipseCTF (long id, int D)
 
String getCTFFile (long id)
 
String getPSDFile (long id)
 
String getPSDEnhanced (long id)
 
CTFDescription getCTFDescription (long id)
 
ColumnInfo getGeoMatrixColumn (ColumnInfo ci)
 
boolean containsGeometryInfo (String type)
 
int getEnabledCount ()
 
boolean isChanged ()
 
String getSetType ()
 
double [] getStatistics (boolean applyGeo, int label)
 
boolean containsMicrographsInfo ()
 
String getSelf ()
 
- Public Member Functions inherited from xmipp.jni.MetaData
 MetaData ()
 
synchronized native void destroy ()
 
native void clear ()
 
native void read_ (String filename)
 
final void read (String filename)
 
native int size ()
 
native void setColumnFormat (boolean format)
 
native void write (String filename)
 
native void writeBlock (String filename)
 
native void print ()
 
native boolean isColumnFormat ()
 
native boolean containsLabel (int label)
 
native boolean removeLabel (int label)
 
boolean containsGeometryInfo (String type)
 
boolean containsLabel (int[] labels)
 
boolean containsMicrographParticles ()
 
boolean containsMicrographsInfo ()
 
native int [] getActiveLabels ()
 
native boolean isMetadataFile ()
 
native void makeAbsPath (int label)
 
native int getValueInt (int label, long objId)
 
native long getValueLong (int label, long objId)
 
native double getValueDouble (int label, long objId)
 
native String getValueString (int label, long objId)
 
String getValueString (int label, long objId, boolean fixPaths)
 
String [] getRowValues (long objId)
 
native void getRow (MDRow mdRow, long objId)
 
native void setRow (MDRow mdRow, long objId)
 
MetaData getMetaDataRow ()
 
String fixPath (String value)
 
String fixPath (String value, String baseDir)
 
native boolean getValueBoolean (int label, long objId)
 
String getFilename ()
 
String getBlock ()
 
String getPath ()
 
String getBaseDir ()
 
native double [] getStatistics (boolean applyGeo, int label)
 
native double [] getColumnValues (int label)
 
boolean setEnabled (boolean value, long objId)
 
boolean getEnabled (long objId)
 
native boolean setValueInt (int label, int value, long objId)
 
native boolean setValueLong (int label, long value, long objId)
 
native boolean setValueDouble (int label, double value, long objId)
 
native boolean setValueString (int label, String value, long objId)
 
native boolean setValueBoolean (int label, boolean value, long objId)
 
native long [] findObjects ()
 
native void sort (int sortLabel, boolean ascending)
 
native void importObjects (MetaData from, long ids[])
 
native long firstObject ()
 
native long addObject ()
 
native boolean removeObject (long objId)
 
native void removeDisabled ()
 
native void addLabel (int label)
 
native void renameColumn (int oldLabel, int newLabel)
 
native void getStatsImages (ImageGeneric imageAvg, ImageGeneric imageStd, boolean applyGeo, boolean wrap, int label)
 
native void writeMdToStack (String filename, boolean applyGeo, boolean wrap, int label)
 
native void getPCAbasis (ImageGeneric basis, int label)
 
native void computeFourierStatistics (MetaData mdIn, int label)
 
native void unionAll (MetaData mdIn)
 
native void fillConstant (int label, String value)
 
native void fillRandom (int label, String mode, double op1, double op2)
 
native void fillLinear (int label, double start, double step)
 
native void enableDebug ()
 
 MetaData (String filename)
 
native void readPlain (String file, String columns)
 
native void operate (String operateStr)
 
native double getColumnMin (int column)
 
native double getColumnMax (int column)
 
boolean isCTFMd ()
 
String getCTFFile (long id)
 
EllipseCTF getEllipseCTF (long id)
 
EllipseCTF getEllipseCTF (long id, int D)
 
String getPSDFile (long id)
 
String getPSDEnhanced (long id)
 
CTFDescription getCTFDescription (long id)
 
boolean hasRecalculateCTF ()
 
void removeCTF (long id)
 
boolean containsCTF (long id)
 
void putCTF (long id, EllipseCTF ellipseCTF)
 
void writeWithException (String xmippFilename) throws IOException
 
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-Static Public Member Functions

static boolean hasIndex (String self)
 
static String getTypeMapping (int type)
 
static int getTypeMapping (String type)
 
static Connection getConnection (String filename) throws ClassNotFoundException, SQLException
 
static Connection getConnectionReadOnly (String filename) throws ClassNotFoundException, SQLException
 
static boolean isScipionMetaData (String filename)
 
- Static Public Member Functions inherited from xmipp.jni.MetaData
static boolean containsBlock (String file, String block)
 
static native String label2Str (int label)
 
static native int str2Label (String labelName)
 
static String getLabelName (int label)
 
static native String [] getBlocksInMetaDataFile (String filename)
 
static native int getLabelType (int label)
 
static Class getClassForType (int type)
 
static Class getLabelClass (int label)
 
static String getLabelTypeString (int labelType)
 
static native String getLabelComment (int label)
 
static native boolean isTextFile (int label)
 
static native boolean isMetadata (int label)
 
static native boolean isCtfParam (int label)
 
static native boolean isImage (int label)
 
static native boolean isStack (int label)
 
static native boolean isMicrograph (int label)
 
static native boolean isPSD (int label)
 
static boolean isPathField (int label)
 
static boolean isPlainPos (String file)
 
- - - - - - -

-Protected Member Functions

void loadValues (Connection c)
 
- Protected Member Functions inherited from xmipp.jni.MetaData
void finalize () throws Throwable
 
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-Protected Attributes

List< ColumnInfo > columns
 
List< EMObject > emobjects
 
ScipionMetaData parent
 
boolean haschilds
 
int labelscount = 0
 
ColumnInfo idci
 
String preffix = ""
 
String [] blocks
 
int enableds
 
Boolean checkTmp
 
HashMap< String, String > properties
 
HashMap< Long, EMObject > idsmap
 
String self
 
- Protected Attributes inherited from xmipp.jni.MetaData
String filename
 
HashMap< Long, EllipseCTF > ctfs = new HashMap<Long, EllipseCTF>()
 
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-Additional Inherited Members

- Static Public Attributes inherited from xmipp.jni.MetaData
static final int LABEL_NOTYPE = -1
 
static final int LABEL_INT = 0
 
static final int LABEL_BOOL = 1
 
static final int LABEL_DOUBLE = 2
 
static final int LABEL_STRING = 3
 
static final int LABEL_VECTOR_DOUBLE = 4
 
static final int LABEL_SIZET = 5
 
static final int LABEL_VECTOR_SIZET = 6
 
static final String FILL_CONSTANT = "constant"
 
static final String FILL_LINEAR = "linear"
 
static final String FILL_RAND_UNIFORM = "random uniform"
 
static final String FILL_RAND_GAUSSIAN = "random gaussian"
 
static final int GEOMETRY_LABELS []
 
static final int GEOMETRY_RELION_LABELS [] = { MDLabel.RLN_ORIENT_ORIGIN_X, MDLabel.RLN_ORIENT_ORIGIN_Y, MDLabel.RLN_ORIENT_PSI, MDLabel.RLN_ORIENT_FLIP}
 
static final int MICROGRAPH_BASIC_LABELS []
 
static final int MD_OVERWRITE = 0
 
static final int MD_APPEND = 1
 
-

Detailed Description

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Author
airen
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Definition at line 37 of file ScipionMetaData.java.

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Constructor & Destructor Documentation

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◆ ScipionMetaData() [1/2]

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xmipp.viewer.scipion.ScipionMetaData.ScipionMetaData (String dbfile)
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Definition at line 54 of file ScipionMetaData.java.

-
54  {
55 
56  this.filename = dbfile;
57  columns = new ArrayList<ColumnInfo>();
58  emobjects = new ArrayList<EMObject>();
59  loadData();
60  if (isClassificationMd()) {
61  String preffix;
62  haschilds = true;
63  List<String> childblocks = new ArrayList<String>();
64  for (EMObject emo : emobjects) {
65  if((Integer)emo.getValue("_size") != 0)
66  {
67  preffix = String.format("Class%03d_", emo.getId());
68  emo.childmd = new ScipionMetaData(dbfile, preffix);
69  emo.childmd.setParent(this);
70  childblocks.add(emo.childmd.getBlock());
71  }
72  }
73  blocks = new String[childblocks.size() + 1];
74  blocks[0] = getBlock();
75  for (int i = 0; i < childblocks.size(); i++) {
76  blocks[i + 1] = childblocks.get(i);
77 
78  }
79  }
80  else
81  blocks = new String[]{getBlock()};
82 
83  }
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◆ ScipionMetaData() [2/2]

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xmipp.viewer.scipion.ScipionMetaData.ScipionMetaData (String dbfile,
String preffix 
)
- 		-inline
-
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Definition at line 85 of file ScipionMetaData.java.

-
85  {
86 
87  this.filename = dbfile;
88  columns = new ArrayList<ColumnInfo>();
89  emobjects = new ArrayList<EMObject>();
90  this.preffix = preffix;
91  loadData();
92  blocks = new String[]{getBlock()};
93 
94  }
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Member Function Documentation

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◆ add()

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void xmipp.viewer.scipion.ScipionMetaData.add (EMObject emo)
- 		-inline
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Definition at line 295 of file ScipionMetaData.java.

-
295  {
296  emobjects.add(emo);
297  if (emo.childmd != null) {
298  haschilds = true;
299  }
300  }
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◆ containsGeometryInfo()

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boolean xmipp.viewer.scipion.ScipionMetaData.containsGeometryInfo (String type)
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-
- -

Definition at line 793 of file ScipionMetaData.java.

-
793  {
794  String column = "_alignment";
795  String value = null;
796  if(properties == null)
797  {
798  if (parent == null)
799  return false;
800  else
801  for(EMObject emo: parent.emobjects)
802  if(preffix.contains(emo.getId().toString()))
803  value = (String)emo.getValue(column);
804  }
805  else
806  value = properties.get(column);
807 
808  if (value == null)
809  return false;
810 
811  return value.equals(type);
812  }
xmipp.viewer.scipion.ScipionMetaData.properties
HashMap< String, String > properties
Definition: ScipionMetaData.java:49
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-
-
- -

◆ containsLabel()

- -
-
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boolean xmipp.viewer.scipion.ScipionMetaData.containsLabel (int label)
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-
- -

Definition at line 323 of file ScipionMetaData.java.

-
323  {
324  for (int i = 0; i < columns.size(); i++) {
325  if (columns.get(i).label == label) {
326  return true;
327  }
328  }
329  return false;
330  }
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◆ containsMicrographsInfo()

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boolean xmipp.viewer.scipion.ScipionMetaData.containsMicrographsInfo ()
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-
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Definition at line 1216 of file ScipionMetaData.java.

-
1217  {
1218  return self.equals("Micrograph") || self.equals("Movie");
1219  }
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-
- -

◆ destroy()

- -
-
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void xmipp.viewer.scipion.ScipionMetaData.destroy ()
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-
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Definition at line 464 of file ScipionMetaData.java.

-
464  {
465  }
-
-
- -

◆ findObjects()

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long [] xmipp.viewer.scipion.ScipionMetaData.findObjects ()
- 		-inline
-
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Definition at line 305 of file ScipionMetaData.java.

-
305  {
306  long[] ids = new long[emobjects.size()];
307  for (int i = 0; i < ids.length; i++) {
308  ids[i] = emobjects.get(i).getId();
309  }
310  return ids;
311 
312  }
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◆ getActiveLabels()

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int [] xmipp.viewer.scipion.ScipionMetaData.getActiveLabels ()
- 		-inline
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- -

Definition at line 314 of file ScipionMetaData.java.

-
314  {
315  int[] labels = new int[columns.size()];
316  for (int i = 0; i < labels.length; i++) {
317  labels[i] = columns.get(i).label;
318  }
319  return labels;
320  }
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◆ getBlock()

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String xmipp.viewer.scipion.ScipionMetaData.getBlock ()
- 		-inline
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Definition at line 241 of file ScipionMetaData.java.

-
241  {
242  String setType = getSetType();
243  if(setType.isEmpty())
244  setType = "noname";
245  String block = setType.replace("SetOf", "");
246 
247  if (preffix == null) {
248  return block;
249  }
250  return preffix + block;
251  }
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◆ getBlocks()

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-
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String [] xmipp.viewer.scipion.ScipionMetaData.getBlocks ()
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- -

Definition at line 235 of file ScipionMetaData.java.

-
235  {
236  return blocks;
237 
238  }
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◆ getChild()

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ScipionMetaData xmipp.viewer.scipion.ScipionMetaData.getChild (String block)
- 		-inline
-
- -

Definition at line 471 of file ScipionMetaData.java.

-
471  {
472  if (!haschilds) {
473  return null;
474  }
475  for (EMObject emo : emobjects) {
476  if (emo.childmd != null && emo.childmd.getBlock().equals(block))//from parent to child
477  {
478  return emo.childmd;
479  }
480  }
481  return null;
482  }
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ColumnInfo xmipp.viewer.scipion.ScipionMetaData.getColumnInfo (int label)
- 		-inline
-
- -

Definition at line 275 of file ScipionMetaData.java.

-
275  {
276 
277  for (ColumnInfo ci : columns) {
278  if (ci.label == label) {
279  return ci;
280  }
281  }
282  return null;
283  }
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ColumnInfo xmipp.viewer.scipion.ScipionMetaData.getColumnInfo (String labelName)
- 		-inline
-
- -

Definition at line 285 of file ScipionMetaData.java.

-
285  {
286  for (ColumnInfo ci : columns) {
287  if (ci.labelName.equals(labelName)) {
288  return ci;
289  }
290  }
291  return null;
292  }
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◆ getColumnsInfo()

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List<ColumnInfo> xmipp.viewer.scipion.ScipionMetaData.getColumnsInfo ()
- 		-inline
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- -

Definition at line 346 of file ScipionMetaData.java.

-
346  {
347  return columns;
348  }
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◆ getConnection()

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static Connection xmipp.viewer.scipion.ScipionMetaData.getConnection (String filename) throws ClassNotFoundException, SQLException
- 		-inlinestatic
-
- -

Definition at line 1058 of file ScipionMetaData.java.

-
1059  {
1060  return getConnection(filename, null);
1061  }
-
xmipp.viewer.scipion.ScipionMetaData.getConnection
static Connection getConnection(String filename)
Definition: ScipionMetaData.java:1058
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◆ getConnectionReadOnly()

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static Connection xmipp.viewer.scipion.ScipionMetaData.getConnectionReadOnly (String filename) throws ClassNotFoundException, SQLException
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-
- -

Definition at line 1062 of file ScipionMetaData.java.

-
1063  {
1064 
1065  SQLiteConfig config = new SQLiteConfig();
1066  config.setReadOnly(true);
1067  Connection c = getConnection(filename, config.toProperties());
1068  c.setReadOnly(true);
1069  return c;
1070  }
-
xmipp.viewer.scipion.ScipionMetaData.getConnection
static Connection getConnection(String filename)
Definition: ScipionMetaData.java:1058
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◆ getCTFDescription()

- -
-
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CTFDescription xmipp.viewer.scipion.ScipionMetaData.getCTFDescription (long id)
- 		-inline
-
- -

Definition at line 770 of file ScipionMetaData.java.

-
771  {
772  try {
773  MetaData md = getEllipseCTF(id).getCTFMd();
774  String file = "ctf.xmd";
775  md.write(file);
776  return new CTFDescription(file);
777  } catch (Exception ex) {
778  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
779  throw new IllegalArgumentException(ex);
780  }
781  }
xmipp.jni.MetaData.write
native void write(String filename)
- -
xmipp.viewer.scipion.ScipionMetaData.getEllipseCTF
EllipseCTF getEllipseCTF(long id, int D)
Definition: ScipionMetaData.java:718
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-
- -

◆ getCTFFile()

- -
-
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String xmipp.viewer.scipion.ScipionMetaData.getCTFFile (long id)
- 		-inline
-
- -

Definition at line 749 of file ScipionMetaData.java.

-
749  {
750  String psde = getPSDEnhanced(id);
751  if(psde != null)
752  {
753  String ctf = psde.replace("_enhanced_psd.xmp", ".ctfparam");
754  if(new File(ctf).exists())
755  return ctf;
756  }
757  return null;
758  }
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-
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◆ getEllipseCTF()

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EllipseCTF xmipp.viewer.scipion.ScipionMetaData.getEllipseCTF (long id,
int D 
)
- 		-inline
-
- -

Definition at line 718 of file ScipionMetaData.java.

-
718  {
719  if (!isCTFMd()) {
720  return null;
721  }
722  try {
723  EMObject emo = getEMObject(id);
724 
725  double Q0, Cs = 0, Ts = 0, kV = 0, defU = 0, defV = 0, defAngle;
726 
727  Q0 = emo.getValueDouble("_micObj._acquisition._amplitudeContrast");
728  Cs = emo.getValueDouble("_micObj._acquisition._sphericalAberration");
729  Ts = emo.getValueDouble("_micObj._samplingRate");
730  kV = emo.getValueDouble("_micObj._acquisition._voltage");
731 
732  defU = emo.getValueDouble("_defocusU");
733  defV = emo.getValueDouble("_defocusV");
734  defAngle = emo.getValueDouble("_defocusAngle");
735  Double downsampleFactor = emo.getValueDouble("_xmipp_CtfDownsampleFactor");
736  if(downsampleFactor == null)
737  downsampleFactor = 1.;
738  //read params from sqlite
739 
740  return new EllipseCTF(id, Q0, Cs, downsampleFactor, Ts, kV, defU, defV, defAngle, D);
741  } catch (Exception ex) {
742  IJ.error(ex.getMessage());
743  throw new IllegalArgumentException(ex);
744  }
745 
746  }
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-
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◆ getEMObject()

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EMObject xmipp.viewer.scipion.ScipionMetaData.getEMObject (long id)
- 		-inline
-
- -

Definition at line 259 of file ScipionMetaData.java.

-
259  {
260  return idsmap.get(id);
261  }
xmipp.viewer.scipion.ScipionMetaData.idsmap
HashMap< Long, EMObject > idsmap
Definition: ScipionMetaData.java:50
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-
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◆ getEMObjects()

- -
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List<EMObject> xmipp.viewer.scipion.ScipionMetaData.getEMObjects ()
- 		-inline
-
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Definition at line 255 of file ScipionMetaData.java.

-
255  {
256  return emobjects;
257  }
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-
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Definition at line 340 of file ScipionMetaData.java.

-
340  {
341  EMObject emo = getEMObject(id);
342  return emo.isEnabled();
343 
344  }
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◆ getEnabledCount()

- -
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int xmipp.viewer.scipion.ScipionMetaData.getEnabledCount ()
- 		-inline
-
- -

Definition at line 816 of file ScipionMetaData.java.

-
817  {
818  return enableds;
819  }
-
-
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- -

◆ getGeoMatrixColumn()

- -
-
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- - - - - - - - -
ColumnInfo xmipp.viewer.scipion.ScipionMetaData.getGeoMatrixColumn (ColumnInfo ci)
- 		-inline
-
- -

Definition at line 783 of file ScipionMetaData.java.

-
784  {
785  String column = "_transform._matrix";
786  if(ci.labelName.contains("."))
787  column = ci.labelName.substring(0, ci.labelName.lastIndexOf(".") + 1) + column;
788  return getColumnInfo(column);
789  }
-
-
-
- -

◆ getParent()

- -
-
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ScipionMetaData xmipp.viewer.scipion.ScipionMetaData.getParent ()
- 		-inline
-
- -

Definition at line 467 of file ScipionMetaData.java.

-
467  {
468  return parent;
469  }
-
-
-
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◆ getPreffix()

- -
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String xmipp.viewer.scipion.ScipionMetaData.getPreffix ()
- 		-inline
-
- -

Definition at line 606 of file ScipionMetaData.java.

-
606  {
607  return preffix;
608  }
-
-
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◆ getPSDEnhanced()

- -
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String xmipp.viewer.scipion.ScipionMetaData.getPSDEnhanced (long id)
- 		-inline
-
- -

Definition at line 766 of file ScipionMetaData.java.

-
766  {
767  return (String) getEMObject(id).getValue("_xmipp_enhanced_psd");
768  }
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-
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◆ getPSDFile()

- -
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String xmipp.viewer.scipion.ScipionMetaData.getPSDFile (long id)
- 		-inline
-
- -

Definition at line 761 of file ScipionMetaData.java.

-
761  {
762  return (String) getEMObject(id).getValue("_psdFile");
763  }
-
-
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◆ getSelf()

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- - - - - - - -
String xmipp.viewer.scipion.ScipionMetaData.getSelf ()
- 		-inline
-
- -

Definition at line 1221 of file ScipionMetaData.java.

-
1222  {
1223  // TODO Auto-generated method stub
1224  return self;
1225  }
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-
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◆ getSetType()

- -
-
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String xmipp.viewer.scipion.ScipionMetaData.getSetType ()
- 		-inline
-
- -

Definition at line 1175 of file ScipionMetaData.java.

-
1175  {
1176  if(properties == null)
1177  return self + "s";//child md from classes set
1178  if(properties.isEmpty())
1179  return "";
1180  return properties.get("self");
1181  }
xmipp.viewer.scipion.ScipionMetaData.properties
HashMap< String, String > properties
Definition: ScipionMetaData.java:49
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-
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double [] xmipp.viewer.scipion.ScipionMetaData.getStatistics (boolean applyGeo)
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Definition at line 614 of file ScipionMetaData.java.

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614  {
615  return null;
616  }
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double [] xmipp.viewer.scipion.ScipionMetaData.getStatistics (boolean applyGeo,
int label 
)
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Definition at line 1183 of file ScipionMetaData.java.

-
1184  {
1185  double[] minMax = new double [2];
1186  ColumnInfo ci = getColumnInfo(label);
1187  if(!ci.render)
1188  throw new IllegalArgumentException("No images to process");
1189  String imageFn, mddir = this.getBaseDir();
1190  ImagePlus imp;
1191  minMax[0] = Double.MAX_VALUE;
1192  minMax[1] = -Double.MAX_VALUE;
1193  double aux;
1194  for (EMObject emo: emobjects)
1195  {
1196  imageFn = emo.getValueString(ci);
1197  if(imageFn != null)
1198  {
1199  imageFn = Filename.findImagePath(imageFn, mddir, true);
1200  if (imageFn != null && Filename.exists(imageFn))
1201  {
1202  imp = new ImagePlusFromFile(imageFn).getImagePlus();
1203  aux = imp.getProcessor().getMin();
1204  if(aux < minMax[0])
1205  minMax[0] = aux;
1206  aux = imp.getProcessor().getMax();
1207  if(aux > minMax[1])
1208  minMax[1] = aux;
1209  }
1210  }
1211  }
1212 
1213  return minMax;
1214  }
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xmipp.jni.MetaData.getBaseDir
String getBaseDir()
Definition: MetaData.java:430
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static String xmipp.viewer.scipion.ScipionMetaData.getTypeMapping (int type)
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Definition at line 581 of file ScipionMetaData.java.

-
581  {
582  if (type == MetaData.LABEL_INT) {
583  return "Integer";
584  }
585  if (type == MetaData.LABEL_DOUBLE) {
586  return "Float";
587  }
588  return "String";
589  }
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static int xmipp.viewer.scipion.ScipionMetaData.getTypeMapping (String type)
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Definition at line 591 of file ScipionMetaData.java.

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591  {
592  if (type.equals("Integer")) {
593  return MetaData.LABEL_INT;
594  }
595  if (type.equals("Float")) {
596  return MetaData.LABEL_DOUBLE;
597  }
598  if(type.equals("Boolean"))
599  return MetaData.LABEL_INT;
600 
601  if(type.equals("String") || type.equals("Matrix") || type.equals("CsvList"))
602  return MetaData.LABEL_STRING;
603  return -1;
604  }
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◆ getValueDouble()

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double xmipp.viewer.scipion.ScipionMetaData.getValueDouble (int label,
long id 
)
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Definition at line 405 of file ScipionMetaData.java.

-
405  {
406  Object value = getValueObject(label, id);
407  if (value != null) {
408  return (Float) value;
409  }
410  return Double.NaN;
411  }
xmipp.viewer.scipion.ScipionMetaData.getValueObject
synchronized Object getValueObject(int label, long id)
Definition: ScipionMetaData.java:388
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◆ getValueFromLabel()

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synchronized String xmipp.viewer.scipion.ScipionMetaData.getValueFromLabel (int index,
int label 
)
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Definition at line 263 of file ScipionMetaData.java.

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263  {
264  if (index >= size()) {
265  return null;
266  }
267  EMObject emo = emobjects.get(index);
268  Object value = emo.getValue(getColumnInfo(label));
269  if (value == null) {
270  return null;
271  }
272  return value.toString();
273  }
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◆ getValueInt()

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int xmipp.viewer.scipion.ScipionMetaData.getValueInt (int label,
long id 
)
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Definition at line 397 of file ScipionMetaData.java.

-
397  {
398  Object value = getValueObject(label, id);
399  if (value != null) {
400  return (Integer) value;
401  }
402  return Integer.MIN_VALUE;
403  }
xmipp.viewer.scipion.ScipionMetaData.getValueObject
synchronized Object getValueObject(int label, long id)
Definition: ScipionMetaData.java:388
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◆ getValueObject()

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synchronized Object xmipp.viewer.scipion.ScipionMetaData.getValueObject (int label,
long id 
)
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Definition at line 388 of file ScipionMetaData.java.

-
388  {
389  EMObject emo = getEMObject(id);
390  ColumnInfo c = getColumnInfo(label);
391  if (c != null) {
392  return emo.getValue(c);
393  }
394  return null;
395  }
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◆ getValueString()

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String xmipp.viewer.scipion.ScipionMetaData.getValueString (int label,
long id 
)
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Definition at line 413 of file ScipionMetaData.java.

-
413  {
414  Object value = getValueObject(label, id);
415  if (value == null)
416  return "";
417  if (value instanceof Float)
418  return String.format("%.2f", value);
419  return value.toString();
420  }
xmipp.viewer.scipion.ScipionMetaData.getValueObject
synchronized Object getValueObject(int label, long id)
Definition: ScipionMetaData.java:388
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◆ hasIndex()

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static boolean xmipp.viewer.scipion.ScipionMetaData.hasIndex (String self)
- 		-inlinestatic
-
- -

Definition at line 377 of file ScipionMetaData.java.

-
377  {
378  if (self.equals("Particle")) {
379  return true;
380  }
381  return false;
382  }
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◆ importObjects()

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void xmipp.viewer.scipion.ScipionMetaData.importObjects (MetaData md,
long [] ids 
)
- 		-inline
-
- -

Definition at line 451 of file ScipionMetaData.java.

-
451  {
452  ScipionMetaData smd = (ScipionMetaData) md;
453  EMObject emo;
454  for (int i = 0; i < ids.length; i++) {
455  emo = smd.getEMObject(ids[i]);
456  add(emo);
457  }
458  }
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◆ isChanged()

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boolean xmipp.viewer.scipion.ScipionMetaData.isChanged ()
- 		-inline
-
- -

Definition at line 896 of file ScipionMetaData.java.

-
897  {
898 
899  for(EMObject emo: emobjects)
900  if(emo.changed)
901  return true;
902  return false;
903  }
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◆ isColumnFormat()

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boolean xmipp.viewer.scipion.ScipionMetaData.isColumnFormat ()
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-
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Definition at line 384 of file ScipionMetaData.java.

-
384  {
385  return true;
386  }
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◆ isCTFMd()

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boolean xmipp.viewer.scipion.ScipionMetaData.isCTFMd ()
- 		-inline
-
- -

Definition at line 713 of file ScipionMetaData.java.

-
713  {
714  return getSetType().equals("SetOfCTF");
715  }
-
-
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◆ isImage()

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boolean xmipp.viewer.scipion.ScipionMetaData.isImage (String label)
- 		-inline
-
- -

Definition at line 350 of file ScipionMetaData.java.

-
350  {
351  String setType = getSetType();
352  if (setType == null)
353  return false;
354  if(label.contains("_filename"))
355  {
356  String indexLabel = label.replace("_filename", "_index");
357  if(getColumnInfo(indexLabel) != null)
358  return true;
359  }
360  if (setType.equals("SetOfMicrographs") || setType.equals("SetOfParticles") || setType.equals("SetOfVolumes")) {
361  if (label.equals("_filename")) {
362  return true;
363  }
364  } else if (setType.equals("SetOfCTF")) {
365  if (label.equals("_micObj._filename") || label.equals("_psdFile") || label.equals("_xmipp_enhanced_psd")
366  ||label.equals("_xmipp_ctfmodel_quadrant") ||label.equals("_xmipp_ctfmodel_halfplane")) {
367  return true;
368  }
369  } else if (setType.equals("SetOfClasses2D") || setType.equals("SetOfClasses3D")) {
370  if (label.equals("_representative._filename")) {
371  return true;
372  }
373  }
374  return false;
375  }
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◆ isScipionMetaData()

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static boolean xmipp.viewer.scipion.ScipionMetaData.isScipionMetaData (String filename)
- 		-inlinestatic
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Definition at line 1227 of file ScipionMetaData.java.

-
1228  {
1229  if (!filename.endsWith(".sqlite") && !filename.endsWith(".db"))
1230  return false;
1231  //Now it will check if contains the required tables to be read as scipion metadata, otherwise will be read as xmipp metadata
1232  Connection c;
1233  Statement stmt;
1234  ResultSet rs;
1235  boolean result = true;
1236  try
1237  {
1238 // c = getConnection(filename);
1239  c = getConnectionReadOnly(filename);
1240  stmt = c.createStatement();
1241  String query = "SELECT name FROM sqlite_master WHERE type='table' AND name='Classes';";
1242  rs = stmt.executeQuery(query);
1243  boolean exists = rs.next();
1244  if (!exists)
1245  result = false;
1246  else
1247  {
1248  query = "SELECT name FROM sqlite_master WHERE type='table' AND name='Objects';";
1249  rs = stmt.executeQuery(query);
1250  exists = rs.next();
1251  if (!exists)
1252  result = false;
1253  }
1254  rs.close();
1255  stmt.close();
1256  c.close();
1257  }
1258  catch (Exception e)
1259  {
1260  // TODO Auto-generated catch block
1261  e.printStackTrace();
1262  return false;
1263  }
1264 
1265  return result;
1266  }
-
xmipp.viewer.scipion.ScipionMetaData.getConnectionReadOnly
static Connection getConnectionReadOnly(String filename)
Definition: ScipionMetaData.java:1062
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◆ loadData()

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void xmipp.viewer.scipion.ScipionMetaData.loadData ()
- 		-inline
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- -

Definition at line 96 of file ScipionMetaData.java.

-
96  {
97  Connection c = null;
98  Statement stmt = null;
99  try {
100  String query;
101 // c = etConnection(filename);
102  c = getConnectionReadOnly(filename);
103  stmt = c.createStatement();
104  ResultSet rs;
105  if (preffix == null || preffix.equals(""))
106  {
107  query = "SELECT name FROM sqlite_master WHERE type='table' AND name='Properties';";
108  rs = stmt.executeQuery(query);
109  boolean exists = rs.next();
110  if(exists)
111  {
112  properties = new HashMap<String, String>();
113  String key, value;
114  query = "SELECT * FROM Properties;";
115  rs = stmt.executeQuery(query);
116 
117  while (rs.next()) {
118  key = rs.getString("key");
119  value = rs.getString("value");
120  properties.put(key, value);
121  }
122  }
123  }
124  String name, alias, clsname;
125  int type;
126  boolean allowRender;
127  ColumnInfo ci;
128 
129  name = alias = "enabled";
130  labelscount++;
131  enabledci = new ColumnInfo(labelscount, name, alias, MetaData.LABEL_INT, false, true);
132  columns.add(enabledci);
133 
134  name = alias = "id";
135  labelscount++;
136  idci = new ColumnInfo(labelscount, name, alias, MetaData.LABEL_INT, false, false);
137  columns.add(idci);
138 
139  name = alias = "label";
140  labelscount++;
141  labelci = new ColumnInfo(labelscount, name, alias, MetaData.LABEL_STRING, false, false);
142  columns.add(labelci);
143 
144  name = alias = "comment";
145  labelscount++;
146  commentci = new ColumnInfo(labelscount, name, alias, MetaData.LABEL_STRING, false, false);
147  columns.add(commentci);
148 
149 
150 
151  loadValues(c);
152 
153 
154  query = String.format("SELECT * FROM %sClasses;", preffix);
155  rs = stmt.executeQuery(query);
156  while (rs.next()) {
157  name = rs.getString("label_property");
158  alias = rs.getString("column_name");
159  clsname = rs.getString("class_name");
160  if(name.equals("self"))
161  {
162  self = clsname;
163  continue;
164  }
165 
166  type = getTypeMapping(clsname);
167  if(type == -1)
168  continue;//complex object is empty, unless is matrix
169  labelscount++;
170  allowRender = isImage(name);
171  ci = new ColumnInfo(labelscount, name, alias, type, allowRender, false);
172  columns.add(ci);
173  }
174 
175 
176  rs.close();
177  stmt.close();
178  c.close();
179  StopWatch.getInstance().printElapsedTime("loaded data");
180  } catch (Exception e) {
181  throw new IllegalArgumentException(e);
182 
183 
184  }
185  }
- - -
xmipp.viewer.scipion.ScipionMetaData.properties
HashMap< String, String > properties
Definition: ScipionMetaData.java:49
- -
xmipp.viewer.scipion.ScipionMetaData.getTypeMapping
static String getTypeMapping(int type)
Definition: ScipionMetaData.java:581
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xmipp.viewer.scipion.ScipionMetaData.getConnectionReadOnly
static Connection getConnectionReadOnly(String filename)
Definition: ScipionMetaData.java:1062
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◆ loadValues()

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void xmipp.viewer.scipion.ScipionMetaData.loadValues (Connection c)
- 		-inlineprotected
-
- -

Definition at line 187 of file ScipionMetaData.java.

-
188  {
189  try {
190  idsmap = new HashMap<Long, EMObject>();
191  Statement stmt = c.createStatement();
192  ResultSet rs;
193  EMObject emo;
194  String alias;
195 
196  String query = String.format("SELECT id, label, comment, enabled FROM %sObjects;", preffix);
197  rs = stmt.executeQuery(query);
198  Object value;
199  int index = 0;
200  while (rs.next()) {
201  emo = new EMObject(index, this);
202  for (ColumnInfo column : columns) {
203  alias = column.comment;
204  switch (column.type) {
205 
206  case MetaData.LABEL_INT:
207  value = rs.getInt(alias);
208  break;
209  case MetaData.LABEL_DOUBLE:
210  value = rs.getFloat(alias);
211  break;
212  default:
213  value = rs.getString(alias);
214  }
215  emo.values.put(column, value);
216  }
217  emobjects.add(emo);
218  idsmap.put(emo.getId(), emo);
219  if(emo.isEnabled())
220  enableds ++;
221  else
222  emo.changed = true;
223  index ++;
224  }
225  } catch (SQLException ex) {
226  throw new IllegalArgumentException(ex);
227 
228  }
229  }
- -
xmipp.viewer.scipion.ScipionMetaData.idsmap
HashMap< Long, EMObject > idsmap
Definition: ScipionMetaData.java:50
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◆ overwrite()

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void xmipp.viewer.scipion.ScipionMetaData.overwrite (String src,
String path,
boolean [] selection 
) throws SQLException
- 		-inline
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Definition at line 634 of file ScipionMetaData.java.

-
634  {
635  try {
636  XmippUtil.copyFile(src, path);
637  // Do not overwrite the parent. This looses the selection. issue #498
638  // if (parent != null) {
639  // parent.overwrite(src, path, null);//this will write parent and siblings
640  // return;
641  // }
642  overwriteBlock(path, selection);
643  if (haschilds) {
644  for (EMObject emo : emobjects) {
645  if (emo.childmd != null) {
646  emo.childmd.overwriteBlock(path, null);
647  }
648  }
649  }
650  } catch (IOException ex) {
651  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
652  }
653 
654  }
- - -
xmipp.viewer.scipion.ScipionMetaData.overwriteBlock
void overwriteBlock(String path, boolean[] selection)
Definition: ScipionMetaData.java:656
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◆ overwriteBlock()

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void xmipp.viewer.scipion.ScipionMetaData.overwriteBlock (String path,
boolean [] selection 
) throws SQLException
- 		-inline
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Definition at line 656 of file ScipionMetaData.java.

-
656  {//overwrites enabled column in existing sqlite objects table
657  Connection c = null;
658  PreparedStatement stmt = null;
659  try {
660 
661 // Class.forName("org.sqlite.JDBC");
662 // c = DriverManager.getConnection("jdbc:sqlite:" + path);
663  c = getConnection(path);
664 
665  c.setAutoCommit(false);
666  stmt = c.prepareStatement(String.format("UPDATE %sObjects SET %s=?, %s=?, %s=? WHERE id=?;", preffix, enabledci.labelName, labelci.labelName, commentci.labelName));
667  boolean enabled;
668  for (EMObject emo : emobjects)
669  {
670  if(selection != null)
671  {
672  enabled = selection[emo.index];
673  stmt.setInt(1, enabled ? 1 : 0);
674  stmt.setString(2, emo.getLabel());
675  stmt.setString(3, emo.getComment());
676  stmt.setInt(4, emo.getId().intValue());
677  stmt.executeUpdate();
678 
679  }
680  else if (emo.changed) {
681  stmt.setInt(1, emo.isEnabled() ? 1 : 0);
682  stmt.setString(2, emo.getLabel());
683  stmt.setString(3, emo.getComment());
684  stmt.setInt(4, emo.getId().intValue());
685  stmt.executeUpdate();
686 
687  }
688  }
689  c.commit();
690 
691  }
692  catch (Exception e) {
693  e.printStackTrace();
694  if (c != null)
695  try {
696  System.err.print("Transaction is being rolled back");
697  c.rollback();
698  }
699  catch(SQLException excep) {
700  excep.printStackTrace();
701  }
702 
703  }
704  finally {
705  if (stmt != null)
706  stmt.close();
707 
708  c.close();
709  }
710  }
- -
xmipp.viewer.scipion.ScipionMetaData.getConnection
static Connection getConnection(String filename)
Definition: ScipionMetaData.java:1058
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◆ print()

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void xmipp.viewer.scipion.ScipionMetaData.print ()
- 		-inline
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Definition at line 610 of file ScipionMetaData.java.

-
610  {
611  System.out.println(toString());
612  }
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◆ setEnabled()

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boolean xmipp.viewer.scipion.ScipionMetaData.setEnabled (boolean isenabled,
long id 
)
- 		-inline
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Definition at line 333 of file ScipionMetaData.java.

-
333  {
334  EMObject emo = getEMObject(id);
335  emo.setEnabled(isenabled);
336  return true;
337  }
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◆ setParent()

- -
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void xmipp.viewer.scipion.ScipionMetaData.setParent (ScipionMetaData md)
- 		-inline
-
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Definition at line 231 of file ScipionMetaData.java.

-
231  {
232  this.parent = md;
233  }
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◆ setValueDouble()

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boolean xmipp.viewer.scipion.ScipionMetaData.setValueDouble (int label,
double value,
long id 
)
- 		-inline
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Definition at line 434 of file ScipionMetaData.java.

-
434  {
435  return setValueObject(label, new Double(value).floatValue(), id);
436  }
xmipp.viewer.scipion.ScipionMetaData.setValueObject
boolean setValueObject(int label, Object value, long id)
Definition: ScipionMetaData.java:443
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◆ setValueInt()

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boolean xmipp.viewer.scipion.ScipionMetaData.setValueInt (int label,
int value,
long id 
)
- 		-inline
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Definition at line 439 of file ScipionMetaData.java.

-
439  {
440  return setValueObject(label, value, id);
441  }
xmipp.viewer.scipion.ScipionMetaData.setValueObject
boolean setValueObject(int label, Object value, long id)
Definition: ScipionMetaData.java:443
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◆ setValueObject()

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boolean xmipp.viewer.scipion.ScipionMetaData.setValueObject (int label,
Object value,
long id 
)
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Definition at line 443 of file ScipionMetaData.java.

-
443  {
444  EMObject emo = getEMObject(id);
445  ColumnInfo ci = getColumnInfo(label);
446  emo.setValue(ci, value);
447  return true;
448  }
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◆ setValueString()

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boolean xmipp.viewer.scipion.ScipionMetaData.setValueString (int label,
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Definition at line 429 of file ScipionMetaData.java.

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429  {
430  return setValueObject(label, value, id);
431  }
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boolean setValueObject(int label, Object value, long id)
Definition: ScipionMetaData.java:443
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Definition at line 424 of file ScipionMetaData.java.

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424  {
425  return emobjects.size();
426  }
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Definition at line 618 of file ScipionMetaData.java.

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618  {
619  ColumnInfo ci = getColumnInfo(sortLabel);
620  try {
621  loadNeighborhoodValues(0, ci, size());
622  } catch (SQLException ex) {
623  Logger.getLogger(ScipionMetaData.class.getName()).log(Level.SEVERE, null, ex);
624  }
625  Comparator<EMObject> comparator = new EMObjectComparator(ci);
626  if(!ascending)
627  comparator = Collections.reverseOrder(comparator);
628  Collections.sort(emobjects, comparator);
629  for (int i = 0; i < emobjects.size(); i++)
630  emobjects.get(i).setIndex(i);
631 
632  }
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void xmipp.viewer.scipion.ScipionMetaData.unionAll (MetaData md)
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Definition at line 460 of file ScipionMetaData.java.

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460  {
461  emobjects.addAll(((ScipionMetaData) md).getEMObjects());
462  }
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Definition at line 484 of file ScipionMetaData.java.

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484  {
485  new File(path).delete();//overwrite file
486  if (path.contains("@")) {
487  writeBlock(path.substring(path.lastIndexOf("@") + 1));
488  return;
489  }
490  if (parent != null) {
491  parent.write(path);//this will write parent and siblings
492  return;
493  }
494  writeBlock(path);
495  if (haschilds) {
496  for (EMObject emo : emobjects) {
497  if (emo.childmd != null) {
498  emo.childmd.writeBlock(path);
499  }
500  }
501  }
502  }
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Definition at line 506 of file ScipionMetaData.java.

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506  {
507  //Might fail if some fixed column was added
508 
509  Connection c = null;
510  Statement stmt = null;
511  try {
512 
513  c = getConnection(path);
514  c.setAutoCommit(false);
515  stmt = c.createStatement();
516 
517  String sql = String.format("DROP TABLE IF EXISTS %1$sClasses; CREATE TABLE %1$sClasses(\n"
518  + "id INTEGER PRIMARY KEY AUTOINCREMENT,\n"
519  + " label_property TEXT UNIQUE,\n"
520  + " column_name TEXT UNIQUE,\n"
521  + " class_name TEXT DEFAULT NULL\n"
522  + " )", preffix);
523  stmt.executeUpdate(sql);
524 
525  String line = ", (%s, \'%s\', \'%s\', \'%s\')";
526  ColumnInfo ci;
527  String createcols = "", cols = "", type;
528  for (int i = 0; i < columns.size(); i++) {
529  ci = columns.get(i);
530  type = getTypeMapping(ci.type);
531  sql += String.format(line, i + 2, ci.labelName, ci.comment, type);
532  createcols += String.format("%s %s DEFAULT NULL,", ci.comment, type);
533  cols += String.format("%s,", ci.comment);
534  }
535  stmt.executeUpdate(sql);
536  createcols = createcols.substring(0, createcols.length() - 1);
537  cols = cols.substring(0, cols.length() - 1);
538  sql = String.format("DROP TABLE IF EXISTS %1$sObjects; CREATE TABLE %1$sObjects(\n"
539  + " %2$s)", preffix, createcols);
540 
541  stmt.executeUpdate(sql);
542  if (size() == 0) {
543  return;
544  }
545  sql = String.format("INSERT INTO %sObjects(%s) VALUES ", preffix, cols);
546  Object value;
547  for (EMObject emo : emobjects) {
548  sql += "(";
549  for (ColumnInfo column : columns) {
550  value = emo.getValue(column);
551  if (value != null) {
552  if (column.type == MetaData.LABEL_STRING) {
553 
554  String str = (String) value;
555  if (str.contains("@")) {
556  str = str.substring(str.lastIndexOf("@") + 1);
557  }
558  value = str;
559  sql += String.format("'%s',", value);
560  } else {
561  sql += String.format("%s,", value);
562  }
563  } else {
564  sql += "NULL,";
565  }
566  }
567  sql = sql.substring(0, sql.length() - 1) + "),";
568  }
569  sql = sql.substring(0, sql.length() - 1);
570  stmt.executeUpdate(sql);
571  c.commit();
572  stmt.close();
573  c.close();
574 
575  } catch (Exception e) {
576  e.printStackTrace();
577 
578  }
579  }
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static String getTypeMapping(int type)
Definition: ScipionMetaData.java:581
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static Connection getConnection(String filename)
Definition: ScipionMetaData.java:1058
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◆ blocks

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Definition at line 46 of file ScipionMetaData.java.

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Definition at line 48 of file ScipionMetaData.java.

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Definition at line 39 of file ScipionMetaData.java.

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Definition at line 40 of file ScipionMetaData.java.

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Definition at line 47 of file ScipionMetaData.java.

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Definition at line 42 of file ScipionMetaData.java.

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◆ idci

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Definition at line 44 of file ScipionMetaData.java.

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Definition at line 50 of file ScipionMetaData.java.

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Definition at line 43 of file ScipionMetaData.java.

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Definition at line 41 of file ScipionMetaData.java.

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Definition at line 45 of file ScipionMetaData.java.

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Definition at line 49 of file ScipionMetaData.java.

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Definition at line 51 of file ScipionMetaData.java.

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- -
-Generated by   -doxygen - 1.8.13 -
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This is the complete list of members for xmipp.viewer.scipion.ScipionMetaData.EMObject, including all inherited members.

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EMObject(int index, ScipionMetaData md)xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
getComment()xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
getEllipseCTF()xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
getId()xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
getLabel()xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
getValueBoolean(String column)xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
isEnabled()xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
setComment(String comment)xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
setEnabled(boolean isenabled)xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
setValue(ColumnInfo ci, Object value)xmipp.viewer.scipion.ScipionMetaData.EMObjectinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject.html b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject.html deleted file mode 100644 index 7963e43f..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject.html +++ /dev/null @@ -1,426 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.scipion.ScipionMetaData.EMObject Class Reference - - - - - - - - - -
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-Public Member Functions

 EMObject (int index, ScipionMetaData md)
 
void setValue (ColumnInfo ci, Object value)
 
Boolean getValueBoolean (String column)
 
boolean isEnabled ()
 
void setEnabled (boolean isenabled)
 
Long getId ()
 
String getLabel ()
 
String getComment ()
 
void setComment (String comment)
 
EllipseCTF getEllipseCTF ()
 
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Definition at line 913 of file ScipionMetaData.java.

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xmipp.viewer.scipion.ScipionMetaData.EMObject.EMObject (int index,
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Definition at line 922 of file ScipionMetaData.java.

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922  {
923  this.index = index;
924  values = new HashMap<ColumnInfo, Object>();
925  this.md = md;
926  changed = false;
927  }
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Definition at line 1009 of file ScipionMetaData.java.

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1009  {
1010  Object value = getValue(commentci);
1011  if (value != null) {
1012  return ((String) getValue(commentci));
1013  }
1014  return null;
1015  }
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Definition at line 1037 of file ScipionMetaData.java.

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1038  {
1039  String comment = getComment();
1040  if(comment == null || comment.isEmpty())
1041  return null;
1042  String[] params = comment.trim().split("\\s+");
1043  double defU = Double.parseDouble(params[0]);
1044  double defV = Double.parseDouble(params[1]);
1045  double angle = Double.parseDouble(params[2]);
1046  double lowFreq = Double.parseDouble(params[3]);
1047  double highFreq = Double.parseDouble(params[4]);
1048  EllipseCTF ctf = md.getEllipseCTF(getId());
1049  ctf.setDefocus(defU, defV, angle);
1050  ctf.setFreqRange(lowFreq, highFreq);
1051  return ctf;
1052  }
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void setDefocus(double defU, double defV, double angle)
Definition: EllipseCTF.java:166
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xmipp.viewer.scipion.ScipionMetaData.getEllipseCTF
EllipseCTF getEllipseCTF(long id, int D)
Definition: ScipionMetaData.java:718
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Definition at line 997 of file ScipionMetaData.java.

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997  {
998  return ((Integer)values.get(idci)).longValue();
999  }
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Definition at line 1001 of file ScipionMetaData.java.

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1001  {
1002  Object value = getValue(labelci);
1003  if (value != null) {
1004  return ((String) getValue(labelci));
1005  }
1006  return null;
1007  }
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Definition at line 971 of file ScipionMetaData.java.

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971  {
972  ColumnInfo ci = getColumnInfo(column);
973  if(column == null)
974  return null;
975  Object value = getValue(ci);
976  if(value == null)
977  return null;
978  return (Integer)value == 1;
979  }
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Definition at line 981 of file ScipionMetaData.java.

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981  {
982  if(!values.containsKey(enabledci))
983  return true;
984  Integer value = (Integer) values.get(enabledci);
985  return value == 1;
986  }
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Definition at line 1017 of file ScipionMetaData.java.

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1017  {
1018  setValue(commentci, comment);
1019  }
xmipp.viewer.scipion.ScipionMetaData.EMObject.setValue
void setValue(ColumnInfo ci, Object value)
Definition: ScipionMetaData.java:964
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void xmipp.viewer.scipion.ScipionMetaData.EMObject.setEnabled (boolean isenabled)
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Definition at line 988 of file ScipionMetaData.java.

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988  {
989  int value = isenabled ? 1 : 0;
990  if(isEnabled() && !isenabled)
991  enableds --;
992  else if( !isEnabled() && isenabled)
993  enableds ++;
994  setValue(enabledci, value);
995  }
xmipp.viewer.scipion.ScipionMetaData.EMObject.setValue
void setValue(ColumnInfo ci, Object value)
Definition: ScipionMetaData.java:964
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void xmipp.viewer.scipion.ScipionMetaData.EMObject.setValue (ColumnInfo ci,
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Definition at line 964 of file ScipionMetaData.java.

-
964  {
965 
966  changed = true;
967  values.put(ci, value);
968 
969  }
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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject__coll__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject__coll__graph.dot deleted file mode 100644 index 43f5a134..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject__coll__graph.dot +++ /dev/null @@ -1,26 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionMetaData.EMObject" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node1 [label="xmipp.viewer.scipion.Scipion\lMetaData.EMObject",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node2 -> Node1 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" childmd\nmd" ,fontname="Helvetica"]; - Node2 [label="xmipp.viewer.scipion.Scipion\lMetaData",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData.html"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.jni.MetaData",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1MetaData.html"]; - Node4 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ctfs" ,fontname="Helvetica"]; - Node4 [label="HashMap\< Long, xmipp.jni.\lEllipseCTF \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" emobjects" ,fontname="Helvetica"]; - Node5 [label="List\< xmipp.viewer.scipion.\lScipionMetaData.EMObject \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" properties" ,fontname="Helvetica"]; - Node6 [label="HashMap\< String, String \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" idsmap" ,fontname="Helvetica"]; - Node7 [label="HashMap\< Long, xmipp.viewer.scipion.\lScipionMetaData.EMObject \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" idci\ncommentci\nlabelci\nenabledci" ,fontname="Helvetica"]; - Node8 [label="xmipp.viewer.models.ColumnInfo",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1ColumnInfo.html"]; - Node9 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" columns" ,fontname="Helvetica"]; - Node9 [label="List\< xmipp.viewer.models.\lColumnInfo \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" parent" ,fontname="Helvetica"]; - Node10 -> Node1 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" values" ,fontname="Helvetica"]; - Node10 [label="Map\< xmipp.viewer.models.\lColumnInfo, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject__coll__graph.md5 deleted file mode 100644 index a3cd5d08..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData_1_1EMObject__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -f1934098b26d82feb7ec533991ca1a09 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__coll__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__coll__graph.dot deleted file mode 100644 index f519bd35..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__coll__graph.dot +++ /dev/null @@ -1,22 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionMetaData" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node2 [label="xmipp.viewer.scipion.Scipion\lMetaData",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.jni.MetaData",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1MetaData.html"]; - Node4 -> Node3 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" ctfs" ,fontname="Helvetica"]; - Node4 [label="HashMap\< Long, xmipp.jni.\lEllipseCTF \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node5 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" emobjects" ,fontname="Helvetica"]; - Node5 [label="List\< xmipp.viewer.scipion.\lScipionMetaData.EMObject \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" properties" ,fontname="Helvetica"]; - Node6 [label="HashMap\< String, String \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" idsmap" ,fontname="Helvetica"]; - Node7 [label="HashMap\< Long, xmipp.viewer.scipion.\lScipionMetaData.EMObject \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" idci\ncommentci\nlabelci\nenabledci" ,fontname="Helvetica"]; - Node8 [label="xmipp.viewer.models.ColumnInfo",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1models_1_1ColumnInfo.html"]; - Node9 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" columns" ,fontname="Helvetica"]; - Node9 [label="List\< xmipp.viewer.models.\lColumnInfo \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node2 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" parent" ,fontname="Helvetica"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__coll__graph.md5 deleted file mode 100644 index 86c3f04b..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -8ef8eea63b130c4ced618fe976106e45 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__inherit__graph.dot deleted file mode 100644 index 07b21ef0..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionMetaData" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.scipion.Scipion\lMetaData",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.jni.MetaData",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1jni_1_1MetaData.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__inherit__graph.md5 deleted file mode 100644 index 6e139e50..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionMetaData__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -8abbaeda44f2652cb70fa78b2c6364d9 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer-members.html b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer-members.html deleted file mode 100644 index 1645e714..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer-members.html +++ /dev/null @@ -1,84 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.scipion.ScipionViewer Member List
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This is the complete list of members for xmipp.viewer.scipion.ScipionViewer, including all inherited members.

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main(String args[])xmipp.viewer.scipion.ScipionViewerinlinestatic
openFile(String filename, ScipionParams parameters)xmipp.viewer.scipion.ScipionViewerinlinestatic
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer.html b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer.html deleted file mode 100644 index 5f025fda..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer.html +++ /dev/null @@ -1,182 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.scipion.ScipionViewer Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Static Public Member Functions | -List of all members
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xmipp.viewer.scipion.ScipionViewer Class Reference
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-Inheritance diagram for xmipp.viewer.scipion.ScipionViewer:
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Inheritance graph
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[legend]
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-Collaboration diagram for xmipp.viewer.scipion.ScipionViewer:
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Collaboration graph
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[legend]
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-Static Public Member Functions

static void main (String args[])
 
static void openFile (String filename, ScipionParams parameters)
 
- Static Public Member Functions inherited from xmipp.viewer.Viewer
static void main (String args[])
 
-

Detailed Description

-
Author
airen
- -

Definition at line 26 of file ScipionViewer.java.

-

Member Function Documentation

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◆ main()

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static void xmipp.viewer.scipion.ScipionViewer.main (String args[])
- 		-inlinestatic
-
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Definition at line 32 of file ScipionViewer.java.

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32  {
33  StopWatch stopWatch = StopWatch.getInstance();
34  stopWatch.printElapsedTime("starting app");
35  // Schedule a job for the event dispatch thread:
36  // creating and showing this application's GUI.
37  final String[] myargs = args;
38 
39  ScipionParams parameters = new ScipionParams(myargs);
40  if(parameters.isScipion())
41  XmippApplication.setIsScipion(true);
42  try {
43  if (parameters.debug) {
44  DEBUG.enableDebug(true);
45  }
46 
47  if (parameters.files != null) {
48  // DEBUG.enableDebug(true);
49  final String[] files = parameters.files;
50 
51  for (int i = 0; i < files.length; i++)
52  openFile(files[i], parameters);
53 
54  }
55 
56  } catch (Exception e) {
57  e.printStackTrace();
58  }
59 
60  }
xmipp.viewer.scipion.ScipionViewer.openFile
static void openFile(String filename, ScipionParams parameters)
Definition: ScipionViewer.java:64
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◆ openFile()

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static void xmipp.viewer.scipion.ScipionViewer.openFile (String filename,
ScipionParams parameters 
)
- 		-inlinestatic
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Definition at line 64 of file ScipionViewer.java.

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64  {
65 
66  try {
67 
68  MetaData md;
69  boolean isscipion = ScipionMetaData.isScipionMetaData(filename);
70  if(isscipion)
71  ImagesWindowFactory.openScipionMetadata(filename, parameters);
72  else if (Filename.isMetadata(filename)) {
73  if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_IMAGE)) {
74  openFileAsImage(null, filename, parameters);
75  } else {
76  //parameters.mode = Params.OPENING_MODE_GALLERY;
77  md = new MetaData(filename);
78  new GalleryJFrame(md, parameters);
79  }
80  } else {
81  ImageGeneric img = new ImageGeneric(filename);
82 
83  if (img.isSingleImage()) {
84  openFileAsImage(null, filename, parameters);
85  } else if (img.isStackOrVolume()) {
86  if (parameters.mode
87  .equalsIgnoreCase(Params.OPENING_MODE_IMAGE)) {
88  openFileAsImage(null, filename, parameters);
89  } else {
90  parameters.mode = Params.OPENING_MODE_GALLERY;
91  new GalleryJFrame(filename, parameters);
92  }
93  }
94  }
95 
96  } catch (Exception e) {
97  XmippDialog.showError(null, String.format(
98  "Couldn't open file: '%s'\nError: %s", filename,
99  e.getMessage()));
100  e.printStackTrace();
101  }
102  }
-
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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__coll__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__coll__graph.dot deleted file mode 100644 index 571546e7..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionViewer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.scipion.Scipion\lViewer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="xmipp.viewer.Viewer",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1Viewer.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__coll__graph.md5 deleted file mode 100644 index 650c0ab1..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -085675bf81e617f347ad9e427ef5910d \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__inherit__graph.dot deleted file mode 100644 index 3e3666cc..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.scipion.ScipionViewer" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.scipion.Scipion\lViewer",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.viewer.Viewer",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1Viewer.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__inherit__graph.md5 deleted file mode 100644 index 04b89c4e..00000000 --- a/html/classxmipp_1_1viewer_1_1scipion_1_1ScipionViewer__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -8667d060fd9a749956a4d3e432be4ede \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1AddFillLabelsJDialog-members.html b/html/classxmipp_1_1viewer_1_1windows_1_1AddFillLabelsJDialog-members.html deleted file mode 100644 index bd7c2526..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1AddFillLabelsJDialog-members.html +++ /dev/null @@ -1,140 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.windows.AddFillLabelsJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.AddFillLabelsJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
AddFillLabelsJDialog(GalleryJFrame parent, List< ColumnInfo > labels)xmipp.viewer.windows.AddFillLabelsJDialoginline
AddFillLabelsJDialog(GalleryJFrame parent, int label)xmipp.viewer.windows.AddFillLabelsJDialoginline
addPair(JPanel panel, String text, int row, Component c)xmipp.viewer.windows.AddFillLabelsJDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.AddFillLabelsJDialoginlineprotected
dictLabelsxmipp.viewer.windows.AddFillLabelsJDialogprotected
dictPanelsxmipp.viewer.windows.AddFillLabelsJDialogprotected
dictTextsxmipp.viewer.windows.AddFillLabelsJDialogprotected
disposeOnClosexmipp.utils.XmippDialogprotected
fillModexmipp.viewer.windows.AddFillLabelsJDialogprotected
galleryxmipp.viewer.windows.AddFillLabelsJDialogprotected
gbcxmipp.viewer.windows.AddFillLabelsJDialogprotected
getFillMode()xmipp.viewer.windows.AddFillLabelsJDialoginline
getLabel()xmipp.viewer.windows.AddFillLabelsJDialoginline
getValue(String key)xmipp.viewer.windows.AddFillLabelsJDialoginline
getValues()xmipp.viewer.windows.AddFillLabelsJDialoginline
handleActionPerformed(ActionEvent evt)xmipp.viewer.windows.AddFillLabelsJDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
isFillMode()xmipp.viewer.windows.AddFillLabelsJDialoginline
jcbLabelxmipp.viewer.windows.AddFillLabelsJDialogprotected
labelxmipp.viewer.windows.AddFillLabelsJDialogprotected
labelsxmipp.viewer.windows.AddFillLabelsJDialogprotected
mainPanelxmipp.viewer.windows.AddFillLabelsJDialogprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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Xmipp -  v20.07 -
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-Public Member Functions

 AddFillLabelsJDialog (GalleryJFrame parent, List< ColumnInfo > labels)
 
 AddFillLabelsJDialog (GalleryJFrame parent, int label)
 
boolean isFillMode ()
 
String getFillMode ()
 
int getLabel ()
 
String getValue (String key)
 
String [] getValues ()
 
void handleActionPerformed (ActionEvent evt)
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void addPair (JPanel panel, String text, int row, Component c)
 
void createContent (JPanel panel)
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Protected Attributes

MetadataGalleryTableModel gallery
 
boolean fillMode = false
 
GridBagConstraints gbc = new GridBagConstraints()
 
int label
 
List< ColumnInfo > labels = null
 
Hashtable< String, JLabel > dictLabels = new Hashtable<String, JLabel>()
 
Hashtable< String, JTextField > dictTexts = new Hashtable<String, JTextField>()
 
Hashtable< String, JPanel > dictPanels = new Hashtable<String, JPanel>()
 
JPanel mainPanel
 
JComboBox jcbLabel
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
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Detailed Description

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Definition at line 53 of file AddFillLabelsJDialog.java.

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Constructor & Destructor Documentation

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◆ AddFillLabelsJDialog() [1/2]

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xmipp.viewer.windows.AddFillLabelsJDialog.AddFillLabelsJDialog (GalleryJFrame parent,
List< ColumnInfo > labels 
)
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Constructor to add a new label the labels present in the metadata are passed

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Definition at line 71 of file AddFillLabelsJDialog.java.

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72  {
73  super(parent, "Add new label", true);
74  this.gallery = (MetadataGalleryTableModel) parent.gallery;
75  this.labels = labels;
76  initComponents();
77  }// constructor AddFillLabelsJDialog
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◆ AddFillLabelsJDialog() [2/2]

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xmipp.viewer.windows.AddFillLabelsJDialog.AddFillLabelsJDialog (GalleryJFrame parent,
int label 
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Constructor to fill an existing label

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Definition at line 80 of file AddFillLabelsJDialog.java.

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80  {
81  super(parent, "Fill label values", true);
82  this.label = label;
83  initComponents();
84  }// constructor AddFillLabelsJDialog
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Member Function Documentation

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◆ addPair()

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void xmipp.viewer.windows.AddFillLabelsJDialog.addPair (JPanel panel,
String text,
int row,
Component c 
)
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Utility function to create a pair of label and other component If the component is null, a textbox will be created and added to the dict

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Definition at line 95 of file AddFillLabelsJDialog.java.

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95  {
96  JLabel label = new JLabel(text);
97  dictLabels.put(text, label);
98  gbc.anchor = GridBagConstraints.EAST;
99  panel.add(label, XmippWindowUtil.getConstraints(gbc, 0, row));
100  if (c == null) {
101  c = new JTextField(10);
102  dictTexts.put(text, (JTextField) c);
103  }
104  gbc.anchor = GridBagConstraints.WEST;
105  panel.add(c, XmippWindowUtil.getConstraints(gbc, 1, row));
106  }
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xmipp.viewer.windows.AddFillLabelsJDialog.dictTexts
Hashtable< String, JTextField > dictTexts
Definition: AddFillLabelsJDialog.java:62
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void xmipp.viewer.windows.AddFillLabelsJDialog.createContent (JPanel panel)
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Definition at line 145 of file AddFillLabelsJDialog.java.

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145  {
146  setResizable(false);
147  mainPanel = new JPanel(new GridBagLayout());
148  gbc.insets = new Insets(5, 5, 0, 0);
149 
150  Component c = null;
151  if (isFillMode()) {
152  JTextField jtext = new JTextField(MetaData.getLabelName(label));
153  jtext.setEditable(false);
154  c = jtext;
155  setPreferredSize(new Dimension(250, 200));
156  } else {
157  c = createLabelsCombo();
158  setPreferredSize(new Dimension(350, 200));
159  }
160  addPair(mainPanel, "Label", 0, c);
161  String[] opts = { MetaData.FILL_CONSTANT, MetaData.FILL_LINEAR, MetaData.FILL_RAND_UNIFORM,
162  MetaData.FILL_RAND_GAUSSIAN };
163  jcbFillMode = new JComboBox(opts);
164  jcbFillMode.addActionListener(this);
165  addPair(mainPanel, "Fill mode", 1, jcbFillMode);
166  addPairsPanel(opts[0], 2, "value").setVisible(true);
167  addPairsPanel(opts[1], 3, "start", "step");
168  addPairsPanel(opts[2], 4, "min", "max");
169  addPairsPanel(opts[3], 5, "mean", "std");
170 
171  panel.add(mainPanel);
172 
173  }// function initComponents
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xmipp.viewer.windows.AddFillLabelsJDialog.addPair
void addPair(JPanel panel, String text, int row, Component c)
Definition: AddFillLabelsJDialog.java:95
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String xmipp.viewer.windows.AddFillLabelsJDialog.getFillMode ()
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some helper functions

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Definition at line 176 of file AddFillLabelsJDialog.java.

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176  {
177  return (String) jcbFillMode.getSelectedItem();
178  }
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int xmipp.viewer.windows.AddFillLabelsJDialog.getLabel ()
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Return the current working label

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Definition at line 181 of file AddFillLabelsJDialog.java.

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181  {
182  if (isFillMode())
183  return label;
184  else {
185  try {
186  return MetaData.str2Label((String) jcbLabel.getSelectedItem());
187  } catch (Exception e) {
188  showException(e);
189  }
190  return MDLabel.MDL_UNDEFINED;
191  }
192  }
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xmipp.utils.XmippDialog.showException
boolean showException(Exception e)
Definition: XmippDialog.java:217
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String xmipp.viewer.windows.AddFillLabelsJDialog.getValue (String key)
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Definition at line 194 of file AddFillLabelsJDialog.java.

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194  {
195  JTextField jtf = dictTexts.get(key);
196  return jtf.getText();
197  }
xmipp.viewer.windows.AddFillLabelsJDialog.dictTexts
Hashtable< String, JTextField > dictTexts
Definition: AddFillLabelsJDialog.java:62
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String [] xmipp.viewer.windows.AddFillLabelsJDialog.getValues ()
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Definition at line 199 of file AddFillLabelsJDialog.java.

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199  {
200  String[] values = null;
201  String mode = getFillMode();
202  if (mode.equalsIgnoreCase(MetaData.FILL_CONSTANT))
203  values = new String[] { getValue("value") };
204  else if (mode.equalsIgnoreCase(MetaData.FILL_LINEAR))
205  values = new String[] { getValue("start"), getValue("step") };
206  else if (mode.equalsIgnoreCase(MetaData.FILL_RAND_UNIFORM))
207  values = new String[] { getValue("min"), getValue("max") };
208  else if (mode.equalsIgnoreCase(MetaData.FILL_RAND_GAUSSIAN))
209  values = new String[] { getValue("mean"), getValue("std") };
210 
211  return values;
212  }
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void xmipp.viewer.windows.AddFillLabelsJDialog.handleActionPerformed (ActionEvent evt)
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Definition at line 215 of file AddFillLabelsJDialog.java.

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215  {
216  JComboBox jcb = (JComboBox) evt.getSource();
217  if (jcb == jcbFillMode) {
218  String fillMode = getFillMode();
219  for (Enumeration<String> keys = dictPanels.keys(); keys
220  .hasMoreElements();) {
221  String keyMode = keys.nextElement();
222  dictPanels.get(keyMode).setVisible(fillMode.equals(keyMode));
223  }
224  }
225  }// function actionPerformed
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boolean xmipp.viewer.windows.AddFillLabelsJDialog.isFillMode ()
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Return if in fill mode

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Definition at line 87 of file AddFillLabelsJDialog.java.

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87  {
88  return this.labels == null;
89  }
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Member Data Documentation

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◆ dictLabels

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Hashtable<String, JLabel> xmipp.viewer.windows.AddFillLabelsJDialog.dictLabels = new Hashtable<String, JLabel>()
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Definition at line 61 of file AddFillLabelsJDialog.java.

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Hashtable<String, JPanel> xmipp.viewer.windows.AddFillLabelsJDialog.dictPanels = new Hashtable<String, JPanel>()
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Definition at line 63 of file AddFillLabelsJDialog.java.

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◆ dictTexts

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Hashtable<String, JTextField> xmipp.viewer.windows.AddFillLabelsJDialog.dictTexts = new Hashtable<String, JTextField>()
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Definition at line 62 of file AddFillLabelsJDialog.java.

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boolean xmipp.viewer.windows.AddFillLabelsJDialog.fillMode = false
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Definition at line 57 of file AddFillLabelsJDialog.java.

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◆ gallery

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MetadataGalleryTableModel xmipp.viewer.windows.AddFillLabelsJDialog.gallery
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Definition at line 55 of file AddFillLabelsJDialog.java.

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GridBagConstraints xmipp.viewer.windows.AddFillLabelsJDialog.gbc = new GridBagConstraints()
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Definition at line 58 of file AddFillLabelsJDialog.java.

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Definition at line 65 of file AddFillLabelsJDialog.java.

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◆ label

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int xmipp.viewer.windows.AddFillLabelsJDialog.label
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Definition at line 59 of file AddFillLabelsJDialog.java.

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List<ColumnInfo> xmipp.viewer.windows.AddFillLabelsJDialog.labels = null
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Definition at line 60 of file AddFillLabelsJDialog.java.

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◆ mainPanel

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JPanel xmipp.viewer.windows.AddFillLabelsJDialog.mainPanel
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Definition at line 64 of file AddFillLabelsJDialog.java.

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The documentation for this class was generated from the following file: -
- -
-Generated by   -doxygen - 1.8.13 -
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xmipp.viewer.windows.AddObjectJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.AddObjectJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
AddObjectJDialog(GalleryJFrame parent)xmipp.viewer.windows.AddObjectJDialoginline
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.AddObjectJDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
handleActionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
mdxmipp.viewer.windows.AddObjectJDialog
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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Xmipp -  v20.07 -
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xmipp.viewer.windows.AddObjectJDialog Class Reference
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-Public Member Functions

 AddObjectJDialog (GalleryJFrame parent)
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Public Attributes

MetaData md
 
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-Protected Member Functions

void createContent (JPanel panel)
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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Detailed Description

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Definition at line 47 of file AddObjectJDialog.java.

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Constructor & Destructor Documentation

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◆ AddObjectJDialog()

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xmipp.viewer.windows.AddObjectJDialog.AddObjectJDialog (GalleryJFrame parent)
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Definition at line 56 of file AddObjectJDialog.java.

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56  {
57  super(parent, "Classes", true);
58  this.gallery = parent.gallery;
59  this.md = gallery.data.getMetaDataRow();
60  initComponents();
61  }// constructor AddObjectJDialog
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Member Function Documentation

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◆ createContent()

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void xmipp.viewer.windows.AddObjectJDialog.createContent (JPanel panel)
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Definition at line 64 of file AddObjectJDialog.java.

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64  {
65  setResizable(false);
66  panel.setLayout(new GridBagLayout());
67  gbc.anchor = GridBagConstraints.EAST;
68 
69  JPanel groupstbpn = new JPanel();
70  JScrollPane sp = new JScrollPane();
71  //groupstbpn.setBorder(BorderFactory.createTitledBorder("Classes"));
72  groupstbpn.add(sp);
73  sp.setOpaque(true);
74  try {
75  model = new MetadataRowTableModel((GalleryJFrame)parent, md);
76  JList rowHeader = new JList();
77  rowHeader.setModel(new GalleryRowHeaderModel(model.data));
78  LookAndFeel.installColorsAndFont(rowHeader, "TableHeader.background",
79  "TableHeader.foreground", "TableHeader.font");
80  rowHeader.setCellRenderer(new RowHeaderRenderer());
81 
82  sp.setRowHeaderView(rowHeader);
83  table = new JTable(model);
84  model.setupTable(table);
85  table.setPreferredScrollableViewportSize(new Dimension(350, 200));
86  sp.setViewportView(table);
87  int h = model.getCellSize().height;
88  rowHeader.setFixedCellHeight(h);
89  table.setRowHeight(h);
90  } catch (Exception e) {
91  // TODO Auto-generated catch block
92  e.printStackTrace();
93  }
94  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
95 
96  // listen to selection changes (only one row selected)
97  table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
98  }// function initComponents
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◆ md

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MetaData xmipp.viewer.windows.AddObjectJDialog.md
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Definition at line 52 of file AddObjectJDialog.java.

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Xmipp -  v20.07 -
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xmipp.viewer.windows.CTFProfileWindow Member List
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This is the complete list of members for xmipp.viewer.windows.CTFProfileWindow, including all inherited members.

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actionPerformed(ActionEvent ae)xmipp.viewer.windows.CTFProfileWindowinline
CTFProfileWindow(ImagePlus imp, String CTFFilename, String PSDFilename)xmipp.viewer.windows.CTFProfileWindowinline
itemStateChanged(ItemEvent ie)xmipp.viewer.windows.CTFProfileWindowinline
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Xmipp -  v20.07 -
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xmipp.viewer.windows.CTFProfileWindow Class Reference
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-Public Member Functions

 CTFProfileWindow (ImagePlus imp, String CTFFilename, String PSDFilename)
 
void itemStateChanged (ItemEvent ie)
 
void actionPerformed (ActionEvent ae)
 
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Detailed Description

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This is the CTF Frame

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Definition at line 73 of file CTFProfileWindow.java.

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Constructor & Destructor Documentation

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◆ CTFProfileWindow()

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xmipp.viewer.windows.CTFProfileWindow.CTFProfileWindow (ImagePlus imp,
String CTFFilename,
String PSDFilename 
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Definition at line 101 of file CTFProfileWindow.java.

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101  {
102 
103  try {
104  //ImageCanvas imc = imp.getCanvas();
105  //imc.setEnabled(false); // Clicks won't remove selection ;)
106 
107  Tm = getSamplingRate(CTFFilename);
108  System.out.println("Tm="+Tm);
109 
110  ctfmodel = new CTFDescription(CTFFilename);
111  ImageGeneric image = new ImageGeneric(PSDFilename);
112  image.setUseLogarithm(false);
113 
114  psdimage = XmippImageConverter.readToImagePlus(image);
115  psdimage.setTitle(PSDFilename);
116 
117  removeAll();
118  GridBagConstraints gc = new GridBagConstraints();
119  setLayout(new GridBagLayout());
120 
121  scrollbar = new JScrollBar(JScrollBar.HORIZONTAL);
122  scrollbar.setMaximum(MAX_VALUE + scrollbar.getVisibleAmount());
123  scrollbar.addAdjustmentListener(new java.awt.event.AdjustmentListener() {
124 
125  public void adjustmentValueChanged(java.awt.event.AdjustmentEvent evt) {
126  updatePlots();
127  }
128  });
129 
130  iconbt = new JButton(XmippUtil.getImageIcon(imp.getImage(), 300, 300));
131  iconbt.setToolTipText("Load CTF Profile");
132  iconbt.setBorderPainted(false);
133  iconbt.setContentAreaFilled(false);
134  iconbt.setFocusPainted(false);
135  iconbt.setOpaque(false);
136 
137  JPanel panelImage = new JPanel(new BorderLayout());
138  panelImage.add(iconbt, BorderLayout.CENTER);
139  panelImage.add(scrollbar, BorderLayout.SOUTH);
140  addMouseWheelListener(new MouseWheelListener() {
141 
142  public void mouseWheelMoved(MouseWheelEvent e) {
143  int MAXSCROLL = scrollbar.getMaximum() - scrollbar.getVisibleAmount();
144 
145  int newValue = (scrollbar.getValue() + e.getUnitsToScroll())
146  % MAXSCROLL;
147 
148  if (newValue < 0) {
149  newValue = newValue + MAXSCROLL;
150  }
151 
152  scrollbar.setValue(newValue);
153  updatePlots();
154  }
155  });
156 
157  JTabbedPane jtpPlots = new JTabbedPane();
158  panelPlot = new JPanel();
159  panelPlotAVG = new JPanel();
160 
161  jtpPlots.add(XmippLabel.LABEL_TAB_PROFILE, panelPlot);
162  jtpPlots.add(XmippLabel.LABEL_TAB_RADIAL_AVERAGE, panelPlotAVG);
163 
164  JPanel pCenter = new JPanel(new BorderLayout());
165  pCenter.add(jtpPlots);
166 
167  // Check boxes for plots
168  rbCTF = new JRadioButton(XmippLabel.CB_PLOT_CTF, true);
169  rbPSD = new JRadioButton(XmippLabel.CB_PLOT_PSD, false);
170  ButtonGroup bg = new ButtonGroup();
171  bg.add(rbCTF);
172  bg.add(rbPSD);
173  cbPSDTheo = new JCheckBox("PSD (Theoretical)", true);
174  cbBgNoise = new JCheckBox(XmippLabel.CB_PLOT_BGNOISE, false);
175  cbEnvelope = new JCheckBox(XmippLabel.CB_PLOT_ENVELOPE, false);
176 
177  cbPSDTheo.addItemListener(this);
178  cbBgNoise.addItemListener(this);
179  cbEnvelope.addItemListener(this);
180  rbPSD.addItemListener(this);
181  rbCTF.addItemListener(this);
182 
183  bExportProfile = XmippWindowUtil.getTextButton(XmippLabel.BUTTON_EXPORT_PROFILE, this);
184  bExportAVG = XmippWindowUtil.getTextButton(XmippLabel.BUTTON_EXPORT_RADIAL_AVERAGE, this);
185 
186  JPanel panelCBoxes = new JPanel(new GridBagLayout());
187  gc.anchor = GridBagConstraints.WEST;
188  panelCBoxes.add(rbCTF, XmippWindowUtil.getConstraints(gc, 0, 0));
189  panelCBoxes.add(rbPSD, XmippWindowUtil.getConstraints(gc, 1, 0));
190  panelCBoxes.add(cbPSDTheo, XmippWindowUtil.getConstraints(gc, 1, 1));
191  panelCBoxes.add(cbBgNoise, XmippWindowUtil.getConstraints(gc, 1, 2));
192  gc.insets = new Insets(0, 0, 10, 10);
193  panelCBoxes.add(cbEnvelope, XmippWindowUtil.getConstraints(gc, 1, 3));
194  gc.weightx = 1.0;
195  panelCBoxes.add(bExportProfile, XmippWindowUtil.getConstraints(gc, 0, 4, 2));
196  panelCBoxes.add(bExportAVG, XmippWindowUtil.getConstraints(gc, 0, 5, 2));
197  // Adds panels.
198  add(panelImage, XmippWindowUtil.getConstraints(gc, 0, 0));
199  add(pCenter, XmippWindowUtil.getConstraints(gc, 1, 0, 2, 2));
200  gc.anchor = GridBagConstraints.EAST;
201  add(panelCBoxes,XmippWindowUtil.getConstraints(gc, 0, 1));
202 // // Store initial values.
203  centerDisplay = new Point(imp.getWidth() / 2, imp.getHeight() / 2);
204  centerPSD = new Point(psdimage.getWidth() / 2, psdimage.getHeight() / 2);
205 
206  displayLength = (int) (imp.getWidth() / 2);
207  samples = (int) (psdimage.getWidth() / 2);
208 
209  xValues = getXValues(samples, Tm);
210 
211  setCBEnableStatus();
212  updatePlots();
213 // updateRadialAverage();
214 
215  // Trick: setting no resizable allows to pack properly.
216  setResizable(false);
217  pack();
218  //setResizable(true);
219  } catch (Exception e) {
220  e.printStackTrace();
221  }
222  }
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Member Function Documentation

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◆ actionPerformed()

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void xmipp.viewer.windows.CTFProfileWindow.actionPerformed (ActionEvent ae)
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Definition at line 241 of file CTFProfileWindow.java.

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241  {
242  if (fc.showSaveDialog(this) == XmippFileChooser.APPROVE_OPTION) {
243  File file = fc.getSelectedFile();
244  if (file != null) {
245  JFreeChart chart = null;
246  if (ae.getSource() == bExportProfile) {
247  chart = chartPanelProfile.getChart();
248  } else if (ae.getSource() == bExportAVG) {
249  chart = chartPanelAVG.getChart();
250  }
251 
252  if (export(file.getAbsolutePath(), chart)) {
253  XmippDialog.showInfo(this, "File saved successfully.");
254  }
255  }
256  }
257  }
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Definition at line 228 of file CTFProfileWindow.java.

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228  {
229  if (ie.getSource() == rbCTF) {
230  setCBEnableStatus();
231  }
232 
233  // Restores general view.
234  chartPanelProfile.restoreAutoBounds();
235  chartPanelAVG.restoreAutoBounds();
236 
237  updatePlots();
238  updateRadialAverage();
239  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1CTFProfileWindow__coll__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1CTFProfileWindow__coll__graph.dot deleted file mode 100644 index 1664b2a2..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1CTFProfileWindow__coll__graph.dot +++ /dev/null @@ -1,27 +0,0 @@ -digraph "xmipp.viewer.windows.CTFProfileWindow" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node4 [label="xmipp.viewer.windows.CTFProfile\lWindow",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node5 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node6 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="ItemListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node4 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" bExportAVG" ,fontname="Helvetica"]; - Node8 [label="JButton",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node4 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" cbPSDTheo\ncbEnvelope" ,fontname="Helvetica"]; - Node9 [label="JCheckBox",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node4 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" chartPanelAVG" ,fontname="Helvetica"]; - Node10 [label="ChartPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node11 -> Node4 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" panelPlotAVG" ,fontname="Helvetica"]; 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- node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.windows.CTFProfile\lWindow",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node2 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="ItemListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1CTFProfileWindow__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1CTFProfileWindow__inherit__graph.md5 deleted file mode 100644 index 2b749a4d..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1CTFProfileWindow__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -29c665d2027238a971ae8dd0db4fd5db \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog-members.html b/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog-members.html deleted file mode 100644 index 42f474f5..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog-members.html +++ /dev/null @@ -1,127 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.windows.ClassesJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.ClassesJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
ClassesJDialog(GalleryJFrame parent)xmipp.viewer.windows.ClassesJDialoginline
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.ClassesJDialoginlineprotected
createToolbarButtons()xmipp.viewer.windows.ClassesJDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
getClassInfo(int index)xmipp.viewer.windows.ClassesJDialoginline
getSelectedClass()xmipp.viewer.windows.ClassesJDialoginline
handleActionPerformed(ActionEvent evt)xmipp.viewer.windows.ClassesJDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resetClasses()xmipp.viewer.windows.ClassesJDialoginline
resultxmipp.utils.XmippDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.viewer.windows.ClassesJDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog.html b/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog.html deleted file mode 100644 index ff9d0eee..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog.html +++ /dev/null @@ -1,459 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.windows.ClassesJDialog Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Classes | -Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.windows.ClassesJDialog Class Reference
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-Inheritance diagram for xmipp.viewer.windows.ClassesJDialog:
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-Classes

class  ClassesTableModel
 
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-Public Member Functions

 ClassesJDialog (GalleryJFrame parent)
 
boolean showDialog ()
 
void resetClasses ()
 
void handleActionPerformed (ActionEvent evt)
 
int getSelectedClass ()
 
ClassInfo getClassInfo (int index)
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void createToolbarButtons ()
 
void createContent (JPanel panel)
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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Detailed Description

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Definition at line 58 of file ClassesJDialog.java.

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Constructor & Destructor Documentation

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◆ ClassesJDialog()

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xmipp.viewer.windows.ClassesJDialog.ClassesJDialog (GalleryJFrame parent)
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Definition at line 69 of file ClassesJDialog.java.

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69  {
70  super(parent, "Classes", true);
71  // this.classes = classes;
72  this.gallery = parent.gallery;
73  this.classes = gallery.data.getClasses();
74  this.btnOkText = "Select";
75  // disposeOnClose = false;
76  initComponents();
77  enableDelete(false);
78  }// constructor ColumnsJDialog
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xmipp.viewer.models.GalleryData.getClasses
ArrayList< ClassInfo > getClasses()
Definition: GalleryData.java:1491
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Member Function Documentation

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◆ createContent()

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void xmipp.viewer.windows.ClassesJDialog.createContent (JPanel panel)
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Definition at line 95 of file ClassesJDialog.java.

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95  {
96  setResizable(false);
97  panel.setLayout(new GridBagLayout());
98  gbc.anchor = GridBagConstraints.EAST;
99 
100  JPanel groupstbpn = new JPanel();
101  JScrollPane sp = new JScrollPane();
102  groupstbpn.setBorder(BorderFactory.createTitledBorder("Classes"));
103  groupstbpn.add(sp);
104  sp.setOpaque(true);
105  model = new ClassesTableModel();
106  tableClasses = new JTable(model);
107  tableClasses
108  .setPreferredScrollableViewportSize(new Dimension(350, 200));
109  sp.setViewportView(tableClasses);
110  tableClasses.setDefaultRenderer(Color.class, new ColorRenderer());
111  tableClasses.setDefaultEditor(Color.class, new ColorEditor());
112  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
113  createToolbarButtons();
114  panel.add(panelButtons, XmippWindowUtil.getConstraints(gbc, 1, 0));
115 
116  // listen to selection changes (only one row selected)
117  tableClasses.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
118  tableClasses.getSelectionModel().addListSelectionListener(
119  new ListSelectionListener() {
120  @Override
121  public void valueChanged(ListSelectionEvent e) {
122  enableDelete(getSelectedClass() >= 0);
123  }
124  });
125  }// function initComponents
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void xmipp.viewer.windows.ClassesJDialog.createToolbarButtons ()
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Definition at line 87 of file ClassesJDialog.java.

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87  {
88  panelButtons = new JPanel();
89  btnAdd = createButton("add.gif");
90  btnDelete = createButton("delete.gif");
91  btnSave = createButton("save.gif");
92  }
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◆ getClassInfo()

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ClassInfo xmipp.viewer.windows.ClassesJDialog.getClassInfo (int index)
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Definition at line 189 of file ClassesJDialog.java.

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189  {
190  return classes.get(index);
191  }
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int xmipp.viewer.windows.ClassesJDialog.getSelectedClass ()
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Definition at line 185 of file ClassesJDialog.java.

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185  {
186  return tableClasses.getSelectedRow();
187  }
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Definition at line 146 of file ClassesJDialog.java.

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146  {
147  JButton btn = (JButton) evt.getSource();
148  if (btn == btnAdd) {
149  model.addNewRow();
150  int row = model.getRowCount() - 1;
151  tableClasses.editCellAt(row, 0);
152  tableClasses.setRowSelectionInterval(row, row);
153  } else if (btn == btnDelete) {
154  int row = getSelectedClass();
155  gallery.removeClass(row);
156  model.fireTableRowsDeleted(row, row);
157  } else if (btn == btnSave) {
158  try {
159  //Read an array of metadatas containing the super-classes selection
160  // the first element will contain the metadata with the 'classes' block
161  // and then one 'images' block for each class
162  MetaData[] mds = gallery.data.getClassesMd();
163  XmippFileChooser fc = new XmippFileChooser();
164  if (fc.showSaveDialog(parent) == JFileChooser.APPROVE_OPTION) {
165  String filename = fc.getSelectedPath();
166  MetaData md = mds[0];
167  md.write("classes" + Filename.SEPARATOR + filename);
168  long[] ids = md.findObjects();
169  // DEBUG.printFormat("mds: %s, ids:%s", mds.length,
170  // ids.length);
171  int i = 1;
172  for (long id : ids) {
173  int ref = md.getValueInt(MDLabel.MDL_REF, id);
174  mds[i].writeBlock(Filename.getClassBlockName(ref)
175  + Filename.SEPARATOR + filename);
176  ++i;
177  }
178  }
179  } catch (Exception e) {
180  showException(e);
181  }
182  }
183  }// function actionPerformed
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boolean showException(Exception e)
Definition: XmippDialog.java:217
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void xmipp.viewer.windows.ClassesJDialog.resetClasses ()
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Definition at line 135 of file ClassesJDialog.java.

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135  {
136  this.classes = null;
137  }
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◆ showDialog()

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Override this method to update the class and image count

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Definition at line 129 of file ClassesJDialog.java.

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129  {
130  gallery.data.updateClassesInfo();
131  this.classes = gallery.data.getClasses();
132  return super.showDialog();
133  }
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ArrayList< ClassInfo > getClasses()
Definition: GalleryData.java:1491
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- Node6 [label="JDialog",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" btnOk\nbtnCancel" ,fontname="Helvetica"]; - Node8 [label="JButton",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" parent" ,fontname="Helvetica"]; - Node9 [label="Window",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" panel\npanelBtn" ,fontname="Helvetica"]; - Node10 [label="JPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node11 -> Node4 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" gbc" ,fontname="Helvetica"]; 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-} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__coll__graph.md5 deleted file mode 100644 index 7648bcae..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -d88521cfe63073ccc598e389c99451b3 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__inherit__graph.dot deleted file mode 100644 index 804a7529..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__inherit__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.windows.ClassesJDialog" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.windows.Classes\lJDialog",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.utils.XmippDialog",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippDialog.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="JDialog",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__inherit__graph.md5 deleted file mode 100644 index e3833270..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ClassesJDialog__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -11a1d9567f50d59bc0849105adb22956 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog-members.html b/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog-members.html deleted file mode 100644 index 11216974..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog-members.html +++ /dev/null @@ -1,127 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.viewer.windows.ColumnsJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.ColumnsJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
ColumnsJDialog(GalleryJFrame parent)xmipp.viewer.windows.ColumnsJDialoginline
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.ColumnsJDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
enableUpDown(boolean value)xmipp.viewer.windows.ColumnsJDialoginlineprotected
formatTable()xmipp.viewer.windows.ColumnsJDialoginlineprotected
getColumnsResult()xmipp.viewer.windows.ColumnsJDialoginline
handleActionPerformed(ActionEvent evt)xmipp.viewer.windows.ColumnsJDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
moveSelection(int deltha)xmipp.viewer.windows.ColumnsJDialoginlineprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog.html b/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog.html deleted file mode 100644 index 5bcf6a75..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog.html +++ /dev/null @@ -1,420 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.windows.ColumnsJDialog Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.viewer.windows.ColumnsJDialog Class Reference
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-Inheritance diagram for xmipp.viewer.windows.ColumnsJDialog:
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-Classes

class  ColumnsTableModel
 
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-Public Member Functions

 ColumnsJDialog (GalleryJFrame parent)
 
List< ColumnInfo > getColumnsResult ()
 
void handleActionPerformed (ActionEvent evt)
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void createContent (JPanel panel)
 
void formatTable ()
 
void enableUpDown (boolean value)
 
void moveSelection (int deltha)
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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Detailed Description

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Definition at line 52 of file ColumnsJDialog.java.

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◆ ColumnsJDialog()

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Definition at line 62 of file ColumnsJDialog.java.

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62  {
63  super(parent, "Columns", true);
64  initComponents();
65  }// constructor ColumnsJDialog
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void xmipp.viewer.windows.ColumnsJDialog.createContent (JPanel panel)
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Definition at line 72 of file ColumnsJDialog.java.

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72  {
73  setResizable(false);
74  panel.setLayout(new GridBagLayout());
75  GridBagConstraints gbc = new GridBagConstraints();
76  gbc.insets = new Insets(10, 10, 10, 10);
77  gbc.anchor = GridBagConstraints.WEST;
78 
79  JPanel groupstbpn = new JPanel();
80  JScrollPane sp = new JScrollPane();
81  groupstbpn.setBorder(BorderFactory
82  .createTitledBorder("Column properties"));
83  groupstbpn.add(sp);
84  sp.setOpaque(true);
85  model = new ColumnsTableModel(((GalleryJFrame)parent).getData().getLabelsInfo());
86  tableColumns = new JTable(model);
87  tableColumns
88  .setPreferredScrollableViewportSize(new Dimension(350, 200));
89  sp.setViewportView(tableColumns);
90  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 0));
91 
92  JPanel panelUpDown = new JPanel();
93  panelUpDown.setLayout(new GridBagLayout());
94  gbc.insets = new Insets(0, 0, 5, 5);
95  btnUp = XmippWindowUtil.getIconButton("up.gif", this);
96  panelUpDown.add(btnUp, XmippWindowUtil.getConstraints(gbc, 0, 0));
97  btnDown = XmippWindowUtil.getIconButton("down.gif", this);
98  panelUpDown.add(btnDown, XmippWindowUtil.getConstraints(gbc, 0, 1));
99  panel.add(panelUpDown, XmippWindowUtil.getConstraints(gbc, 1, 0));
100  // this buttons will be enabled after selection
101  enableUpDown(false);
102  // listen to selection changes (only one row selected)
103  tableColumns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
104  tableColumns.getSelectionModel().addListSelectionListener(
105  new ListSelectionListener() {
106  @Override
107  public void valueChanged(ListSelectionEvent e) {
108  enableUpDown(true);
109  }
110  });
111  formatTable();
112  }// function initComponents
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Definition at line 123 of file ColumnsJDialog.java.

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123  {
124  btnUp.setEnabled(value);
125  btnDown.setEnabled(value);
126  }// function enableUpDown
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Definition at line 114 of file ColumnsJDialog.java.

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114  {
115  tableColumns.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
116  tableColumns.getColumnModel().getColumn(0).setPreferredWidth(200);
117  tableColumns.getColumnModel().getColumn(1).setPreferredWidth(50);
118  tableColumns.getColumnModel().getColumn(2).setPreferredWidth(50);
119  tableColumns.getColumnModel().getColumn(3).setPreferredWidth(50);
120 
121  }
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Definition at line 67 of file ColumnsJDialog.java.

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67  {
68  return rows;
69  }
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Definition at line 139 of file ColumnsJDialog.java.

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139  {
140  JButton btn = (JButton) evt.getSource();
141 
142  if (btn == btnUp && tableColumns.getSelectedRow() > 0)
143  moveSelection(-1);
144  else if (btn == btnDown && tableColumns.getSelectedRow() < rows.size() - 1)
145  moveSelection(1);
146  }// function actionPerformed
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void xmipp.viewer.windows.ColumnsJDialog.moveSelection (int deltha)
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Definition at line 129 of file ColumnsJDialog.java.

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129  {
130  int pos = tableColumns.getSelectedRow();
131  ColumnInfo ci = rows.remove(pos);
132  pos += deltha;
133  rows.add(pos, ci);
134  model.fireTableDataChanged();
135  tableColumns.setRowSelectionInterval(pos, pos);
136  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__coll__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__coll__graph.dot deleted file mode 100644 index c7e17fab..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__coll__graph.dot +++ /dev/null @@ -1,18 +0,0 @@ -digraph "xmipp.viewer.windows.ColumnsJDialog" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node4 [label="xmipp.viewer.windows.Columns\lJDialog",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node5 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node5 [label="xmipp.utils.XmippDialog",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippDialog.html"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="JDialog",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node7 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node7 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node8 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" btnOk\nbtnCancel" ,fontname="Helvetica"]; - Node8 [label="JButton",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node9 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" parent" ,fontname="Helvetica"]; - Node9 [label="Window",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node10 -> Node5 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" panel\npanelBtn" ,fontname="Helvetica"]; - Node10 [label="JPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__coll__graph.md5 deleted file mode 100644 index 07183b5a..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -d1242e1d9a93201896c376df661c6bea \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__inherit__graph.dot deleted file mode 100644 index 0974b2ee..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__inherit__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.windows.ColumnsJDialog" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.windows.Columns\lJDialog",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.utils.XmippDialog",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippDialog.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="JDialog",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node3 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__inherit__graph.md5 deleted file mode 100644 index 8c9b14c8..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1ColumnsJDialog__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -739a61a9f3f64462527341cc6655bbc1 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1EditLabelsJDialog-members.html b/html/classxmipp_1_1viewer_1_1windows_1_1EditLabelsJDialog-members.html deleted file mode 100644 index 78dc4859..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1EditLabelsJDialog-members.html +++ /dev/null @@ -1,126 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.windows.EditLabelsJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.EditLabelsJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.EditLabelsJDialoginlineprotected
createToolbarButtons()xmipp.viewer.windows.EditLabelsJDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
EditLabelsJDialog(GalleryJFrame parent)xmipp.viewer.windows.EditLabelsJDialoginline
getSelectedRows()xmipp.viewer.windows.EditLabelsJDialoginline
handleActionPerformed(ActionEvent evt)xmipp.viewer.windows.EditLabelsJDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
rowToLabel(int row)xmipp.viewer.windows.EditLabelsJDialoginline
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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-Generated by   -doxygen - 1.8.13 -
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-Classes

class  ColumnsTableModel
 
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-Public Member Functions

 EditLabelsJDialog (GalleryJFrame parent)
 
void handleActionPerformed (ActionEvent evt)
 
int [] getSelectedRows ()
 
int rowToLabel (int row)
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void createToolbarButtons ()
 
void createContent (JPanel panel)
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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Detailed Description

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Definition at line 50 of file EditLabelsJDialog.java.

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◆ EditLabelsJDialog()

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Definition at line 62 of file EditLabelsJDialog.java.

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62  {
63  super(parent, "Edit labels", true);
64  this.rows = parent.getData().getLabelsInfo();
65  this.gallery = parent.gallery;
66  btnOkText = "Close";
67  btnCancelDisplay = false;
68  initComponents();
69  enableDelete(false);
70  enableFill(false);
71  }// constructor ColumnsJDialog
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◆ createContent()

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void xmipp.viewer.windows.EditLabelsJDialog.createContent (JPanel panel)
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Definition at line 89 of file EditLabelsJDialog.java.

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89  {
90  setResizable(false);
91  panel.setLayout(new GridBagLayout());
92  gbc.anchor = GridBagConstraints.EAST;
93 
94  JPanel groupstbpn = new JPanel();
95  JScrollPane sp = new JScrollPane();
96  groupstbpn.setBorder(BorderFactory.createTitledBorder("Labels"));
97  groupstbpn.add(sp);
98  sp.setOpaque(true);
99  model = new ColumnsTableModel();
100  tableColumns = new JTable(model);
101  tableColumns
102  .setPreferredScrollableViewportSize(new Dimension(350, 200));
103  sp.setViewportView(tableColumns);
104  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
105  createToolbarButtons();
106  panel.add(panelButtons, XmippWindowUtil.getConstraints(gbc, 1, 0));
107 
108  // listen to selection changes (only one row selected)
109  // tableColumns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
110  tableColumns.getSelectionModel().addListSelectionListener(
111  new ListSelectionListener() {
112  @Override
113  public void valueChanged(ListSelectionEvent e) {
114  int n = getSelectedRows().length;
115  enableDelete(n > 0);
116  enableFill(n == 1);
117  }
118  });
119  }// function initComponents
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Definition at line 81 of file EditLabelsJDialog.java.

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81  {
82  panelButtons = new JPanel();
83  btnAdd = createButton("add.gif", "Add new label");
84  btnDelete = createButton("delete.gif", "Delete label");
85  btnFill = createButton("fill.png", "Fill label");
86  }
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Definition at line 171 of file EditLabelsJDialog.java.

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171  {
172  return tableColumns.getSelectedRows();
173  }
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Definition at line 145 of file EditLabelsJDialog.java.

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145  {
146  try {
147  JButton btn = (JButton) evt.getSource();
148  if (btn == btnAdd) {
149  showAddFillDialog(new AddFillLabelsJDialog(
150  (GalleryJFrame) parent, rows));
151  } else if (btn == btnDelete) {
152  System.out.println("Here testing java...");
153  if (showWarning("Are you sure to remove this label?")) {
154  int [] rows = getSelectedRows();
155  System.out.println("Rows: " + Integer.toString(rows.length));
156  for (int row: rows) {
157  ((GalleryJFrame) parent).removeLabel(rowToLabel(row));
158  }
159  rowsChanged();
160  }
161  } else if (btn == btnFill) {
162  int [] rows = getSelectedRows();
163  showAddFillDialog(new AddFillLabelsJDialog(
164  (GalleryJFrame) parent, rowToLabel(rows[0])));
165  }
166  } catch (Exception e) {
167  showException(e);
168  }
169  }// function actionPerformed
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boolean showException(Exception e)
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Definition at line 176 of file EditLabelsJDialog.java.

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176  {
177  return rows.get(row).label;
178  }
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-Generated by   -doxygen - 1.8.13 -
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xmipp.viewer.windows.ExportImagesJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.ExportImagesJDialog, including all inherited members.

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ExportImagesJDialog(GalleryJFrame parent)xmipp.viewer.windows.ExportImagesJDialoginline
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xmipp.viewer.windows.ExportImagesJDialog Class Reference
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-Public Member Functions

 ExportImagesJDialog (GalleryJFrame parent)
 
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Detailed Description

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Author
airen
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Definition at line 39 of file ExportImagesJDialog.java.

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Constructor & Destructor Documentation

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◆ ExportImagesJDialog()

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xmipp.viewer.windows.ExportImagesJDialog.ExportImagesJDialog (GalleryJFrame parent)
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Definition at line 54 of file ExportImagesJDialog.java.

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55  {
56  super(parent);
57  this.frame = parent;
58 
59  path = parent.data.getFileName();
60  if(path == null)
61  path = "images";
62  path = Filename.removeExtension(path) + "_export.stk";
63  label = parent.data.getRenderLabel();
64  initComponents();
65  }
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The documentation for this class was generated from the following file: -
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This is the complete list of members for xmipp.viewer.windows.FSCJFrame, including all inherited members.

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FSCJFrame(GalleryData data, MetaData imagesmd, int label)xmipp.viewer.windows.FSCJFrameinline
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-Public Member Functions

 FSCJFrame (GalleryData data, MetaData imagesmd, int label)
 
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Detailed Description

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Definition at line 39 of file FSCJFrame.java.

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Constructor & Destructor Documentation

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◆ FSCJFrame()

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xmipp.viewer.windows.FSCJFrame.FSCJFrame (GalleryData data,
MetaData imagesmd,
int label 
)
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Definition at line 41 of file FSCJFrame.java.

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41  {
42  super(XmippLabel.TITLE_FSC + data.getFileName());
43 
44  try {
45  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
46  setLayout(new BorderLayout());
47 
48  MetaData mdout = new MetaData();
49 
50  mdout.computeFourierStatistics(imagesmd, label);
51 
52  double xValues[] = mdout.getColumnValues(MDLabel.MDL_RESOLUTION_FREQ);
53  double y1s[] = mdout.getColumnValues(MDLabel.MDL_RESOLUTION_FRC);
54  double y2s[] = mdout.getColumnValues(MDLabel.MDL_RESOLUTION_DPR);
55 
56  //String labelX = MetaData.label2Str(MDLabel.MDL_RESOLUTION_FREQ);
57  String labelY1 = MetaData.label2Str(MDLabel.MDL_RESOLUTION_FRC);
58  String labelY2 = MetaData.label2Str(MDLabel.MDL_RESOLUTION_DPR);
59 
60  XYSeriesCollection dataset1 = new XYSeriesCollection(
61  createSeries(labelY1, xValues, y1s));
62  XYSeriesCollection dataset2 = new XYSeriesCollection(
63  createSeries(labelY2, xValues, y2s));
64 
65  JFreeChart chart = ChartFactory.createXYLineChart(
66  "", XmippLabel.LABEL_DIGITAL_FREQUENCY, "",
67  dataset1, PlotOrientation.VERTICAL,
68  true, true, false);
69 
70  // Sets second axis.
71  XYPlot plot = chart.getXYPlot();
72  ValueAxis axisDPR = plot.getRangeAxis();
73  axisDPR.setLabel(labelY1);
74 
75  NumberAxis axisFSC = new NumberAxis();
76  axisFSC.setLabel(labelY2);
77  axisFSC.setAutoRangeIncludesZero(false);
78 
79  plot.setRangeAxis(1, axisFSC);
80  plot.setDataset(1, dataset2);
81  plot.mapDatasetToRangeAxis(1, 1);
82 
83  // Sets a new renderer, so series color will be different.
84  plot.setRenderer(1, new StandardXYItemRenderer());
85 
86  add(createChartPanel(chart), BorderLayout.CENTER);
87  pack();
88  XmippWindowUtil.centerWindows(this);
89 
90  imagesmd.destroy();
91  mdout.destroy();
92 
93  } catch (Exception e) {
94  DEBUG.printException(e);
95  }
96  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__coll__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__coll__graph.dot deleted file mode 100644 index 169c8183..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__coll__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.windows.FSCJFrame" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node2 [label="xmipp.viewer.windows.FSCJFrame",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__coll__graph.md5 deleted file mode 100644 index ca9f07d1..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -441b6e4c6d1252b852efe6d9ccb6550b \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__inherit__graph.dot deleted file mode 100644 index 9b3e9982..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__inherit__graph.dot +++ /dev/null @@ -1,8 +0,0 @@ -digraph "xmipp.viewer.windows.FSCJFrame" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.windows.FSCJFrame",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="JFrame",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; -} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__inherit__graph.md5 deleted file mode 100644 index ba1c61fd..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1FSCJFrame__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -de191edb52d2923884eb748ebef47bc4 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame-members.html b/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame-members.html deleted file mode 100644 index e79f13ba..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame-members.html +++ /dev/null @@ -1,158 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.windows.GalleryJFrame Member List
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This is the complete list of members for xmipp.viewer.windows.GalleryJFrame, including all inherited members.

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buttonspnxmipp.viewer.windows.GalleryJFrameprotected
cbPanelxmipp.viewer.windows.GalleryJFrameprotected
changeView()xmipp.viewer.windows.GalleryJFrameinlineprotected
CHIMERA_LAUNCHERxmipp.viewer.windows.GalleryJFramestatic
chimerabtxmipp.viewer.windows.GalleryJFrameprotected
close()xmipp.viewer.windows.GalleryJFrameinline
close(boolean ask)xmipp.viewer.windows.GalleryJFrameinline
createCombos()xmipp.viewer.windows.GalleryJFrameinlineprotected
createGUI()xmipp.viewer.windows.GalleryJFrameinlineprotected
createModel()xmipp.viewer.windows.GalleryJFrameinlineprotected
createModel(boolean[] selection)xmipp.viewer.windows.GalleryJFrameinlineprotected
createToolbar()xmipp.viewer.windows.GalleryJFrameinlineprotected
ctfTasksxmipp.viewer.windows.GalleryJFrameprotected
dataxmipp.viewer.windows.GalleryJFrameprotected
DIM_RATExmipp.viewer.windows.GalleryJFrameprotectedstatic
done()xmipp.viewer.windows.GalleryJFrameinline
enableToolBarActions()xmipp.viewer.windows.GalleryJFrameinlineprotected
fcxmipp.viewer.windows.GalleryJFrameprotected
fillLabel(int label, String mode, String... values)xmipp.viewer.windows.GalleryJFrameinline
findReplace()xmipp.viewer.windows.GalleryJFrameinline
fireTableRowsUpdated(int from, int to)xmipp.viewer.windows.GalleryJFrameinline
galleryxmipp.viewer.windows.GalleryJFrameprotected
GalleryJFrame(String filename, Params parameters)xmipp.viewer.windows.GalleryJFrameinline
GalleryJFrame(MetaData md, Params parameters)xmipp.viewer.windows.GalleryJFrameinline
GalleryJFrame(GalleryData data)xmipp.viewer.windows.GalleryJFrameinline
getBlock()xmipp.viewer.windows.GalleryJFrameinline
getData()xmipp.viewer.windows.GalleryJFrameinline
getFilename()xmipp.viewer.windows.GalleryJFrameinline
getKeyAssist()xmipp.viewer.windows.GalleryJFrameinline
getTasksEngine()xmipp.viewer.windows.GalleryJFrameinline
initGalleryMenu()xmipp.viewer.windows.GalleryJFrameinlineprotected
initResliceButtonMenu()xmipp.viewer.windows.GalleryJFrameinlineprotected
jcbBlocksxmipp.viewer.windows.GalleryJFrameprotected
jcbVolumesxmipp.viewer.windows.GalleryJFrameprotected
jlBlocksxmipp.viewer.windows.GalleryJFrameprotected
jlVolumesxmipp.viewer.windows.GalleryJFrameprotected
jpBottomxmipp.viewer.windows.GalleryJFrameprotected
jsColumnsxmipp.viewer.windows.GalleryJFrameprotected
jsGoToImagexmipp.viewer.windows.GalleryJFrameprotected
jsRowsxmipp.viewer.windows.GalleryJFrameprotected
jsZoomxmipp.viewer.windows.GalleryJFrameprotected
MAX_HEIGHTxmipp.viewer.windows.GalleryJFrameprotectedstatic
MAX_HEIGHT_RATExmipp.viewer.windows.GalleryJFrameprotectedstatic
MAX_WIDTHxmipp.viewer.windows.GalleryJFrameprotectedstatic
menuxmipp.viewer.windows.GalleryJFrameprotected
MIN_HEIGHTxmipp.viewer.windows.GalleryJFrameprotectedstatic
MIN_WIDTHxmipp.viewer.windows.GalleryJFrameprotectedstatic
openChimera(String file, boolean link)xmipp.viewer.windows.GalleryJFrameinlineprotected
openMetadata(final MetaData md)xmipp.viewer.windows.GalleryJFrameinline
openMicrographs()xmipp.viewer.windows.GalleryJFrameinline
openWithChimera()xmipp.viewer.windows.GalleryJFrameinlineprotected
plotbtxmipp.viewer.windows.GalleryJFrameprotected
plotColumns()xmipp.viewer.windows.GalleryJFrameinlineprotected
proceedWithChanges()xmipp.viewer.windows.GalleryJFrameinline
refreshActive(long id, boolean enabled)xmipp.viewer.windows.GalleryJFrameinline
reloadFile(String file, boolean changed)xmipp.viewer.windows.GalleryJFrameinline
reloadTableData()xmipp.viewer.windows.GalleryJFrameinline
reloadTableData(boolean[] selection)xmipp.viewer.windows.GalleryJFrameinline
reloadTableData(boolean changed, boolean[] selection)xmipp.viewer.windows.GalleryJFrameinline
removeLabel(int label)xmipp.viewer.windows.GalleryJFrameinline
removeObjects(boolean selected)xmipp.viewer.windows.GalleryJFrameinline
runInBackground(int operation)xmipp.viewer.windows.GalleryJFrameinline
saveMd()xmipp.viewer.windows.GalleryJFrameinlineprotected
saveMd(String path, boolean saveall, boolean isoverwrite, boolean reload)xmipp.viewer.windows.GalleryJFrameinlineprotected
screenSizexmipp.viewer.windows.GalleryJFrameprotectedstatic
searchbtxmipp.viewer.windows.GalleryJFrameprotected
selectBlock(String block)xmipp.viewer.windows.GalleryJFrameinline
selectItem(int row, int col)xmipp.viewer.windows.GalleryJFrameinline
setAutoAdjustColumns(boolean autoAdjustColumns)xmipp.viewer.windows.GalleryJFrameinline
setRowBusy(int row)xmipp.viewer.windows.GalleryJFrameinline
setRowIdle(int row)xmipp.viewer.windows.GalleryJFrameinline
setRunning(boolean running)xmipp.viewer.windows.GalleryJFrameinline
setupButton(AbstractButton btn, String icon, String text, ActionListener listener)xmipp.viewer.windows.GalleryJFrameinlineprotected
showException(Exception e)xmipp.viewer.windows.GalleryJFrameinline
tableMouseClicked(MouseEvent evt)xmipp.viewer.windows.GalleryJFrameinlineprotected
updateVisibleCombos()xmipp.viewer.windows.GalleryJFrameinlineprotected
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-Classes

class  GalleryMenu
 
class  GalleryPopupMenu
 
class  GalleryScroll
 
class  ResliceActionListener
 
class  VolumesComboBoxModel
 
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 GalleryJFrame (String filename, Params parameters)
 
 GalleryJFrame (MetaData md, Params parameters)
 
 GalleryJFrame (GalleryData data)
 
void openMetadata (final MetaData md)
 
GalleryData getData ()
 
void close ()
 
void close (boolean ask)
 
boolean proceedWithChanges ()
 
void fireTableRowsUpdated (int from, int to)
 
void setAutoAdjustColumns (boolean autoAdjustColumns)
 
void runInBackground (int operation)
 
void reloadTableData ()
 
void reloadTableData (boolean[] selection)
 
void reloadTableData (boolean changed, boolean[] selection)
 
void fillLabel (int label, String mode, String... values) throws Exception
 
void removeObjects (boolean selected)
 
void findReplace ()
 
void removeLabel (int label) throws Exception
 
void selectBlock (String block)
 
void selectItem (int row, int col)
 
void showException (Exception e)
 
void setRunning (boolean running)
 
void setRowBusy (int row)
 
void setRowIdle (int row)
 
void done ()
 
String getFilename ()
 
void openMicrographs ()
 
void refreshActive (long id, boolean enabled)
 
String getBlock ()
 
void reloadFile (String file, boolean changed) throws Exception
 
Map< Object, Object > getKeyAssist ()
 
TasksEngine getTasksEngine ()
 
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static final String CHIMERA_LAUNCHER = "CHIMERA_LAUNCHER"
 
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void createModel () throws Exception
 
void createModel (boolean[] selection)
 
void createGUI ()
 
void initGalleryMenu ()
 
void setupButton (AbstractButton btn, String icon, String text, ActionListener listener)
 
void changeView ()
 
void createToolbar ()
 
void createCombos ()
 
void enableToolBarActions ()
 
void updateVisibleCombos ()
 
void tableMouseClicked (MouseEvent evt)
 
void plotColumns ()
 
void saveMd () throws Exception
 
void saveMd (String path, boolean saveall, boolean isoverwrite, boolean reload)
 
void initResliceButtonMenu ()
 
void openChimera (String file, boolean link)
 
void openWithChimera ()
 
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-Protected Attributes

ImageGalleryTableModel gallery
 
GalleryMenu menu
 
XmippFileChooser fc
 
JPanel jpBottom
 
JSpinner jsColumns
 
JSpinner jsGoToImage
 
JSpinner jsRows
 
JSpinner jsZoom
 
JPanel cbPanel
 
JComboBox jcbBlocks
 
JComboBox jcbVolumes
 
JLabel jlBlocks
 
JLabel jlVolumes
 
TasksEngine ctfTasks
 
GalleryData data
 
JPanel buttonspn
 
JButton searchbt
 
JButton plotbt
 
JButton chimerabt
 
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-Static Protected Attributes

static final float MAX_HEIGHT_RATE = 2.0f / 3.0f
 
static final float DIM_RATE = 4.0f / 3.0f
 
static final int MIN_WIDTH = 800
 
static int MIN_HEIGHT
 
static int MAX_HEIGHT
 
static int MAX_WIDTH
 
static Dimension screenSize
 
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Detailed Description

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This is the main frame used in showj

Author
airen
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Definition at line 127 of file GalleryJFrame.java.

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◆ GalleryJFrame() [1/3]

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xmipp.viewer.windows.GalleryJFrame.GalleryJFrame (String filename,
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Definition at line 236 of file GalleryJFrame.java.

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237  {
238  super();
239  init(new GalleryData(this, filename, parameters));
240  }
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Definition at line 242 of file GalleryJFrame.java.

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243  {
244  super();
245  init(new GalleryData(this, parameters, md));
246  }
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Definition at line 248 of file GalleryJFrame.java.

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249  {
250  super();
251  init(data);
252  }
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◆ changeView()

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Definition at line 985 of file GalleryJFrame.java.

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986  {
987  data.changeMode();
988  boolean[] selection = null;
989  if(!data.isVolumeMd())
990  selection = gallery.getSelection();
991  reloadTableData(selection);
992  if(gallery.getSelTo() != -1)
993  {
994  Point coords = gallery.getCoords(gallery.getSelTo());
995  makeVisible(coords.y, coords.x);
996  }
997 
998  }
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Close the application, check if changes first

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Definition at line 302 of file GalleryJFrame.java.

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303  {
304  close(true);
305  }// function close
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void xmipp.viewer.windows.GalleryJFrame.close (boolean ask)
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-

Close the application, check if changes first

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Definition at line 308 of file GalleryJFrame.java.

-
309  {
310  boolean isclose = true;
311  if(ask)
312  isclose = proceedWithChanges();
313  if (isclose)
314  {
315  setVisible(false);
316  dispose();
317  XmippApplication.removeInstance(false);
318 
319  }
320  }// function close
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◆ createCombos()

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void xmipp.viewer.windows.GalleryJFrame.createCombos ()
- 		-inlineprotected
-
-

Create combos for selection of block and volume if its the case

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Definition at line 1160 of file GalleryJFrame.java.

-
1161  {
1162  cbPanel = new JPanel();
1163  // add some padding
1164  cbPanel.setBorder(new EmptyBorder(5, 5, 5, 5));
1165  cbPanel.setLayout(new BoxLayout(cbPanel,BoxLayout.LINE_AXIS));
1166 
1167  // Add blocks selector combo
1168  jlBlocks = new JLabel(XmippLabel.LABEL_BLOCK);
1169  jcbBlocks = new JComboBox();
1170  DEBUG.printFormat("data.getNumberOfBlocks: %d\n", data.getNumberOfBlocks());
1171 
1172  if (data.getNumberOfBlocks() > 0)
1173  {
1174  cbPanel.add(jlBlocks);
1175  jcbBlocks.setModel(new ComboBoxModel()
1176  {
1177 
1178  @Override
1179  public int getSize()
1180  {
1181  return data.getNumberOfBlocks();
1182  }
1183 
1184  @Override
1185  public Object getElementAt(int index)
1186  {
1187  return data.getBlock(index);
1188  }
1189 
1190  @Override
1191  public void setSelectedItem(Object item)
1192  {
1193  if (proceedWithChanges())
1194  selectBlock((String)item);
1195  }
1196 
1197  @Override
1198  public Object getSelectedItem()
1199  {
1200  return data.getSelectedBlock();
1201  }
1202 
1203  @Override
1204  public void removeListDataListener(ListDataListener arg0)
1205  {
1206  }
1207 
1208  @Override
1209  public void addListDataListener(ListDataListener arg0)
1210  {
1211  // TODO Auto-generated method stub
1212  }
1213  });
1214 
1215  cbPanel.add(jcbBlocks);
1216  }
1217  // Add volumes selector combo
1218  cbPanel.add(Box.createRigidArea(new Dimension(5,0)));
1219  jlVolumes = new JLabel(XmippLabel.LABEL_VOLUME);
1220  cbPanel.add(jlVolumes);
1221  jcbVolumes = new JComboBox();
1222  jcbVolumes.setModel(new VolumesComboBoxModel());
1223  cbPanel.add(jcbVolumes);
1224  }
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◆ createGUI()

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void xmipp.viewer.windows.GalleryJFrame.createGUI ()
- 		-inlineprotected
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Function to create general GUI base on a TableModel. It will use helper functions to create different components of the GUI

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Definition at line 354 of file GalleryJFrame.java.

-
355  {
356  // Create file chooser and set current dir
357  //setIconImage(XmippResource.getIcon("xmipp_logo.png").getImage());
358  if (data.getFileName() != null)
359  fc = new XmippFileChooser(new File(data.getFileName()));
360  else
361  fc = new XmippFileChooser();
362  ctfTasks = new TasksEngine(GalleryJFrame.this);
363 
364  isUpdating = true; // avoid handling some changes events
365 
366  setGalleryTitle();
367  setDefaultCloseOperation(DO_NOTHING_ON_CLOSE);
368  setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
369  addWindowListener(new WindowAdapter()
370  {
371  @Override
372  public void windowClosing(WindowEvent arg0)
373  {
374  close();
375  }
376  });
377 
378  // Get main pane and set layout
379  Container pane = getContentPane();
380  JPanel container = new JPanel(new GridBagLayout());
381  pane.add(container);
382  // container.setLayout(new GridBagLayout());
383  GridBagConstraints c = new GridBagConstraints();
384 
385  // Create toolbar buttons
386  createToolbar();
387  container.add(toolBar, XmippWindowUtil.getConstraints(c, 0, 0, 1, 1, GridBagConstraints.HORIZONTAL));
388  setInitialValues();
389 
390  // Create combos for selection of blocks and/or volumes
391  createCombos();
392  container.add(cbPanel, XmippWindowUtil.getConstraints(c, 0, 1, 1, 1, GridBagConstraints.HORIZONTAL));
393  updateVisibleCombos();
394 
395  jspContent = new GalleryScroll();
396  // Create table
397  createTable();
398 
399  c.weightx = 1.0;
400  c.weighty = 1.0;
401  container.add(jspContent, XmippWindowUtil.getConstraints(c, 0, 2, 1, 1, GridBagConstraints.BOTH));
402  c.weightx = 0;
403  c.weighty = 0;
404 
405  buttonspn = new JPanel(new FlowLayout(FlowLayout.TRAILING));
406  container.add(buttonspn, XmippWindowUtil.getConstraints(c, 0, 3, 1, 1, GridBagConstraints.HORIZONTAL));
407 
408  // Create the menu for table
409  initGalleryMenu();
410  setJMenuBar(menu.getMenuBar());
411  jpopUpMenuTable = new GalleryPopupMenu();
412  menu.update();
413 
414  // pack();
415  isUpdating = false;
416 
417  // Zoom in with Ctrl + P
418  InputMap imap = container.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
419  ActionMap amap = container.getActionMap();
420  imap.put(KeyStroke.getKeyStroke("ctrl released P"), "zoomIn");
421  amap.put("zoomIn", new AbstractAction()
422  {
423  @Override
424  public void actionPerformed(ActionEvent e)
425  {
426  zoomChange(true);
427  }
428 
429  });
430  // Zoom in with Ctrl + O
431  imap.put(KeyStroke.getKeyStroke("ctrl released M"), "zoomOut");
432  amap.put("zoomOut", new AbstractAction()
433  {
434  @Override
435  public void actionPerformed(ActionEvent e)
436  {
437  zoomChange(false);
438  }
439 
440  });
441 
442  // Change view with Ctrl + Tab
443  imap.put(KeyStroke.getKeyStroke("ctrl released I"), "changeView");
444  amap.put("changeView", new AbstractAction()
445  {
446  @Override
447  public void actionPerformed(ActionEvent e)
448  {
449  changeView();
450  }
451  });
452  enableToolBarActions();
453  pack();
454  XmippWindowUtil.centerWindows(this);
455  setVisible(true);
456  SwingUtilities.invokeLater(new Runnable()
457  {
458  public void run()
459  {
460  addComponentListener(new java.awt.event.ComponentAdapter()
461  {
462  public void componentResized(java.awt.event.ComponentEvent evt)
463  {
464  formComponentResized(evt);
465  }
466  });
467  }
468  });
469  XmippWindowUtil.setScipionImageIcon(this);
470  }
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xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
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◆ createModel() [1/2]

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void xmipp.viewer.windows.GalleryJFrame.createModel () throws Exception
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Definition at line 277 of file GalleryJFrame.java.

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278  {
279  createModel(null);
280  }
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◆ createModel() [2/2]

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void xmipp.viewer.windows.GalleryJFrame.createModel (boolean [] selection)
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Function to create the gallery type depending on the filename

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Definition at line 284 of file GalleryJFrame.java.

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285  {
286  gallery = data.createModel(selection);
287  if (data.getModelColumns() != null)
288  gallery.setColumns(data.getModelColumns());
289  else if (data.getModelRows() != null)
290  gallery.setRows(data.getModelRows());
291  int index = gallery.getSelTo();
292  if(jsGoToImage != null)
293  jsGoToImage.setValue(index + 1);
294  }
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ImageGalleryTableModel createModel(boolean[] selection)
Definition: GalleryData.java:665
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◆ createToolbar()

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void xmipp.viewer.windows.GalleryJFrame.createToolbar ()
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Definition at line 1000 of file GalleryJFrame.java.

-
1000  {
1001  // Create Main TOOLBAR
1002  toolBar = new JToolBar();
1003  toolBar.setFloatable(false);
1004  toolBar.setRollover(true);
1005  toolBar.setLayout(new FlowLayout(FlowLayout.LEFT));
1006 
1007  btnChangeView = new JButton();
1008  // updateViewState();
1009  btnChangeView.addActionListener(new ActionListener() {
1010  @Override
1011  public void actionPerformed(ActionEvent e) {
1012  changeView();
1013  }
1014  });
1015 
1016  toolBar.add(btnChangeView);
1017  toolBar.addSeparator();
1018 
1019  jlZoom = new javax.swing.JLabel();
1020  jsZoom = new javax.swing.JSpinner();
1021  jlZoom.setIcon(XmippResource.getIcon(XmippResource.ZOOM));
1022  jlZoom.setToolTipText(XmippLabel.LABEL_ZOOM);
1023  toolBar.add(jlZoom);
1024 
1025  jsZoom.setModel(new javax.swing.SpinnerNumberModel(Integer.valueOf(1), Integer.valueOf(1), null, Integer.valueOf(1)));
1026  jsZoom.addChangeListener(new javax.swing.event.ChangeListener() {
1027  public void stateChanged(javax.swing.event.ChangeEvent evt) {
1028  Integer zoom = (Integer) jsZoom.getValue();
1029  if (gallery.getCellSize().getHeight() < 30 && zoom < gallery.data.getZoom()) {
1030  jsZoom.setValue(gallery.data.getZoom());//keep previous zoom
1031  return;
1032  }
1033  gallery.setZoom(zoom);
1034  makeVisible(gallery.getFirstSelectedIndex(), 0);
1035  // gallery.updateTableSelection(table);
1036  }
1037  });
1038 
1039  toolBar.add(jsZoom);
1040  toolBar.addSeparator();
1041 
1042  jlGoToImage = new javax.swing.JLabel();
1043  jsGoToImage = new javax.swing.JSpinner();
1044  jlGoToImage.setIcon(XmippResource.getIcon(XmippResource.GOTO));
1045  jlGoToImage.setToolTipText(XmippLabel.LABEL_GOTO_ITEM);
1046  toolBar.add(jlGoToImage);
1047 
1048  if (gallery.getSize() > 0)
1049  jsGoToImage.setValue(1);
1050 
1051  jsGoToImage.addChangeListener(new javax.swing.event.ChangeListener() {
1052  public void stateChanged(javax.swing.event.ChangeEvent evt) {
1053  jsGoToImageStateChanged(evt);
1054  }
1055  });
1056  toolBar.add(jsGoToImage);
1057 
1058  toolBar.addSeparator();
1059 
1060  jcbAutoAdjustColumns = new JToggleButton();
1061  setupButton(jcbAutoAdjustColumns, XmippResource.ADJUST_COLS, XmippLabel.MSG_ADJUST_COLS, new java.awt.event.ActionListener() {
1062  public void actionPerformed(java.awt.event.ActionEvent evt) {
1063  autoAdjustColumns(jcbAutoAdjustColumns.isSelected());
1064  }
1065  });
1066  jcbAutoAdjustColumns.setSelected(data.isAutoAdjust());
1067  jlRows = new javax.swing.JLabel();
1068  jsRows = new javax.swing.JSpinner();
1069  jlColumns = new javax.swing.JLabel();
1070  jsColumns = new javax.swing.JSpinner();
1071  toolBar.add(jcbAutoAdjustColumns);
1072 
1073  jlColumns.setText(XmippLabel.LABEL_COLUMNS);
1074  toolBar.add(jlColumns);
1075 
1076  jsColumns.addChangeListener(new javax.swing.event.ChangeListener() {
1077  public void stateChanged(javax.swing.event.ChangeEvent evt) {
1078  jsColumnsStateChanged(evt);
1079  }
1080  });
1081  toolBar.add(jsColumns);
1082 
1083  jlRows.setText(XmippLabel.LABEL_ROWS);
1084  toolBar.add(jlRows);
1085 
1086  jsRows.addChangeListener(new javax.swing.event.ChangeListener() {
1087  public void stateChanged(javax.swing.event.ChangeEvent evt) {
1088  jsRowsStateChanged(evt);
1089  }
1090  });
1091  toolBar.add(jsRows);
1092 
1093  // Some settings of the spinners
1094 
1095 // if (gallery.getSize() > 0)
1096 // {
1097 //
1098 // jsRows.setModel(new SpinnerNumberModel(1, 1, gallery.getSize(), 1));
1099 // jsColumns.setModel(new SpinnerNumberModel(1, 1, gallery.getSize(), 1));
1100 // jsGoToImage.setModel(new SpinnerNumberModel(1, 1, gallery.getSize(), 1));
1101 // }
1102 
1103  int TEXTWIDTH = 4;
1104  ((JSpinner.NumberEditor) jsZoom.getEditor()).getTextField().setColumns(TEXTWIDTH);
1105  ((JSpinner.NumberEditor) jsGoToImage.getEditor()).getTextField().setColumns(TEXTWIDTH);
1106  ((JSpinner.NumberEditor) jsRows.getEditor()).getTextField().setColumns(TEXTWIDTH);
1107  ((JSpinner.NumberEditor) jsColumns.getEditor()).getTextField().setColumns(TEXTWIDTH);
1108 
1109  initResliceButtonMenu();
1110  toolBar.add(reslicebt);
1111  searchbt = new JButton(XmippResource.getIcon("binocular.png"));
1112  searchbt.setEnabled(data.isTableMode());
1113  searchbt.addActionListener(new ActionListener() {
1114 
1115  @Override
1116  public void actionPerformed(ActionEvent ae) {
1117  try {
1118  findReplace();
1119  } catch (Exception ex) {
1120  Logger.getLogger(GalleryJFrame.class.getName()).log(Level.SEVERE, null, ex);
1121  }
1122  }
1123  });
1124  toolBar.add(searchbt);
1125  plotbt = new JButton(XmippResource.getIcon("plot.png"));
1126  plotbt.setEnabled(data.isTableMode());
1127  plotbt.addActionListener(new ActionListener() {
1128 
1129  @Override
1130  public void actionPerformed(ActionEvent ae) {
1131  try {
1132  plotColumns();
1133  } catch (Exception ex) {
1134  Logger.getLogger(GalleryJFrame.class.getName()).log(Level.SEVERE, null, ex);
1135  }
1136  }
1137  });
1138 
1139  toolBar.add(plotbt);
1140  chimerabt = new JButton(XmippResource.getIcon("chimera.png"));
1141  chimerabt.setEnabled(data.isVolumeMode());
1142 
1143  if ( getChimera() == null){
1144  chimerabt.setEnabled(false);
1145  chimerabt.setToolTipText("ChimeraX not available, looking at " + CHIMERA_LAUNCHER);
1146  }
1147 
1148  chimerabt.addActionListener(new ActionListener() {
1149 
1150  @Override
1151  public void actionPerformed(ActionEvent ae) {
1152  openWithChimera();
1153  }
1154  });
1155  toolBar.add(chimerabt);
1156 
1157  }// function createToolbar
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xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
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xmipp.viewer.windows.GalleryJFrame.setupButton
void setupButton(AbstractButton btn, String icon, String text, ActionListener listener)
Definition: GalleryJFrame.java:813
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◆ done()

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void xmipp.viewer.windows.GalleryJFrame.done ()
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Implements xmipp.viewer.ctf.iCTFGUI.

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Definition at line 2152 of file GalleryJFrame.java.

-
2153  {
2154  XmippDialog.showInfo(this, "Calculating ctf: DONE");
2155  }
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◆ enableToolBarActions()

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void xmipp.viewer.windows.GalleryJFrame.enableToolBarActions ()
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Definition at line 1244 of file GalleryJFrame.java.

-
1245  {
1246  boolean hasRender = data.allowGallery();
1247  boolean isCol = data.isColumnFormat();
1248 
1249  btnChangeView.setEnabled(hasRender && isCol && data.renderImages());
1250  jsZoom.setEnabled(hasRender);
1251  jlZoom.setEnabled(hasRender);
1252 
1253  jsGoToImage.setEnabled(isCol && gallery.getSize() > 0);
1254  jlGoToImage.setEnabled(isCol);
1255 
1256  }
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◆ fillLabel()

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void xmipp.viewer.windows.GalleryJFrame.fillLabel (int label,
String mode,
String... values 
) throws Exception
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Fill some label mode can be: "constant", "linear", "uniform", "gaussian" values is a list of string

- -

Definition at line 920 of file GalleryJFrame.java.

-
921  {
922  if (mode.equalsIgnoreCase(MetaData.FILL_CONSTANT))
923  data.fillConstant(label, values[0]);
924  else
925  {
926  double v1 = Double.parseDouble(values[0]);
927  double v2 = Double.parseDouble(values[1]);
928  if (mode.equalsIgnoreCase(MetaData.FILL_LINEAR))
929  data.fillLinear(label, v1, v2);
930  else if (mode.equalsIgnoreCase(MetaData.FILL_RAND_UNIFORM))
931  data.fillRandom(label, "uniform", v1, v2);
932  else if (mode.equalsIgnoreCase(MetaData.FILL_RAND_GAUSSIAN))
933  data.fillRandom(label, "gaussian", v1, v2);
934  else
935  throw new Exception("Unknown label fill mode: " + mode);
936  }
937  reloadMd();
938  }
-
xmipp.viewer.models.GalleryData.fillConstant
void fillConstant(int label, String value)
Definition: GalleryData.java:1399
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xmipp.viewer.models.GalleryData.fillLinear
void fillLinear(int label, Double start, Double step)
Definition: GalleryData.java:1403
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xmipp.viewer.models.GalleryData.fillRandom
void fillRandom(int label, String mode, double op1, double op2)
Definition: GalleryData.java:1407
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◆ findReplace()

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void xmipp.viewer.windows.GalleryJFrame.findReplace ()
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-

Find and replace in metadata

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Definition at line 968 of file GalleryJFrame.java.

-
969  {
970  MDSearchJDialog dlg = new MDSearchJDialog(this, table, data);
971  dlg.setVisible(true);
972  }
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◆ fireTableRowsUpdated()

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void xmipp.viewer.windows.GalleryJFrame.fireTableRowsUpdated (int from,
int to 
)
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Definition at line 502 of file GalleryJFrame.java.

-
502  {
503  gallery.fireTableRowsUpdated(from, to);
504  }
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◆ getBlock()

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String xmipp.viewer.windows.GalleryJFrame.getBlock ()
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Definition at line 2282 of file GalleryJFrame.java.

-
2283  {
2284  return (String) jcbBlocks.getSelectedItem();
2285  }
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◆ getData()

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Definition at line 296 of file GalleryJFrame.java.

-
297  {
298  return data;
299  }
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◆ getFilename()

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String xmipp.viewer.windows.GalleryJFrame.getFilename ()
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Implements xmipp.viewer.ctf.iCTFGUI.

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Definition at line 2194 of file GalleryJFrame.java.

-
2195  {
2196  return data.getFileName();
2197  }
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◆ getKeyAssist()

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Map<Object, Object> xmipp.viewer.windows.GalleryJFrame.getKeyAssist ()
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Definition at line 2351 of file GalleryJFrame.java.

-
2352  {
2353  Map<Object, Object> map = Collections.synchronizedMap(new LinkedHashMap<>());
2354  map.put("Shift + scroll up/ctrl + P", "Zoom in if images displayed");
2355  map.put("Shift + scroll down/ctrl + M", "Zoom out if images displayed");
2356  map.put("Left click", "Selects a cell in gallery mode and a row in table mode");
2357  map.put("Right click", "Selects a row in table mode and displays row menu");
2358  map.put("Supr", "Delete selected cell in gallery mode and row in table mode");
2359  map.put("Up", "Select previous row in table mode and cell in previous row in gallery mode");
2360  map.put("Down", "Select next row in table mode and cell in next row in gallery mode");
2361  map.put("Left", "Select previous cell in gallery mode");
2362  map.put("Right", "Select next cell in gallery mode");
2363  map.put("Ctrl + O", "Open file");
2364  map.put("Ctrl + J", "Open with ImageJ");
2365  map.put("Ctrl + S", "Save");
2366  map.put("F5", "Refresh");
2367  map.put("Ctrl + Q", "Exit");
2368  map.put("Ctrl + N", "Display global normalization");
2369  map.put("Ctrl + L", "Display labels");
2370  map.put("Ctrl + R", "Render images");
2371  map.put("Ctrl + G", "Apply geometry");
2372  map.put("Ctrl + W", "Wrap");
2373  map.put("Space Bar", "Enable/Disable selection");
2374 
2375  return map;
2376  }
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◆ getTasksEngine()

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Definition at line 2378 of file GalleryJFrame.java.

-
2379  {
2380  return ctfTasks;
2381  }
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◆ initGalleryMenu()

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Definition at line 508 of file GalleryJFrame.java.

-
508  {
509  menu = new GalleryMenu();
510 
511  }
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◆ initResliceButtonMenu()

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void xmipp.viewer.windows.GalleryJFrame.initResliceButtonMenu ()
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Definition at line 2301 of file GalleryJFrame.java.

-
2302  {
2303  // Create the popup menu.
2304  String reslice;
2305  final JPopupMenu popup = new JPopupMenu();
2306  JRadioButtonMenuItem mi;
2307  reslicegroup = new ButtonGroup();
2308  for (int i = 0; i < reslices.length; i++)
2309  {
2310  reslice = reslices[i];
2311  mi = new JRadioButtonMenuItem(reslice);
2312  reslicegroup.add(mi);
2313  if (i == 0)
2314  reslicegroup.setSelected(mi.getModel(), true);
2315  mi.setActionCommand(String.valueOf(ImageGeneric.VIEWS[i]));
2316  popup.add(mi);
2317  mi.addActionListener(new ResliceActionListener());
2318 
2319  }
2320  reslicebt = new JButton(XmippResource.getIcon("topview.png"));
2321  reslicebt.setToolTipText("Reslice");
2322  reslicebt.setContentAreaFilled(false);
2323  reslicebt.setFocusPainted(false);
2324  reslicebt.setOpaque(false);
2325 
2326  reslicebt.addMouseListener(new MouseAdapter()
2327  {
2328  public void mousePressed(MouseEvent e)
2329  {
2330  popup.show(e.getComponent(), e.getX(), e.getY());
2331  }
2332  });
2333 
2334  }
-
-
- -

◆ openChimera()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.openChimera (String file,
boolean link 
)
- 		-inlineprotected
-
- -

Definition at line 2385 of file GalleryJFrame.java.

-
2386  {
2387  try
2388  {
2389  // CHIMERA_LAUNCHER will be any String ready to place a file name having %1 in it
2390  String chimera_launcher = getChimera();
2391  if(chimera_launcher == null)
2392  {
2393  XmippDialog.showError(GalleryJFrame.this, "ChimeraX is not available");
2394  return;
2395  }
2396 
2397  // There must be a better way to "clean" :mrc annotations
2398  if(file.endsWith(":mrc"))
2399  file = file.replace(":mrc", "");
2400 
2401  // make file absolute
2402  // Create a file object
2403  File f = new File(file);
2404 
2405  String run = String.format(chimera_launcher, f.getAbsolutePath());
2406  HashMap<String, String> chimeraEnv = new HashMap<String, String>() {
2407  {
2408  put("LD_LIBRARY_PATH", "");
2409  }
2410  };
2411  String output = XmippWindowUtil.executeCommand(run, false, chimeraEnv);
2412 
2413  }
2414  catch (Exception ex)
2415  {
2416  ex.printStackTrace();
2417  }
2418  }
xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
-
-
-
- -

◆ openMetadata()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.openMetadata (final MetaData md)
- 		-inline
-
-

Open another metadata separately *

- -

Definition at line 257 of file GalleryJFrame.java.

-
258  {
259  try
260  {
261  SwingUtilities.invokeLater(new Runnable() {
262 
263  @Override
264  public void run() {
265  new GalleryJFrame(md, new Params());
266  }
267  });
268 
269  }
270  catch(Exception e)
271  {
272  XmippDialog.showError(this, e.getMessage());
273  }
274 
275  }
xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
-
-
-
- -

◆ openMicrographs()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.openMicrographs ()
- 		-inline
-
- -

Definition at line 2253 of file GalleryJFrame.java.

-
2254  {
2255  if (extractframe == null || !extractframe.isVisible())
2256  extractframe = ExtractParticlePicker.open(getBlock(), data.getFileName(), gallery.getImageWidth(), this);
2257  refreshExtractFrame();
2258  }
- - - - -
-
-
- -

◆ openWithChimera()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.openWithChimera ()
- 		-inlineprotected
-
- -

Definition at line 2424 of file GalleryJFrame.java.

-
2425  {
2426  if(data.containsGeometryInfo("3D") || data.containsGeometryInfo("Projection") )
2427  {
2428  fc.setApproveButtonText("Open");
2429  fc.setDialogTitle("Open with ChimeraX");
2430  fc.setApproveButtonToolTipText("Choose a chimera compatible file.");
2431  int result = fc.showOpenDialog(GalleryJFrame.this);
2432  if(result != XmippFileChooser.CANCEL_OPTION)
2433  {
2434  String path = fc.getSelectedPath();
2435  if(!Filename.isVolumeExt(path))
2436  {
2437  XmippDialog.showError(GalleryJFrame.this, XmippMessage.getFileTypeNotSupportedMsg(path));
2438  return;
2439  }
2440  openChimera(path, true);
2441  }
2442  }
2443  else
2444  openChimera(data.getSelVolumeFile(), false);
2445  }
- -
xmipp.viewer.windows.GalleryJFrame.openChimera
void openChimera(String file, boolean link)
Definition: GalleryJFrame.java:2385
- - - -
xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
-
-
-
- -

◆ plotColumns()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.plotColumns ()
- 		-inlineprotected
-
- -

Definition at line 1547 of file GalleryJFrame.java.

-
1547  {
1548  PlotJDialog dlg = new PlotJDialog(GalleryJFrame.this);
1549  dlg.showDialog();
1550  }
xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
-
-
-
- -

◆ proceedWithChanges()

- -
-
- - - - - -
- - - - - - - -
boolean xmipp.viewer.windows.GalleryJFrame.proceedWithChanges ()
- 		-inline
-
-

Check if there are changes to proceed

- -

Definition at line 323 of file GalleryJFrame.java.

-
324  {
325  boolean proceed = true;
326  if (data.hasMdChanges())
327  {
328  XmippQuestionDialog dlg = new XmippQuestionDialog(GalleryJFrame.this, "Do you want to save metadata changes?");
329  if (dlg.showDialog())
330  try
331  {
332  save();
333  }
334  catch (Exception e)
335  {
336  showException(e);
337  }
338  else
339  proceed = !dlg.isCanceled();
340  }
341  return proceed;
342  }
-
xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
- - -
-
-
- -

◆ refreshActive()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.refreshActive (long id,
boolean enabled 
)
- 		-inline
-
- -

Definition at line 2271 of file GalleryJFrame.java.

-
2272  {
2273  for (int i = 0; i < data.size(); i++)
2274  if (id == data.getId(i))
2275  {
2276  goToImage(i);
2277  gallery.setSelectionEnabled(enabled);
2278  }
2279 
2280  }
- - - - -
-
-
- -

◆ reloadFile()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.reloadFile (String file,
boolean changed 
) throws Exception
- 		-inline
-
- -

Definition at line 2287 of file GalleryJFrame.java.

-
2288  {
2289  createModel(gallery.getSelection());
2290  reloadMd(changed);
2291  reloadCombos();
2292  }
- - -
-
-
- -

◆ reloadTableData() [1/3]

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.reloadTableData ()
- 		-inline
-
- -

Definition at line 851 of file GalleryJFrame.java.

-
852  {
853  reloadTableData(true, null);
854  }
-
-
-
- -

◆ reloadTableData() [2/3]

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.reloadTableData (boolean [] selection)
- 		-inline
-
- -

Definition at line 856 of file GalleryJFrame.java.

-
857  {
858  reloadTableData(true, selection);
859  }
-
-
-
- -

◆ reloadTableData() [3/3]

- -
-
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- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.reloadTableData (boolean changed,
boolean [] selection 
)
- 		-inline
-
-

Reload table data

- -

Definition at line 862 of file GalleryJFrame.java.

-
863  {
864  try
865  {
866  //DEBUG.printMessage("reloadTableData...");
867  if (table != null)
868  table.removeAll();
869  createModel(selection);
870  // gallery.setShowLabels(menu.getShowLabel());
871  createTable();
872 
873  menu.update();
874  updateVisibleCombos();
875  searchbt.setEnabled(data.isTableMode());
876  plotbt.setEnabled(data.isTableMode());
877  if (dlgSave != null && changed)
878  dlgSave.setInitialValues();
879 
880  this.saved = !changed;
881  setGalleryTitle();
882  Integer rows = data.getModelRows();
883  Integer cols = data.getModelColumns();
884  if (rows != null)
885  gallery.setRows(rows);
886  if (cols != null)
887  gallery.setColumns(cols);
888 
889 
890  }
891  catch (Exception e)
892  {
893  e.printStackTrace();
894  }
895  }
- - - - - - - - - - - - - -
-
-
- -

◆ removeLabel()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.removeLabel (int label) throws Exception
- 		-inline
-
-

Drop some label from the metadata

- -

Definition at line 975 of file GalleryJFrame.java.

-
976  {
977  data.removeLabel(label);
978  reloadMd();
979  }
- -
-
-
- -

◆ removeObjects()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.removeObjects (boolean selected)
- 		-inline
-
-

Delete selected or disabled items if 'selected' is true, selection is removed if false, the disabled items

- -

Definition at line 944 of file GalleryJFrame.java.

-
945  {
946  try
947  {
948  String type = selected ? "selected" : "disabled";
949  if (XmippDialog.showWarning(this, String.format("Are you sure to delete %s items?", type)))
950  {
951  if (selected)
952  data.removeSelection(gallery.getSelection());
953  else
954  data.removeDisabled();
955  gallery.clearSelection();
956  reloadMd();
957  }
958  }
959  catch (Exception ex)
960  {
961  showException(ex);
962  }
963  }
- - -
xmipp.viewer.models.GalleryData.removeSelection
void removeSelection(boolean[] selection)
Definition: GalleryData.java:1211
- - - -
-
-
- -

◆ runInBackground()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.runInBackground (int operation)
- 		-inline
-
-

Function to create and launch the worker, blocking the gui

- -

Definition at line 766 of file GalleryJFrame.java.

-
767  {
768 
769  boolean selected = false;
770  if(gallery.hasSelection())
771  {
772  int result = XmippDialog.showQuestionYesNoCancel(this, "This operation processes all images by default. Would you like to use selection instead?");
773 
774  if(result == XmippQuestionDialog.YES_OPTION)
775  selected = true;
776  else if(result == XmippQuestionDialog.CANCEL_OPTION)
777 
778  return;
779  }
780 
781 
782 
783  Worker w = new Worker(operation, selected, this);
784  XmippWindowUtil.blockGUI(this, w.getMessage());
785  Thread thr = new Thread(w);
786  thr.start();
787  }
- -
-
-
- -

◆ saveMd() [1/2]

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.saveMd () throws Exception
- 		-inlineprotected
-
- -

Definition at line 2157 of file GalleryJFrame.java.

-
2158  {
2159  saveMd(dlgSave.getMdFilename(), false, dlgSave.isOverwrite(), true );
2160  }
- - -
-
-
- -

◆ saveMd() [2/2]

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-
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void xmipp.viewer.windows.GalleryJFrame.saveMd (String path,
boolean saveall,
boolean isoverwrite,
boolean reload 
)
- 		-inlineprotected
-
- -

Definition at line 2164 of file GalleryJFrame.java.

-
2165  {
2166  try
2167  {
2168  data.saveMd(path, saveall, isoverwrite);
2169  String file;
2170  if (path.contains("@"))
2171  file = path.substring(path.lastIndexOf("@") + 1);
2172  else
2173  {
2174  file = path;
2175  path = getBlock() + "@" + file;
2176  }
2177  if(reload)
2178  {
2179  gallery.data.setFileName(file);
2180  if (path.contains("@"))
2181  gallery.data.selectBlock(path.substring(0, path.lastIndexOf("@")));
2182  reloadFile(file, false);
2183  setGalleryTitle();
2184  }
2185  }
2186  catch (Exception e)
2187  {
2188  e.printStackTrace();
2189  }
2190  }// function saveMd
-
xmipp.viewer.windows.GalleryJFrame.reloadFile
void reloadFile(String file, boolean changed)
Definition: GalleryJFrame.java:2287
- -
xmipp.viewer.models.GalleryData.saveMd
void saveMd(String path, boolean saveall, boolean isoverwrite)
Definition: GalleryData.java:1573
-
xmipp.viewer.models.GalleryData.selectBlock
void selectBlock(String block)
Definition: GalleryData.java:654
- - - -
-
-
- -

◆ selectBlock()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.selectBlock (String block)
- 		-inline
-
- -

Definition at line 1226 of file GalleryJFrame.java.

-
1227  {
1228  data.selectBlock(block);
1229  jcbVolumes.invalidate();
1230  try
1231  {
1232  data.loadMd();
1233  reloadTableData();
1234  autoAdjustColumns(data.isAutoAdjust());
1235  enableToolBarActions();
1236  }
1237  catch (Exception e)
1238  {
1239  // TODO Auto-generated catch block
1240  e.printStackTrace();
1241  }
1242  }
- - - -
xmipp.viewer.models.GalleryData.selectBlock
void selectBlock(String block)
Definition: GalleryData.java:654
- - -
-
-
- -

◆ selectItem()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.selectItem (int row,
int col 
)
- 		-inline
-
- -

Definition at line 1433 of file GalleryJFrame.java.

-
1434  {
1435  if (row < 0 || row > table.getRowCount() - 1 || col < 0 || col > table.getColumnCount())
1436  return;
1437 
1438  if (gallery.data.isGalleryMode() && row * table.getColumnCount() + col + 1 > gallery.getSize())
1439  {
1440  Point coords = gallery.getCoords(gallery.getSize() - 1);
1441  row = coords.y;
1442  col = coords.x;
1443  }
1444  gallery.clearSelection();
1445  gallery.touchItem(row, col);
1446  makeVisible(row, col);
1447 
1448  }
- - - - - - -
-
-
- -

◆ setAutoAdjustColumns()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.setAutoAdjustColumns (boolean autoAdjustColumns)
- 		-inline
-
- -

Definition at line 734 of file GalleryJFrame.java.

-
735  {
736  jcbAutoAdjustColumns.setSelected(autoAdjustColumns);
737  jcbAutoAdjustColumns.setEnabled(!data.isTableMode());
738  jsColumns.setEnabled(!autoAdjustColumns);
739  jsRows.setEnabled(!autoAdjustColumns);
740  }
- - - -
-
-
- -

◆ setRowBusy()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.setRowBusy (int row)
- 		-inline
-
- -

Implements xmipp.viewer.ctf.iCTFGUI.

- -

Definition at line 2136 of file GalleryJFrame.java.

-
2137  {
2138 
2139  gallery.setRowBusy(row);
2140  }
- -
-
-
- -

◆ setRowIdle()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.setRowIdle (int row)
- 		-inline
-
- -

Implements xmipp.viewer.ctf.iCTFGUI.

- -

Definition at line 2143 of file GalleryJFrame.java.

-
2144  {
2145  gallery.setRowIdle(row);
2146 
2147  }
- -
-
-
- -

◆ setRunning()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.setRunning (boolean running)
- 		-inline
-
- -

Implements xmipp.viewer.ctf.iCTFGUI.

- -

Definition at line 2129 of file GalleryJFrame.java.

-
2130  {
2131  // XmippDialog.showInfo(this, String.format("Calculating ctf"));
2132  // XmippWindowUtil.blockGUI(getRootPane(), "Calculating CTF");
2133  }
-
-
- -

◆ setupButton()

- -
-
- - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.setupButton (AbstractButton btn,
String icon,
String text,
ActionListener listener 
)
- 		-inlineprotected
-
- -

Definition at line 813 of file GalleryJFrame.java.

-
814  {
815  // Add toggle button to set/unset global normalization
816  // JToggleButton btn = new javax.swing.JToggleButton();
817  btn.setFocusable(false);
818  btn.setIcon(XmippResource.getIcon(icon));
819  btn.setToolTipText(text);
820  btn.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
821  btn.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
822  btn.addActionListener(listener);
823  // return btn;
824  }
-
-
- -

◆ showException()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.showException (Exception e)
- 		-inline
-
- -

Definition at line 2123 of file GalleryJFrame.java.

-
2124  {
2125  XmippDialog.showException(this, e);
2126  }
-
-
- -

◆ tableMouseClicked()

- -
-
- - - - - -
- - - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.tableMouseClicked (MouseEvent evt)
- 		-inlineprotected
-
- -

Definition at line 1450 of file GalleryJFrame.java.

-
1451  {
1452  final Point p = evt.getPoint();
1453  int row = table.rowAtPoint(p);
1454  int col = table.columnAtPoint(p);
1455  col = table.convertColumnIndexToModel(col);
1456  int index = gallery.getIndex(row, col);
1457  if (!gallery.isValidIndex(index))
1458  return;
1459  if (evt.getButton() == MouseEvent.BUTTON1 && evt.getClickCount() > 1)
1460  {
1461  try
1462  {
1463  gallery.handleDoubleClick(row, col);
1464  }
1465  catch (Exception e)
1466  {
1467  XmippDialog.showError(this, e.getMessage());
1468  }
1469  }
1470  else
1471  {
1472  isUpdating = true;
1473  jsGoToImage.setValue(index + 1);
1474  isUpdating = false;
1475  // Ctrl adds items to selection, otherwise previous ones are removed.
1476  if (!evt.isControlDown() && !evt.isShiftDown())
1477  {
1478  if(evt.getButton() == MouseEvent.BUTTON1)
1479  {
1480  gallery.clearSelection();
1481  gallery.touchItem(row, col);
1482 
1483  }
1484  else
1485  {
1486  if(!gallery.isSelected(row, col))
1487  gallery.clearSelection();
1488  gallery.touchItem(row, col, true);
1489  }
1490 
1491  }
1492  else
1493  {
1494  if (evt.isShiftDown())
1495  gallery.selectRange(previousSelectedRow, previousSelectedCol, row, col);
1496  else if (evt.isControlDown())
1497  {
1498  gallery.touchItem(row, col);
1499  jsGoToImage.setValue(gallery.getSelTo() + 1);
1500  }
1501  }
1502 
1503  if (!evt.isShiftDown())
1504  {
1505  previousSelectedRow = row;
1506  previousSelectedCol = col;
1507  }
1508 
1509  final MouseEvent me = evt;
1510  if (evt.getButton() == MouseEvent.BUTTON3 && gallery.handleRightClick(row, col, jpopUpMenuTable))
1511  {
1512  SwingUtilities.invokeLater(new Runnable()
1513  {
1514  public void run()
1515  {
1516  jpopUpMenuTable.show(me.getComponent(), p);
1517  }
1518  });
1519  }
1520  }
1521  table.invalidate();
1522  table.repaint();
1523  refreshExtractFrame();
1524  }// function tableMouseClicked
xmipp.viewer.models.ImageGalleryTableModel.selectRange
void selectRange(int first_index, int last_index, boolean value)
Definition: ImageGalleryTableModel.java:421
- -
xmipp.viewer.models.ImageGalleryTableModel.handleRightClick
abstract boolean handleRightClick(int row, int col, XmippPopupMenuCreator xpopup)
-
xmipp.viewer.models.ImageGalleryTableModel.handleDoubleClick
abstract boolean handleDoubleClick(int row, int col)
- - - - - - - -
-
-
- -

◆ updateVisibleCombos()

- -
-
- - - - - -
- - - - - - - -
void xmipp.viewer.windows.GalleryJFrame.updateVisibleCombos ()
- 		-inlineprotected
-
- -

Definition at line 1351 of file GalleryJFrame.java.

-
1352  {
1353 
1354  boolean showBlocks = data.getNumberOfBlocks() > 0;
1355  boolean showVols = data.size() > 1 && data.isVolumeMode();
1356  jcbBlocks.setVisible(showBlocks);
1357  jcbVolumes.setVisible(showVols);
1358  jlBlocks.setVisible(showBlocks);
1359  jlVolumes.setVisible(showVols);
1360  cbPanel.setVisible(showBlocks || showVols);
1361  //pack();
1362  }
- - - - - - - - -
-
-
-

Member Data Documentation

- -

◆ buttonspn

- -
-
- - - - - -
- - - - -
JPanel xmipp.viewer.windows.GalleryJFrame.buttonspn
- 		-protected
-
- -

Definition at line 194 of file GalleryJFrame.java.

- -
-
- -

◆ cbPanel

- -
-
- - - - - -
- - - - -
JPanel xmipp.viewer.windows.GalleryJFrame.cbPanel
- 		-protected
-
- -

Definition at line 164 of file GalleryJFrame.java.

- -
-
- -

◆ CHIMERA_LAUNCHER

- -
-
- - - - - -
- - - - -
final String xmipp.viewer.windows.GalleryJFrame.CHIMERA_LAUNCHER = "CHIMERA_LAUNCHER"
- 		-static
-
- -

Definition at line 132 of file GalleryJFrame.java.

- -
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Definition at line 197 of file GalleryJFrame.java.

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Definition at line 169 of file GalleryJFrame.java.

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Definition at line 191 of file GalleryJFrame.java.

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Definition at line 181 of file GalleryJFrame.java.

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Definition at line 146 of file GalleryJFrame.java.

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Definition at line 137 of file GalleryJFrame.java.

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Definition at line 165 of file GalleryJFrame.java.

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Definition at line 166 of file GalleryJFrame.java.

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Definition at line 167 of file GalleryJFrame.java.

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Definition at line 168 of file GalleryJFrame.java.

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Definition at line 157 of file GalleryJFrame.java.

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Definition at line 158 of file GalleryJFrame.java.

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Definition at line 159 of file GalleryJFrame.java.

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Definition at line 161 of file GalleryJFrame.java.

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Definition at line 162 of file GalleryJFrame.java.

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Definition at line 179 of file GalleryJFrame.java.

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Definition at line 185 of file GalleryJFrame.java.

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Definition at line 145 of file GalleryJFrame.java.

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Definition at line 183 of file GalleryJFrame.java.

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Definition at line 182 of file GalleryJFrame.java.

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Definition at line 196 of file GalleryJFrame.java.

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Definition at line 186 of file GalleryJFrame.java.

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Definition at line 195 of file GalleryJFrame.java.

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xmipp.viewer.windows.GalleryJFrame.GalleryMenu Member List
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This is the complete list of members for xmipp.viewer.windows.GalleryJFrame.GalleryMenu, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippMenuCreatorinline
addDisplayLabelItems()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinlineprotected
addExtraMenuItems()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinline
addItem(String key, String text, String... values)xmipp.utils.XmippMenuCreatorinline
addRenderImageColumnItems()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinlineprotected
addSeparator(String key)xmipp.utils.XmippMenuBarCreatorinline
createItems()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinlineprotected
CTF_PROFILExmipp.utils.XmippMenuCreatorstatic
CTF_RECALCULATExmipp.utils.XmippMenuCreatorstatic
DISABLEDxmipp.utils.XmippMenuCreatorstatic
DISPLAYxmipp.utils.XmippMenuCreator
DISPLAY_APPLYGEOxmipp.utils.XmippMenuCreator
DISPLAY_COLUMNSxmipp.utils.XmippMenuCreator
DISPLAY_INVERTYxmipp.utils.XmippMenuCreator
DISPLAY_NORMALIZExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGExmipp.utils.XmippMenuCreator
DISPLAY_RENDERIMAGESxmipp.utils.XmippMenuCreator
DISPLAY_RESLICExmipp.utils.XmippMenuCreator
DISPLAY_RESLICE_VIEWSxmipp.utils.XmippMenuCreator
DISPLAY_SHOWLABELSxmipp.utils.XmippMenuCreator
DISPLAY_WRAPxmipp.utils.XmippMenuCreator
ENABLEDxmipp.utils.XmippMenuCreatorstatic
FILExmipp.utils.XmippMenuCreator
FILE_EXITxmipp.utils.XmippMenuCreator
FILE_EXPORTIMAGESxmipp.utils.XmippMenuCreator
FILE_INFOxmipp.utils.XmippMenuCreator
FILE_LINK_CHIMERAxmipp.utils.XmippMenuCreator
FILE_LOAD_SELxmipp.utils.XmippMenuCreator
FILE_OPENxmipp.utils.XmippMenuCreator
FILE_OPENMICROGRAPHSxmipp.utils.XmippMenuCreator
FILE_OPENWITH_CHIMERAxmipp.utils.XmippMenuCreator
FILE_OPENWITH_IJxmipp.utils.XmippMenuCreator
FILE_REFRESHxmipp.utils.XmippMenuCreator
FILE_SAVExmipp.utils.XmippMenuCreator
FILE_SAVE_SELxmipp.utils.XmippMenuCreator
FILE_SAVEASxmipp.utils.XmippMenuCreator
getItem(String key)xmipp.utils.XmippMenuCreatorinline
getItemEnabled(String key)xmipp.utils.XmippMenuCreatorinline
getItemSelected(String key)xmipp.utils.XmippMenuCreatorinline
getMenuBar()xmipp.utils.XmippMenuBarCreatorinline
groupsxmipp.utils.XmippMenuCreatorprotected
handleActionPerformed(ActionEvent evt)xmipp.viewer.windows.GalleryJFrame.GalleryMenuinlineprotected
HELPxmipp.utils.XmippMenuCreator
HELP_ONLINExmipp.utils.XmippMenuCreator
initItems()xmipp.utils.XmippMenuCreatorinline
INVERT_SELECTxmipp.utils.XmippMenuCreatorstatic
itemsxmipp.utils.XmippMenuCreatorprotected
KEY_ASSISTxmipp.utils.XmippMenuCreator
MD_ADD_OBJECTxmipp.utils.XmippMenuCreator
MD_CLASSESxmipp.utils.XmippMenuCreator
MD_EDIT_COLSxmipp.utils.XmippMenuCreator
MD_FIND_REPLACExmipp.utils.XmippMenuCreator
MD_REMOVE_DISABLEDxmipp.utils.XmippMenuCreator
MD_REMOVE_SELECTIONxmipp.utils.XmippMenuCreator
MD_SAVE_SELECTIONxmipp.utils.XmippMenuCreator
menuxmipp.utils.XmippMenuCreatorprotected
METADATAxmipp.utils.XmippMenuCreator
OPENxmipp.utils.XmippMenuCreatorstatic
OPEN_ASTEXTxmipp.utils.XmippMenuCreatorstatic
OPEN_IMAGESxmipp.utils.XmippMenuCreatorstatic
quickhelpdlgxmipp.viewer.windows.GalleryJFrame.GalleryMenuprotected
REFRESHxmipp.utils.XmippMenuCreatorstatic
SAVE_IMAGESxmipp.utils.XmippMenuCreatorstatic
SELECTxmipp.utils.XmippMenuCreatorstatic
SELECT_ALLxmipp.utils.XmippMenuCreatorstatic
SELECT_FROMHERExmipp.utils.XmippMenuCreatorstatic
SELECT_TOHERExmipp.utils.XmippMenuCreatorstatic
SET_CLASSxmipp.utils.XmippMenuCreatorstatic
setItemEnabled(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemSelected(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
setItemVisible(String key, boolean value)xmipp.utils.XmippMenuCreatorinline
TOOLSxmipp.utils.XmippMenuCreator
TOOLS_AVGSTDxmipp.utils.XmippMenuCreator
TOOLS_FSCxmipp.utils.XmippMenuCreator
TOOLS_PCAxmipp.utils.XmippMenuCreator
TOOLS_PLOTxmipp.utils.XmippMenuCreator
update()xmipp.viewer.windows.GalleryJFrame.GalleryMenuinline
XmippMenuBarCreator()xmipp.utils.XmippMenuBarCreatorinline
XmippMenuCreator(JComponent menu)xmipp.utils.XmippMenuCreatorinline
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- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu.html b/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu.html deleted file mode 100644 index 6f7a0a6f..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu.html +++ /dev/null @@ -1,652 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.windows.GalleryJFrame.GalleryMenu Class Reference - - - - - - - - - -
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-Classes

class  DisplayLabelActionListener
 
class  RenderColumnActionListener
 
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-Public Member Functions

void addExtraMenuItems ()
 
void update ()
 
- Public Member Functions inherited from xmipp.utils.XmippMenuBarCreator
 XmippMenuBarCreator ()
 
JMenuBar getMenuBar ()
 
void addSeparator (String key)
 
- Public Member Functions inherited from xmipp.utils.XmippMenuCreator
 XmippMenuCreator (JComponent menu)
 
JMenuItem addItem (String key, String text, String... values)
 
JMenuItem getItem (String key)
 
boolean getItemEnabled (String key)
 
void setItemEnabled (String key, boolean value)
 
boolean getItemSelected (String key)
 
void setItemSelected (String key, boolean value)
 
void setItemVisible (String key, boolean value)
 
void actionPerformed (ActionEvent evt)
 
void initItems ()
 
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-Protected Member Functions

void createItems () throws Exception
 
void handleActionPerformed (ActionEvent evt)
 
void addRenderImageColumnItems ()
 
void addDisplayLabelItems ()
 
- Protected Member Functions inherited from xmipp.utils.XmippMenuCreator
abstract void handleActionPerformed (ActionEvent evt)
 
abstract void createItems () throws Exception
 
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-Protected Attributes

QuickHelpJDialog quickhelpdlg
 
- Protected Attributes inherited from xmipp.utils.XmippMenuCreator
Map< String, JMenuItem > items
 
Map< String, ButtonGroup > groups
 
JComponent menu
 
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-Additional Inherited Members

- Public Attributes inherited from xmipp.utils.XmippMenuCreator
final String FILE = "File"
 
final String FILE_OPEN = "File.Open_mi"
 
final String FILE_OPENWITH_IJ = "File.OpenWithIJ_mi"
 
final String FILE_OPENMICROGRAPHS = "File.OpenMicrographs_mi"
 
final String FILE_OPENWITH_CHIMERA = "File.OpenWithChimera_mi"
 
final String FILE_INFO = "File.FileInfo_mi"
 
final String FILE_SAVE = "File.Save_mi"
 
final String FILE_SAVEAS = "File.SaveAs_mi"
 
final String FILE_LOAD_SEL = "File.LoadSel_mi"
 
final String FILE_SAVE_SEL = "File.SaveSel_mi"
 
final String FILE_EXPORTIMAGES = "File.ExportImages_mi"
 
final String FILE_REFRESH = "File.Refresh_mi"
 
final String FILE_EXIT = "File.Exit_mi"
 
final String FILE_LINK_CHIMERA = "File.LinkWithChimera_mi"
 
final String DISPLAY = "Display"
 
final String DISPLAY_SHOWLABELS = "Display.ShowLabel"
 
final String DISPLAY_RENDERIMAGES = "Display.RenderImages_cb"
 
final String DISPLAY_RENDERIMAGE = "Display.RenderImage"
 
final String DISPLAY_INVERTY = "Display.InvertY_cb"
 
final String DISPLAY_APPLYGEO = "Display.ApplyGeo_cb"
 
final String DISPLAY_WRAP = "Display.Wrap_cb"
 
final String DISPLAY_NORMALIZE = "Display.Normalize_cb"
 
final String DISPLAY_COLUMNS = "Display.Columns_mi"
 
final String DISPLAY_RESLICE = "Display.Reslice"
 
final String DISPLAY_RESLICE_VIEWS []
 
final String METADATA = "Metadata"
 
final String MD_CLASSES = "Metadata.Classes_mi"
 
final String MD_EDIT_COLS = "Metadata.EditCols_mi"
 
final String MD_ADD_OBJECT = "Metadata.AddObject_mi"
 
final String MD_REMOVE_SELECTION = "Metadata.RemoveSelection_mi"
 
final String MD_SAVE_SELECTION = "Metadata.SaveSelection_mi"
 
final String MD_REMOVE_DISABLED = "Metadata.RemoveDisabled_mi"
 
final String TOOLS = "Tools"
 
final String TOOLS_AVGSTD = "Tools.AvgStd_mi"
 
final String TOOLS_PCA = "Tools.Pca_mi"
 
final String TOOLS_FSC = "Tools.Fsc_mi"
 
final String TOOLS_PLOT = "Tools.Plot_mi"
 
final String MD_FIND_REPLACE = "Tools.FindReplace_mi"
 
final String HELP = "Help"
 
final String HELP_ONLINE = "Help.Online_mi"
 
final String KEY_ASSIST = "Help.Key_mi"
 
- Static Public Attributes inherited from xmipp.utils.XmippMenuCreator
static final String ENABLED = "Enabled_mi"
 
static final String DISABLED = "Disabled_mi"
 
static final String REFRESH = "Refresh_mi"
 
static final String OPEN = "Open_mi"
 
static final String OPEN_ASTEXT = "OpenAsText_mi"
 
static final String CTF_PROFILE = "CTFProfile_mi"
 
static final String CTF_RECALCULATE = "CTFRecalculate_cb"
 
static final String SELECT = "Select"
 
static final String SELECT_ALL = "Select.All_mi"
 
static final String SELECT_TOHERE = "Select.ToHere_mi"
 
static final String SELECT_FROMHERE = "Select.FromHere_mi"
 
static final String INVERT_SELECT = "Select.InvertSelection_mi"
 
static final String SET_CLASS = "SetClass_mi"
 
static final String OPEN_IMAGES = "OpenImages_mi"
 
static final String SAVE_IMAGES = "SaveImages_mi"
 
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Detailed Description

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Definition at line 1552 of file GalleryJFrame.java.

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Member Function Documentation

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◆ addDisplayLabelItems()

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void xmipp.viewer.windows.GalleryJFrame.GalleryMenu.addDisplayLabelItems ()
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Definition at line 1882 of file GalleryJFrame.java.

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1883  {
1884  JMenuItem mi = getItem(DISPLAY_SHOWLABELS);
1885  if(mi == null)
1886  mi = addItem(DISPLAY_SHOWLABELS, "Display label");
1887  else
1888  mi.removeAll();
1889 
1890  // Create the popup menu.
1891  String id, column;
1892  List<String> displayLabels = null;
1893  if(data.parameters.getDisplayLabels() != null)
1894  displayLabels = Arrays.asList(data.parameters.getDisplayLabels());
1895  for(ColumnInfo ci: data.getColumns())
1896  {
1897  if(ci.visible)
1898  {
1899  column = ci.labelName;
1900  id = String.format("Display.ShowLabel.%s_cb", column.replace(".", ""));
1901  mi = addItem(id, column);
1902  mi.addActionListener(new DisplayLabelActionListener());
1903 
1904  if(displayLabels!= null && displayLabels.contains(column))
1905  setItemSelected(id, true);
1906  }
1907  }
1908 
1909  }
xmipp.utils.XmippMenuCreator.setItemSelected
void setItemSelected(String key, boolean value)
Definition: XmippMenuCreator.java:151
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JMenuItem getItem(String key)
Definition: XmippMenuCreator.java:130
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xmipp.utils.Params.getDisplayLabels
String [] getDisplayLabels()
Definition: Params.java:313
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JMenuItem addItem(String key, String text, String... values)
Definition: XmippMenuCreator.java:56
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List< ColumnInfo > getColumns()
Definition: GalleryData.java:293
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◆ addExtraMenuItems()

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Definition at line 1622 of file GalleryJFrame.java.

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Definition at line 1854 of file GalleryJFrame.java.

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1855  {
1856  JMenuItem mi = getItem(DISPLAY_RENDERIMAGE);
1857  if(mi == null)
1858  mi = addItem(DISPLAY_RENDERIMAGE, "Render label");
1859  else
1860  mi.removeAll();
1861  boolean rendercolumn = false;
1862 
1863  // Create the popup menu.
1864  String id, column;
1865  for(ColumnInfo ci: data.getColumns())
1866  {
1867  if(ci.render)
1868  {
1869  column = ci.labelName;
1870  id = String.format("Display.RenderImage.%s_rb", column.replace(".", ""));
1871  mi = addItem(id, column);
1872  mi.addActionListener(new RenderColumnActionListener());
1873  if(data.getRenderColumn().toString().equals(column))
1874  setItemSelected(id, true);
1875  rendercolumn = true;
1876  }
1877  }
1878  setItemEnabled(DISPLAY_RENDERIMAGE, rendercolumn);
1879 
1880  }
xmipp.utils.XmippMenuCreator.setItemSelected
void setItemSelected(String key, boolean value)
Definition: XmippMenuCreator.java:151
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JMenuItem getItem(String key)
Definition: XmippMenuCreator.java:130
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JMenuItem addItem(String key, String text, String... values)
Definition: XmippMenuCreator.java:56
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List< ColumnInfo > getColumns()
Definition: GalleryData.java:293
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xmipp.utils.XmippMenuCreator.setItemEnabled
void setItemEnabled(String key, boolean value)
Definition: XmippMenuCreator.java:138
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void xmipp.viewer.windows.GalleryJFrame.GalleryMenu.createItems () throws Exception
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Definition at line 1558 of file GalleryJFrame.java.

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1559  {
1560  // File
1561  addItem(FILE, "File");
1562  addItem(FILE_OPEN, "Open ...", null, "control released O");
1563  addItem(FILE_OPENWITH_IJ, "Open with ImageJ", "ij.gif", "control released J");
1564  addItem(FILE_OPENWITH_CHIMERA, "Open with ChimeraX", "chimera.png", "control released H");
1565  addItem(FILE_OPENMICROGRAPHS, "Open colored particles");
1566  addItem(FILE_INFO, "File info ...");
1567  addExtraMenuItems();
1568 
1569  addSeparator(FILE);
1570  addItem(FILE_SAVE, "Save", "save.gif", "control released S");
1571  addItem(FILE_SAVEAS, "Save as", "save_as.gif");
1572 
1573  addItem(FILE_EXPORTIMAGES, "Export images ...", "export_wiz.gif");
1574  addItem(FILE_REFRESH, "Refresh", "refresh.gif", "released F5");
1575  addSeparator(FILE);
1576  addItem(FILE_EXIT, "Exit", null, "control released Q");
1577  // Display
1578 
1579 
1580  addItem(DISPLAY, "Display");
1581  addItem(DISPLAY_APPLYGEO, "Apply geometry", null, "control released G");
1582  addItem(DISPLAY_WRAP, "Wrap", null, "control released W");
1583  addItem(DISPLAY_NORMALIZE, "Normalize", null, "control released N");
1584  addItem(DISPLAY_INVERTY, "Render positive Y up");
1585  addSeparator(DISPLAY);
1586  addItem(DISPLAY_RENDERIMAGES, "Render images", null, "control released R");
1587 
1588  addRenderImageColumnItems();
1589  addDisplayLabelItems();
1590 
1591  addItem(DISPLAY_RESLICE, "Reslice");
1592  for (int i = 0; i < ImageGeneric.VIEWS.length; ++i)
1593  addItem(DISPLAY_RESLICE_VIEWS[i], reslices[i]);
1594  addItem(DISPLAY_COLUMNS, "Columns ...", "columns.gif");
1595 
1596 
1597  addItem(TOOLS, "Tools");
1598  addItem(TOOLS_AVGSTD, "Avg & Std images");
1599  addItem(TOOLS_PCA, "PCA");
1600  addItem(TOOLS_FSC, "FSC");
1601  addItem(TOOLS_PLOT, "Plot", "plot.png");
1602  addItem(MD_FIND_REPLACE, "Find & Replace", "binocular.png", "control released F");
1603 
1604  // Metadata operations
1605  addItem(METADATA, "Metadata");
1606 
1607 
1608  addItem(MD_CLASSES, "Classes");
1609  addItem(MD_EDIT_COLS, "Edit labels", "edit.gif");
1610  addItem(MD_ADD_OBJECT, "Add new object", "new_object.gif");
1611  addItem(MD_REMOVE_DISABLED, "Remove disabled", "delete.gif");
1612  addItem(MD_REMOVE_SELECTION, "Remove selection");
1613  addItem(MD_SAVE_SELECTION, "Save state", "save.gif");
1614  addSeparator(METADATA);
1615  // Help
1616  addItem(HELP, "Help");
1617  addItem(HELP_ONLINE, "Online help", "online_help.gif");
1618  addItem(KEY_ASSIST, "Tips...", "bulb.png");
1619  }// function createItems
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xmipp.utils.XmippMenuCreator.addItem
JMenuItem addItem(String key, String text, String... values)
Definition: XmippMenuCreator.java:56
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◆ handleActionPerformed()

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void xmipp.viewer.windows.GalleryJFrame.GalleryMenu.handleActionPerformed (ActionEvent evt)
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Definition at line 1671 of file GalleryJFrame.java.

-
1672  {
1673  String cmd = evt.getActionCommand();
1674  try
1675  {
1676  if (cmd.equals(DISPLAY_INVERTY))
1677  {
1678  gallery.setInvertY(getItemSelected(DISPLAY_INVERTY));
1679  }
1680  else if (cmd.equals(DISPLAY_NORMALIZE))
1681  {
1682  gallery.setNormalized(getItemSelected(DISPLAY_NORMALIZE));
1683  }
1684  else if (cmd.equals(DISPLAY_APPLYGEO) || cmd.equals(DISPLAY_WRAP))
1685  {
1686  if (data.containsGeometryInfo())
1687  {
1688  ((MetadataGalleryTableModel) gallery).setUseGeometry(getItemSelected(DISPLAY_APPLYGEO), getItemSelected(DISPLAY_WRAP));
1689  setItemEnabled(DISPLAY_WRAP, data.containsGeometryInfo() && data.useGeo());
1690 
1691  }
1692  }
1693 
1694  else if (cmd.equals(DISPLAY_RENDERIMAGES))
1695  {
1696  if(gallery instanceof MetadataTableModel)
1697  {
1698  ((MetadataTableModel) gallery).setRenderImages(getItemSelected(DISPLAY_RENDERIMAGES));
1699  setItemEnabled(DISPLAY_SHOWLABELS, gallery.showLabels());
1700  btnChangeView.setEnabled(data.hasRenderLabel() && data.renderImages());
1701  }
1702  makeVisible(gallery.getFirstSelectedIndex(), 0);
1703  }
1704 
1705  else if (cmd.equals(DISPLAY_COLUMNS))
1706  {
1707  ColumnsJDialog dialog = new ColumnsJDialog(GalleryJFrame.this);
1708  boolean result = dialog.showDialog();
1709  if (result)
1710  {
1711  List<ColumnInfo> columns = dialog.getColumnsResult();
1712  isUpdating = true;
1713  ((MetadataGalleryTableModel) gallery).updateColumnInfo(columns);
1714  gallery.fireTableDataChanged();
1715  //setItemEnabled(DISPLAY_RENDERIMAGES, data.renderImages());
1716  // menu.enableRenderImages(data.globalRender);
1717  isUpdating = false;
1718  }
1719  }
1720  else if (cmd.equals(TOOLS_AVGSTD))
1721  runInBackground(Worker.STATS);
1722  else if (cmd.equals(TOOLS_PCA))
1723  runInBackground(Worker.PCA);
1724  else if (cmd.equals(TOOLS_FSC))
1725  runInBackground(Worker.FSC);
1726  else if (cmd.equals(FILE_OPEN))
1727  {
1728  fc.setDialogTitle("Open");
1729  fc.setApproveButtonToolTipText("File to open");
1730  fc.setApproveButtonText("Open");
1731  if (fc.showOpenDialog(GalleryJFrame.this) != XmippFileChooser.CANCEL_OPTION)
1732  {
1733  if (Filename.exists(fc.getSelectedFile().getPath()))
1734  ImagesWindowFactory.openFileAsDefault(fc.getSelectedPath());
1735  else
1736  XmippDialog.showError(GalleryJFrame.this, String.format("File: '%s' doesn't exist.", fc.getSelectedPath()));
1737  }
1738  }
1739  else if (cmd.equals(FILE_SAVE))
1740  {
1741  save();
1742  }
1743  else if (cmd.equals(FILE_SAVEAS))
1744  {
1745  saveAs();
1746  }
1747  else if (cmd.equals(FILE_EXPORTIMAGES))
1748  {
1749  exportImages();
1750  }
1751  else if (cmd.equals(FILE_EXIT))
1752  {
1753  close();
1754  }
1755  else if (cmd.equals(FILE_OPENWITH_CHIMERA))
1756  {
1757  openWithChimera();
1758  }
1759  else if (cmd.equals(FILE_OPENMICROGRAPHS))
1760  {
1761  openMicrographs();
1762  }
1763 
1764  else if (cmd.equals(FILE_INFO))
1765  {
1766  XmippDialog.showInfo(GalleryJFrame.this, data.getFileInfo());
1767  }
1768 
1769  else if (cmd.equals(FILE_OPENWITH_IJ))
1770  {
1771  try
1772  {
1773  XmippUtil.showImageJ(Tool.VIEWER);
1774  ImagePlusLoader loader = gallery.getImageLoader();
1775  ImagesWindowFactory.openXmippImageWindow(loader, data.parameters);
1776  }
1777  catch (Exception e1)
1778  {
1779  e1.printStackTrace();
1780  }
1781  }
1782  else if (cmd.equals(FILE_REFRESH))
1783  {
1784  data.readMd();
1785  reloadTableData();
1786 
1787  }
1788  else if (cmd.contains(DISPLAY_RESLICE))
1789  {
1790  for (int i = 0; i < ImageGeneric.VIEWS.length; ++i)
1791  if (cmd.equals(DISPLAY_RESLICE_VIEWS[i]))
1792  {
1793  setResliceView(ImageGeneric.VIEWS[i]);
1794  break;
1795  }
1796  }
1797  else if (cmd.equals(TOOLS_PLOT))
1798  {
1799  plotColumns();
1800  }
1801  else if (cmd.equals(MD_CLASSES))
1802  {
1803  openClassesDialog();
1804  }
1805  else if (cmd.equals(MD_EDIT_COLS))
1806  {
1807  EditLabelsJDialog dlg = new EditLabelsJDialog(GalleryJFrame.this);
1808  dlg.showDialog();
1809  }
1810  else if (cmd.equals(MD_REMOVE_SELECTION))
1811  {
1812  if (gallery.getSelectionCount() > 0)
1813  removeObjects(true);
1814  }
1815  else if (cmd.equals(MD_REMOVE_DISABLED))
1816  {
1817  removeObjects(false);
1818  }
1819  else if (cmd.equals(MD_SAVE_SELECTION))
1820  {
1821  if(gallery.hasSelection())
1822  data.saveSelection(gallery.getSelection());
1823  }
1824  else if (cmd.equals(MD_FIND_REPLACE))
1825  {
1826  findReplace();
1827  }
1828  else if (cmd.equals(MD_ADD_OBJECT))
1829  {
1830  boolean added = data.addObject();
1831  if(added)
1832  reloadMd();
1833  }
1834  else if (cmd.equals(HELP_ONLINE))
1835  {
1836  XmippWindowUtil.openURI("http://github.com/I2PC/scipion/wiki/ShowJ");
1837  }
1838  else if (cmd.equals(KEY_ASSIST))
1839  {
1840  if (quickhelpdlg == null)
1841  quickhelpdlg = new QuickHelpJDialog(GalleryJFrame.this, false, "Tips", getKeyAssist());
1842  quickhelpdlg.setVisible(true);
1843 
1844  }
1845 
1846  }
1847  catch (Exception e)
1848  {
1849  showException(e);
1850  }
1851  }// function handleActionPerformed
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xmipp.viewer.windows.GalleryJFrame.getKeyAssist
Map< Object, Object > getKeyAssist()
Definition: GalleryJFrame.java:2351
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xmipp.utils.XmippMenuCreator.getItemSelected
boolean getItemSelected(String key)
Definition: XmippMenuCreator.java:142
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xmipp.viewer.windows.GalleryJFrame.removeObjects
void removeObjects(boolean selected)
Definition: GalleryJFrame.java:944
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xmipp.viewer.models.GalleryData.saveSelection
void saveSelection(boolean[] selection)
Definition: GalleryData.java:1353
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xmipp.viewer.windows.GalleryJFrame.GalleryJFrame
GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
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xmipp.utils.XmippMenuCreator.setItemEnabled
void setItemEnabled(String key, boolean value)
Definition: XmippMenuCreator.java:138
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◆ update()

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void xmipp.viewer.windows.GalleryJFrame.GalleryMenu.update ()
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Definition at line 1625 of file GalleryJFrame.java.

-
1626  {
1627 
1628  boolean isscipion = data.isScipionInstance();
1629  boolean galMode = data.isGalleryMode();
1630  boolean volMode = !data.getSelVolumeFile().isEmpty();
1631  setItemEnabled(FILE_OPENWITH_CHIMERA, volMode || data.containsGeometryInfo("3D")|| data.containsGeometryInfo("Projection"));
1632  setItemEnabled(FILE_OPENMICROGRAPHS, data.hasMicrographParticles());
1633  setItemEnabled(FILE_EXPORTIMAGES, data.hasRenderLabel() && !volMode);
1634  setItemEnabled(FILE_SAVE, !volMode && !isscipion);
1635  setItemEnabled(FILE_SAVEAS, !volMode && !isscipion);
1636 
1637  setItemEnabled(DISPLAY_APPLYGEO, data.containsGeometryInfo());
1638  setItemEnabled(DISPLAY_WRAP, data.containsGeometryInfo() && data.useGeo());
1639  setItemSelected(DISPLAY_WRAP, data.containsGeometryInfo() && data.isWrap());
1640  setItemSelected(DISPLAY_APPLYGEO, data.useGeo());
1641  setItemSelected(DISPLAY_INVERTY, data.isInvertY());
1642  setItemEnabled(DISPLAY_RENDERIMAGES, data.isTableMode() && data.isColumnFormat());
1643  setItemSelected(DISPLAY_RENDERIMAGES, data.renderImages());
1644  setItemEnabled(DISPLAY_SHOWLABELS, gallery.showLabels());
1645  setItemEnabled(DISPLAY_RENDERIMAGE, galMode);
1646  for (int i = 0; i < ImageGeneric.VIEWS.length; ++i)
1647  setItemSelected(DISPLAY_RESLICE_VIEWS[i], (data.getResliceView() == ImageGeneric.VIEWS[i]));
1648  setItemEnabled(DISPLAY_COLUMNS, !galMode);
1649  setItemEnabled(DISPLAY_RESLICE, data.isVolumeMode());
1650  setItemSelected(DISPLAY_NORMALIZE, data.getNormalized());
1651  setItemEnabled(MD_CLASSES, data.isClassificationMd());
1652  setItemEnabled(TOOLS_PLOT, data.isTableMode());
1653  boolean isCol = data.isColumnFormat();
1654  boolean doStats = isCol && !volMode;
1655  setItemEnabled(TOOLS_AVGSTD, doStats);
1656  setItemEnabled(TOOLS_FSC, doStats);
1657  setItemEnabled(TOOLS_PCA, doStats);
1658  setItemEnabled(MD_ADD_OBJECT, isCol);
1659  setItemEnabled(MD_REMOVE_DISABLED, isCol);
1660  setItemEnabled(MD_REMOVE_SELECTION, isCol);
1661  setItemEnabled(MD_SAVE_SELECTION, isCol);
1662  setItemEnabled(MD_FIND_REPLACE, isCol && !galMode);
1663  reslicebt.setEnabled(data.isVolumeMode());
1664  chimerabt.setEnabled(volMode && getChimera() != null);
1665  setItemVisible(METADATA, !isscipion);
1666  addDisplayLabelItems();
1667  addRenderImageColumnItems();
1668  }// function update
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xmipp.utils.XmippMenuCreator.setItemSelected
void setItemSelected(String key, boolean value)
Definition: XmippMenuCreator.java:151
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xmipp.utils.XmippMenuCreator.setItemVisible
void setItemVisible(String key, boolean value)
Definition: XmippMenuCreator.java:160
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xmipp.utils.XmippMenuCreator.setItemEnabled
void setItemEnabled(String key, boolean value)
Definition: XmippMenuCreator.java:138
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Member Data Documentation

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◆ quickhelpdlg

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QuickHelpJDialog xmipp.viewer.windows.GalleryJFrame.GalleryMenu.quickhelpdlg
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Definition at line 1555 of file GalleryJFrame.java.

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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__coll__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__coll__graph.dot deleted file mode 100644 index 053aaf72..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__coll__graph.dot +++ /dev/null @@ -1,35 +0,0 @@ -digraph "xmipp.viewer.windows.GalleryJFrame.GalleryMenu" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node5 [label="xmipp.viewer.windows.Gallery\lJFrame.GalleryMenu",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node6 -> Node5 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node6 [label="xmipp.utils.XmippMenuBar\lCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuBarCreator.html"]; 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- Node16 -> Node15 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node16 [label="JPanel",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node17 -> Node15 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helptb" ,fontname="Helvetica"]; - Node17 [label="JTable",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node16 -> Node15 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" buttonspn" ,fontname="Helvetica"]; - Node18 -> Node15 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helpmap" ,fontname="Helvetica"]; - Node18 [label="Map\< Object, Object \>",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node18 -> Node12 [dir="back",color="darkorchid3",fontsize="10",style="dashed",label=" helpmap" ,fontname="Helvetica"]; -} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__coll__graph.md5 deleted file mode 100644 index 6d44dc34..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -f9bb20bcb168da358e8d018a84fcf458 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__inherit__graph.dot deleted file mode 100644 index d930c48f..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__inherit__graph.dot +++ /dev/null @@ -1,14 +0,0 @@ -digraph "xmipp.viewer.windows.GalleryJFrame.GalleryMenu" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.windows.Gallery\lJFrame.GalleryMenu",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; - Node1 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node1 [label="xmipp.utils.XmippMenuBar\lCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuBarCreator.html"]; - Node2 -> Node1 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node2 [label="xmipp.utils.XmippMenuCreator",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1XmippMenuCreator.html"]; - Node3 -> Node2 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node3 [label="ActionListener",height=0.2,width=0.4,color="grey75", fillcolor="white", style="filled"]; - Node0 -> Node4 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node4 [label="xmipp.viewer.scipion.Scipion\lGalleryJFrame.ScipionGalleryMenu",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1viewer_1_1scipion_1_1ScipionGalleryJFrame_1_1ScipionGalleryMenu.html"]; -} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__inherit__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__inherit__graph.md5 deleted file mode 100644 index 5bd18da8..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryMenu__inherit__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -00bf8794d6783b495994adbfe773e122 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryScroll.html b/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryScroll.html deleted file mode 100644 index 6281ab3a..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1GalleryJFrame_1_1GalleryScroll.html +++ /dev/null @@ -1,100 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.windows.GalleryJFrame.GalleryScroll Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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xmipp.viewer.windows.GalleryJFrame.GalleryScroll Class Reference
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-Inheritance diagram for xmipp.viewer.windows.GalleryJFrame.GalleryScroll:
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Inheritance graph
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[legend]
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-Collaboration diagram for xmipp.viewer.windows.GalleryJFrame.GalleryScroll:
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Detailed Description

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Some tweaks over traditional JTable

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Definition at line 514 of file GalleryJFrame.java.

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The documentation for this class was generated from the following file: -
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xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel Member List
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This is the complete list of members for xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel, including all inherited members.

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addListDataListener(ListDataListener arg0)xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModelinline
getElementAt(int index)xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModelinline
getSelectedItem()xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModelinline
getSize()xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModelinline
getVolumeName(String volume)xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModelinline
removeListDataListener(ListDataListener arg0)xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModelinline
setSelectedItem(Object anItem)xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModelinline
VolumesComboBoxModel()xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModelinline
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-Public Member Functions | -List of all members
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xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel Class Reference
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-Public Member Functions

 VolumesComboBoxModel ()
 
int getSize ()
 
Object getElementAt (int index)
 
void setSelectedItem (Object anItem)
 
String getVolumeName (String volume)
 
Object getSelectedItem ()
 
void addListDataListener (ListDataListener arg0)
 
void removeListDataListener (ListDataListener arg0)
 
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Detailed Description

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Definition at line 1258 of file GalleryJFrame.java.

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Constructor & Destructor Documentation

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◆ VolumesComboBoxModel()

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xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel.VolumesComboBoxModel ()
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Definition at line 1264 of file GalleryJFrame.java.

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1265  {
1266  String volume;
1267  size = data.allowsVolumeMode()? data.size(): 0;
1268  indexToVolume = new HashMap(size);
1269  volumeToIndex = new HashMap(size);
1270  for(int i = 0; i < size; i ++)
1271  {
1272  volume = data.getVolumeAt(i);
1273  volume = getVolumeName(volume);
1274  indexToVolume.put(i, volume);
1275  volumeToIndex.put(volume, i);
1276  }
1277  }
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◆ addListDataListener()

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void xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel.addListDataListener (ListDataListener arg0)
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Definition at line 1337 of file GalleryJFrame.java.

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1338  {
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1341  }
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◆ getElementAt()

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Object xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel.getElementAt (int index)
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Definition at line 1289 of file GalleryJFrame.java.

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1290  {
1291  return indexToVolume.get(index);
1292  }
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◆ getSelectedItem()

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Object xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel.getSelectedItem ()
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Definition at line 1331 of file GalleryJFrame.java.

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1332  {
1333  return getVolumeName(data.getSelVolumeFile());
1334  }
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int xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel.getSize ()
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Definition at line 1282 of file GalleryJFrame.java.

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1283  {
1284 
1285  return size;
1286  }
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◆ getVolumeName()

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String xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel.getVolumeName (String volume)
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Definition at line 1310 of file GalleryJFrame.java.

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1311  {
1312 
1313  if(Filename.hasPrefix(volume))//is stack
1314  return volume;
1315  String base = Filename.getBaseName(volume);
1316  int count = 0;
1317  for(int i = 0; i < getSize(); i ++)
1318  if(base.equals(Filename.getBaseName(data.getVolumeAt(i))))
1319  {
1320  count ++;
1321  if (count > 1)// if volumes use same name you need to keep preffix
1322  break;
1323  }
1324  if(count == 1)
1325  return base;
1326 
1327  return volume;//needs full path to differentiate volumes
1328  }
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Definition at line 1344 of file GalleryJFrame.java.

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1346  // TODO Auto-generated method stub
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1348  }
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void xmipp.viewer.windows.GalleryJFrame.VolumesComboBoxModel.setSelectedItem (Object anItem)
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Definition at line 1295 of file GalleryJFrame.java.

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1296  {
1297  try
1298  {
1299  int index = volumeToIndex.get(anItem);
1300  data.selectVolumeAt(index);
1301  reloadTableData();
1302  }
1303  catch(Exception e)
1304  {
1305  XmippDialog.showError(GalleryJFrame.this, e.getMessage());
1306  }
1307 
1308  }
xmipp.viewer.models.GalleryData.selectVolumeAt
void selectVolumeAt(int selectedIndex)
Definition: GalleryData.java:167
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GalleryJFrame(String filename, Params parameters)
Definition: GalleryJFrame.java:236
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xmipp.viewer.windows.ImagesWindowFactory Member List
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This is the complete list of members for xmipp.viewer.windows.ImagesWindowFactory, including all inherited members.

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getSortTitle(String title, int width, FontMetrics fontMetrics)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFileAsDefault(String filename)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFileAsDefault(String filename, Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFileAsImage(String path)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFileAsImage(Frame pframe, String filename, Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFileAsImagePlus(String path, Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFileAsText(String filename, Component parent)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFilesAsDefault(String filenames[], Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFilesAsGallery(String filenames[], boolean useSameTable)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFilesAsGallery(String filenames[], boolean useSameTable, Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openFilesAsImages(String filenames[], Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openImagePlusAs3D(ImagePlus ip)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openMetadata(String filename, MetaData md, Params parameters, String mode)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openMetadata(String filename, Params parameters, String mode)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openScipionMetadata(String filename, Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openXmippImageWindow(ImagePlus imp, Params params)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openXmippImageWindow(ImagePlusLoader impLoader, Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
openXmippImageWindow(ImagePlusLoader impLoader, String title, Params parameters)xmipp.viewer.windows.ImagesWindowFactoryinlinestatic
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Xmipp -  v20.07 -
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-Classes | -Static Public Member Functions | -List of all members
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xmipp.viewer.windows.ImagesWindowFactory Class Reference
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-Classes

class  Worker
 
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-Static Public Member Functions

static void openFilesAsDefault (String filenames[], Params parameters)
 
static void openFileAsDefault (String filename)
 
static void openFileAsDefault (String filename, Params parameters)
 
static void openFilesAsImages (String filenames[], Params parameters)
 
static void openFileAsImage (String path)
 
static void openFileAsImage (Frame pframe, String filename, Params parameters)
 
static ImagePlus openFileAsImagePlus (String path, Params parameters) throws Exception
 
static XmippIJWindow openXmippImageWindow (ImagePlus imp, Params params)
 
static XmippIJWindow openXmippImageWindow (ImagePlusLoader impLoader, Params parameters)
 
static XmippIJWindow openXmippImageWindow (ImagePlusLoader impLoader, String title, Params parameters)
 
static GalleryJFrame openMetadata (String filename, MetaData md, Params parameters, String mode)
 
static void openMetadata (String filename, Params parameters, String mode) throws Exception
 
static void openScipionMetadata (String filename, Params parameters) throws Exception
 
static void openFilesAsGallery (String filenames[], boolean useSameTable) throws Exception
 
static void openFilesAsGallery (String filenames[], boolean useSameTable, Params parameters) throws Exception
 
static void openImagePlusAs3D (ImagePlus ip)
 
static void openFileAsText (String filename, Component parent)
 
static String getSortTitle (String title, int width, FontMetrics fontMetrics)
 
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Detailed Description

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Author
Juanjo Vega
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Definition at line 43 of file ImagesWindowFactory.java.

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Member Function Documentation

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◆ getSortTitle()

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static String xmipp.viewer.windows.ImagesWindowFactory.getSortTitle (String title,
int width,
FontMetrics fontMetrics 
)
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Definition at line 289 of file ImagesWindowFactory.java.

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290  {
291  String sort = title;
292  int strlenght = fontMetrics.stringWidth(sort);
293  int index = 0;
294 
295  while (strlenght > width) {
296  index++;
297  sort = "..." + title.substring(index);
298  strlenght = fontMetrics.stringWidth(sort);
299  }
300 
301  return sort;
302  }
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◆ openFileAsDefault() [1/2]

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static void xmipp.viewer.windows.ImagesWindowFactory.openFileAsDefault (String filename)
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Definition at line 53 of file ImagesWindowFactory.java.

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53  {
54 
55  Params params = new Params();
56 
57  if (ScipionMetaData.isScipionMetaData(filename)) {
58  params = new ScipionParams();
59  }
60 
61  openFileAsDefault(filename, params);
62  }
xmipp.viewer.windows.ImagesWindowFactory.openFileAsDefault
static void openFileAsDefault(String filename)
Definition: ImagesWindowFactory.java:53
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◆ openFileAsDefault() [2/2]

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static void xmipp.viewer.windows.ImagesWindowFactory.openFileAsDefault (String filename,
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Definition at line 64 of file ImagesWindowFactory.java.

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64  {
65  try {
66  if (Filename.isMetadata(filename)) {
67  if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_IMAGE))
68  openFileAsImage(null, filename, parameters);
69  else
70  openMetadata(filename, parameters,
71  Params.OPENING_MODE_GALLERY);
72  } else {
73  ImageGeneric img = new ImageGeneric(filename);
74 
75  if (img.isSingleImage()) {
76  openFileAsImage(null, filename, parameters);
77  } else if (img.isStackOrVolume()) {
78  if (parameters.mode
79  .equalsIgnoreCase(Params.OPENING_MODE_IMAGE))
80  openFileAsImage(null, filename, parameters);
81  else
82  openMetadata(filename, parameters, Params.OPENING_MODE_GALLERY);
83  }
84  }
85  } catch (Exception e) {
86  XmippDialog.showError(null, String.format(
87  "Couldn't open file: '%s'\nError: %s", filename,
88  e.getMessage()));
89  e.printStackTrace();
90  }
91  }
xmipp.viewer.windows.ImagesWindowFactory.openMetadata
static GalleryJFrame openMetadata(String filename, MetaData md, Params parameters, String mode)
Definition: ImagesWindowFactory.java:180
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Definition at line 99 of file ImagesWindowFactory.java.

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99  {
100  openFileAsImage(null, path, new Params());
101  }
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static void xmipp.viewer.windows.ImagesWindowFactory.openFileAsImage (Frame pframe,
String filename,
Params parameters 
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Definition at line 103 of file ImagesWindowFactory.java.

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104  {
105  try {
106  ImagePlusLoader ipl = new ImagePlusLoader(filename, false);
107  XmippIJWindow xiw = openXmippImageWindow(ipl,
108  parameters);
109  if (parameters.mask_toolbar)
110  xiw.openMaskToolbar();
111  } catch (Exception e) {
112  XmippDialog.showError(null, String.format(
113  "Couldn't open file: '%s'\nError: %s", filename,
114  e.getMessage()));
115  e.printStackTrace();
116  }
117  }
xmipp.viewer.windows.ImagesWindowFactory.openXmippImageWindow
static XmippIJWindow openXmippImageWindow(ImagePlus imp, Params params)
Definition: ImagesWindowFactory.java:134
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◆ openFileAsImagePlus()

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static ImagePlus xmipp.viewer.windows.ImagesWindowFactory.openFileAsImagePlus (String path,
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Definition at line 119 of file ImagesWindowFactory.java.

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120  {
121  ImagePlus imp;
122  if (Filename.isMetadata(path)) {
123  MetaData md = new MetaData(path);
124  imp = XmippImageConverter.readMetadataToImagePlus(
125  MDLabel.MDL_IMAGE, md, parameters.useGeo, parameters.wrap, parameters.inverty);
126  md.destroy();
127  } else {
128  imp = XmippImageConverter.loadImage(path,
129  parameters.zoom != null ? parameters.zoom : 100);
130  }
131  return imp;
132  }
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◆ openFileAsText()

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static void xmipp.viewer.windows.ImagesWindowFactory.openFileAsText (String filename,
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Definition at line 281 of file ImagesWindowFactory.java.

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281  {
282  TextfileJFrame frameText = new TextfileJFrame(filename);
283  if (parent != null)
284  frameText.setLocationRelativeTo(null);
285  frameText.setVisible(true);
286  }
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static void xmipp.viewer.windows.ImagesWindowFactory.openFilesAsDefault (String filenames[],
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Definition at line 47 of file ImagesWindowFactory.java.

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47  {
48  for (int i = 0; i < filenames.length; i++) {
49  openFileAsDefault(filenames[i], parameters);
50  }
51  }
xmipp.viewer.windows.ImagesWindowFactory.openFileAsDefault
static void openFileAsDefault(String filename)
Definition: ImagesWindowFactory.java:53
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static void xmipp.viewer.windows.ImagesWindowFactory.openFilesAsGallery (String filenames[],
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Definition at line 233 of file ImagesWindowFactory.java.

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234  {
235  openFilesAsGallery(filenames, useSameTable, new Params());
236  }
xmipp.viewer.windows.ImagesWindowFactory.openFilesAsGallery
static void openFilesAsGallery(String filenames[], boolean useSameTable)
Definition: ImagesWindowFactory.java:233
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Definition at line 238 of file ImagesWindowFactory.java.

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239  {
240  GalleryJFrame gallery = null;
241 
242  if (useSameTable) {
243  MetaData md = new MetaData();
244  for (int i = 0; i < filenames.length; ++i)
245  md.setValueString(MDLabel.MDL_IMAGE, filenames[i],
246  md.addObject());
247  openMetadata(null, md, parameters, null);
248  } else {
249  for (int i = 0; i < filenames.length; i++) {
250  openMetadata(filenames[i], parameters,
251  Params.OPENING_MODE_GALLERY);
252  }
253  }
254 
255  }
xmipp.viewer.windows.ImagesWindowFactory.openMetadata
static GalleryJFrame openMetadata(String filename, MetaData md, Params parameters, String mode)
Definition: ImagesWindowFactory.java:180
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◆ openFilesAsImages()

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static void xmipp.viewer.windows.ImagesWindowFactory.openFilesAsImages (String filenames[],
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Definition at line 93 of file ImagesWindowFactory.java.

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93  {
94  for (int i = 0; i < filenames.length; i++) {
95  openFileAsImage(null, filenames[i], parameters);
96  }
97  }
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◆ openImagePlusAs3D()

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static void xmipp.viewer.windows.ImagesWindowFactory.openImagePlusAs3D (ImagePlus ip)
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Definition at line 257 of file ImagesWindowFactory.java.

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257  {
258  try {
259  // Checks if java3D is available or not.
260  Class.forName("javax.media.j3d.J3DBuffer");
261 
262  new StackConverter(ip).convertToRGB();
263 
264  Image3DUniverse universe = new Image3DUniverse(UNIVERSE_W,
265  UNIVERSE_H);
266 
267  // Adds the sphere image plus to universe.
268  Content c = universe.addSurfacePlot(ip, new Color3f(1f, 165f / 255,
269  82f / 255), "1", 50, new boolean[] { true, true, true }, 1);
270  c.displayAs(Content.SURFACE);
271  c.setColor(new Color3f(1f, 165f / 255, 82f / 255));
272 
273  universe.show(); // Shows...
274  } catch (final ClassNotFoundException e) {
275  IJ.error("Java 3D not found. Please, check your installation.");
276  }
277  }
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Definition at line 180 of file ImagesWindowFactory.java.

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181  {
182 
183  if (parameters.mode.equalsIgnoreCase(Params.OPENING_MODE_DEFAULT))
184  parameters.mode = mode;
185  return new GalleryJFrame(md, parameters);
186  }
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Definition at line 188 of file ImagesWindowFactory.java.

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190  {
191  if(filename.endsWith(".sqlite") || filename.endsWith(".db"))
192  openScipionMetadata(filename, parameters);
193  else
194  openMetadata(filename, new MetaData(filename), parameters, mode);
195  }
xmipp.viewer.windows.ImagesWindowFactory.openMetadata
static GalleryJFrame openMetadata(String filename, MetaData md, Params parameters, String mode)
Definition: ImagesWindowFactory.java:180
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Definition: ImagesWindowFactory.java:197
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Definition at line 197 of file ImagesWindowFactory.java.

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198  {
199  if(!(filename.endsWith(".sqlite") || filename.endsWith(".db")))
200  throw new IllegalArgumentException(XmippMessage.getIllegalValueMsg("scipion metadata", filename));
201  else
202  {
203  ScipionMetaData md;
204  if(filename.contains("@"))
205  {
206  int sep = filename.indexOf('@');
207  final String preffix = filename.substring(0, sep);
208  filename = filename.substring(sep + 1);
209  md = new ScipionMetaData(filename);
210  final ScipionGalleryData data = new ScipionGalleryData(null, parameters, md);
211  SwingUtilities.invokeLater(new Runnable() {
212 
213  @Override
214  public void run() {
215  ScipionGalleryJFrame frame = new ScipionGalleryJFrame(data);
216  frame.selectBlock(preffix);
217  }
218  });
219 
220  }
221  else
222  {
223  md = new ScipionMetaData(filename);
224  ScipionGalleryData data = new ScipionGalleryData(null, parameters, md);
225  new ScipionGalleryJFrame(data);
226  }
227  }
228  }
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135  {
136  return openXmippImageWindow(new ImagePlusLoader(imp), params);
137  }
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static XmippIJWindow openXmippImageWindow(ImagePlus imp, Params params)
Definition: ImagesWindowFactory.java:134
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Definition at line 139 of file ImagesWindowFactory.java.

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140  {
141  return openXmippImageWindow(impLoader, impLoader.getName(), parameters);
142 
143  }
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static XmippIJWindow openXmippImageWindow(ImagePlus imp, Params params)
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Definition at line 144 of file ImagesWindowFactory.java.

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145  {
146 
147  XmippIJWindow iw;
148 
149  if (impLoader.isStackOrVolume())
150  iw = (title != null)? new XmippStackWindow(impLoader, title, parameters): new XmippStackWindow(impLoader, parameters);
151  else
152  iw = (title != null )? new XmippImageWindow(impLoader, title, parameters): new XmippImageWindow(impLoader, parameters);
153 
154  SwingUtilities.invokeLater(new Worker(iw));
155  return iw;
156  }
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- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1MDSearchJDialog-members.html b/html/classxmipp_1_1viewer_1_1windows_1_1MDSearchJDialog-members.html deleted file mode 100644 index cbfde632..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1MDSearchJDialog-members.html +++ /dev/null @@ -1,134 +0,0 @@ - - - - - - - -Xmipp: Member List - - - - - - - - - -
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xmipp.viewer.windows.MDSearchJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.MDSearchJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
addPair(JPanel panel, String text, Component c, int col, int row)xmipp.viewer.windows.MDSearchJDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.MDSearchJDialoginlineprotected
dataxmipp.viewer.windows.MDSearchJDialogprotected
disposeOnClosexmipp.utils.XmippDialogprotected
enableActions()xmipp.viewer.windows.MDSearchJDialoginlineprotected
gbcxmipp.viewer.windows.MDSearchJDialogprotected
handleActionPerformed(ActionEvent evt)xmipp.viewer.windows.MDSearchJDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
idsxmipp.viewer.windows.MDSearchJDialogprotected
initComponents()xmipp.utils.XmippDialoginlineprotected
jcbLabelxmipp.viewer.windows.MDSearchJDialogprotected
labelxmipp.viewer.windows.MDSearchJDialogprotected
labelsxmipp.viewer.windows.MDSearchJDialogprotected
mainPanelxmipp.viewer.windows.MDSearchJDialogprotected
MDSearchJDialog(JFrame parent, JTable table, GalleryData data)xmipp.viewer.windows.MDSearchJDialoginline
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.viewer.windows.MDSearchJDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
selected_indexxmipp.viewer.windows.MDSearchJDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
tablexmipp.viewer.windows.MDSearchJDialogprotected
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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-Public Member Functions

 MDSearchJDialog (JFrame parent, JTable table, GalleryData data)
 
void handleActionPerformed (ActionEvent evt)
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void addPair (JPanel panel, String text, Component c, int col, int row)
 
void createContent (JPanel panel)
 
void enableActions ()
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Protected Attributes

GalleryJFrame parent
 
GalleryData data
 
JTable table
 
long [] ids
 
int selected_index = -1
 
ColumnInfo label
 
List< ColumnInfo > labels
 
GridBagConstraints gbc = new GridBagConstraints()
 
JPanel mainPanel
 
JComboBox jcbLabel
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
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Detailed Description

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Definition at line 58 of file MDSearchJDialog.java.

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Constructor & Destructor Documentation

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◆ MDSearchJDialog()

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xmipp.viewer.windows.MDSearchJDialog.MDSearchJDialog (JFrame parent,
JTable table,
GalleryData data 
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Constructor to add a new label the labels present in the metadata are passed

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Definition at line 86 of file MDSearchJDialog.java.

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86  {
87  super(parent, "Find and Replace", false);
88 
89  this.parent = (GalleryJFrame) parent;
90  this.data = data;
91  this.table = table;
92  this.ids = data.getIds();
93  this.labels = data.getColumns();
94  this.label = labels.get(0);
95  btnOkText = "Close";
96  btnCancelDisplay = false;
97  initComponents();
98  }// constructor MDSearchJDialog
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Definition: GalleryData.java:293
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◆ addPair()

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void xmipp.viewer.windows.MDSearchJDialog.addPair (JPanel panel,
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int col,
int row 
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Utility function to create a pair of label and other component If the component is null, a textbox will be created and added to the dict

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Definition at line 104 of file MDSearchJDialog.java.

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105  {
106  JLabel label = new JLabel(text);
107  gbc.anchor = GridBagConstraints.EAST;
108  panel.add(label, XmippWindowUtil.getConstraints(gbc, col, row));
109  gbc.anchor = GridBagConstraints.WEST;
110  panel.add(c, XmippWindowUtil.getConstraints(gbc, col + 1, row));
111  }
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Definition at line 114 of file MDSearchJDialog.java.

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114  {
115  setResizable(false);
116  mainPanel = new JPanel(new GridBagLayout());
117  gbc.insets = new Insets(5, 5, 0, 0);
118 
119  jtFind = new JTextField(15);
120  jtReplace = new JTextField(15);
121 
122  int row = 0;
123  addPair(mainPanel, "Find", jtFind, 0, row++);
124  addPair(mainPanel, "Replace", jtReplace, 0, row++);
125 
126  jtFind.addActionListener(this);
127 
128  // setPreferredSize(new Dimension(350, 180));
129  setIconImage(XmippResource.getIcon("search.gif").getImage());
130 
131  JPanel optPanel = new JPanel(new GridBagLayout());
132  mainPanel.add(optPanel,
133  XmippWindowUtil.getConstraints(gbc, 0, row++, 2));
134  optPanel.setBorder(BorderFactory.createTitledBorder("Options"));
135 
136  // Create labels combo
137  jcbLabel = new JComboBox();
138  for (ColumnInfo l : labels) {
139  jcbLabel.addItem(l.labelName);
140  }
141  jcbLabel.addActionListener(this);
142  addPair(optPanel, "Label", jcbLabel, 0, 0);
143  jchCase = new JCheckBox();
144  addPair(optPanel, "Case sensitive", jchCase, 0, 1);
145  ButtonGroup btnGroup = new ButtonGroup();
146  jrbForward = new JRadioButton("Forward");
147  jrbForward.setSelected(true);
148  btnGroup.add(jrbForward);
149  JRadioButton jrb = new JRadioButton("Backward");
150  btnGroup.add(jrb);
151  addPair(optPanel, "Direction", jrbForward, 0, 2);
152  addPair(optPanel, "", jrb, 0, 3);
153 
154  // Add buttons
155  JPanel btnPanel = new JPanel(new GridBagLayout());
156 
157  btnFind = XmippWindowUtil.getTextButton("Find", this);
158  btnReplace = XmippWindowUtil.getTextButton("Replace", this);
159  btnReplaceFind = XmippWindowUtil.getTextButton("Replace/Find", this);
160  btnReplaceAll = XmippWindowUtil.getTextButton("Replace All", this);
161 
162  btnPanel.add(btnFind, XmippWindowUtil.getConstraints(gbc, 0, 0, 2));
163  btnPanel.add(btnReplaceFind,
164  XmippWindowUtil.getConstraints(gbc, 2, 0, 2));
165  btnPanel.add(btnReplace, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
166  btnPanel.add(btnReplaceAll,
167  XmippWindowUtil.getConstraints(gbc, 2, 1, 2));
168  gbc.anchor = GridBagConstraints.EAST;
169  mainPanel.add(btnPanel,
170  XmippWindowUtil.getConstraints(gbc, 0, row++, 2));
171 
172  panel.add(mainPanel);
173  enableActions();
174  }// function initComponents
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Definition: MDSearchJDialog.java:104
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Definition at line 177 of file MDSearchJDialog.java.

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178  {
179  boolean isenabled = !data.isScipionInstance();
180  jtReplace.setEnabled(isenabled);
181  btnReplace.setEnabled(isenabled);
182  btnReplaceFind.setEnabled(isenabled);
183  btnReplaceAll.setEnabled(isenabled);
184  }
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Definition at line 187 of file MDSearchJDialog.java.

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187  {
188  Object o = evt.getSource();
189  if (o == jtFind || o == btnFind)
190  find();
191  else if (o == jcbLabel)
192  {
193  column = jcbLabel.getSelectedIndex();
194  label = labels.get(column);
195  }
196  else if (o == btnReplace)
197  replace(selected_index);
198  else if (o == btnReplaceFind) {
199  replace(selected_index);
200  find();
201  } else if (o == btnReplaceAll)
202  replaceAll();
203 
204  }// function actionPerformed
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Definition at line 61 of file MDSearchJDialog.java.

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Definition at line 68 of file MDSearchJDialog.java.

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Definition at line 69 of file MDSearchJDialog.java.

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Definition at line 62 of file MDSearchJDialog.java.

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Xmipp -  v20.07 -
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xmipp.viewer.windows.PlotJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.PlotJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.PlotJDialoginlineprotected
createEntries()xmipp.viewer.windows.PlotJDialoginlineprotected
disposeOnClosexmipp.utils.XmippDialogprotected
getBins()xmipp.viewer.windows.PlotJDialoginline
getPlotTitle()xmipp.viewer.windows.PlotJDialoginline
getXColumn()xmipp.viewer.windows.PlotJDialoginline
getXLabel()xmipp.viewer.windows.PlotJDialoginline
handleActionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
handleCancel()xmipp.viewer.windows.PlotJDialoginline
handleOk()xmipp.viewer.windows.PlotJDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
isHistogram()xmipp.viewer.windows.PlotJDialoginline
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
parentxmipp.utils.XmippDialogprotected
PlotJDialog(GalleryJFrame parent)xmipp.viewer.windows.PlotJDialoginline
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog.html b/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog.html deleted file mode 100644 index 2d645570..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog.html +++ /dev/null @@ -1,515 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.windows.PlotJDialog Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Classes | -Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.windows.PlotJDialog Class Reference
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-Classes

class  ColumnsTableModel
 
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-Public Member Functions

 PlotJDialog (GalleryJFrame parent)
 
boolean isHistogram ()
 
void handleCancel ()
 
void handleOk ()
 
String getXColumn ()
 
String getXLabel ()
 
String getPlotTitle ()
 
String getBins ()
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void createEntries ()
 
void createContent (JPanel panel)
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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Detailed Description

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Definition at line 70 of file PlotJDialog.java.

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Constructor & Destructor Documentation

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◆ PlotJDialog()

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xmipp.viewer.windows.PlotJDialog.PlotJDialog (GalleryJFrame parent)
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Definition at line 89 of file PlotJDialog.java.

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89  {
90  super(parent, "Plot columns", false);
91 
92  rows = new ArrayList<ColumnInfo>();
93  rowsExtra = new HashMap<ColumnInfo, ColumnInfo.ColumnExtraInfo>();
94  int i = 0;
95  for (ColumnInfo ci : parent.getData().getLabelsInfo())
96  if (ci.type == MetaData.LABEL_INT || ci.type == MetaData.LABEL_DOUBLE) {// int or double
97 
98  rows.add(ci);
99  rowsExtra.put(ci, ci.new ColumnExtraInfo(COLORS[i % COLORS.length]));
100  ++i;
101  }
102  this.gallery = parent.gallery;
103  btnOkText = "Plot";
104  closeOnAction = false;
105  initComponents();
106  }// constructor ColumnsJDialog
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◆ createContent()

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void xmipp.viewer.windows.PlotJDialog.createContent (JPanel panel)
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Definition at line 171 of file PlotJDialog.java.

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171  {
172  setResizable(false);
173  panel.setLayout(new GridBagLayout());
174  gbc.anchor = GridBagConstraints.EAST;
175  gbc.insets = new Insets(5, 5, 5, 5);
176 
177  JPanel groupstbpn = new JPanel();
178  JScrollPane sp = new JScrollPane();
179  groupstbpn.setBorder(BorderFactory.createTitledBorder("Labels"));
180  groupstbpn.add(sp);
181  sp.setOpaque(true);
182  model = new ColumnsTableModel();
183  tableColumns = new JTable(model);
184  tableColumns.getColumnModel().getColumn(0).setPreferredWidth(250);
185  tableColumns.setPreferredScrollableViewportSize(new Dimension(450, 200));
186  sp.setViewportView(tableColumns);
187  panel.add(groupstbpn, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
188  createEntries();
189  panel.add(panelEntries, XmippWindowUtil.getConstraints(gbc, 1, 0));
190 
191  tableColumns.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
192  tableColumns.setDefaultRenderer(Color.class, new ColorRenderer());
193  tableColumns.setDefaultEditor(Color.class, new ColorEditor());
194  setComboEditor(3, "solid", "dashed", "dotted");
195  setComboEditor(4, "none", ".", ",", "o", "v", "^", "<", ">", "1", "2",
196  "3", "4", "s", "p", "h", "H", "+", "x", "D", "d", "|", "_");
197  }// function initComponents
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◆ createEntries()

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void xmipp.viewer.windows.PlotJDialog.createEntries ()
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Definition at line 120 of file PlotJDialog.java.

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120  {
121  tfTitle = new JTextField(20);
122  tfXLabel = new JTextField(20);
123  tfYLabel = new JTextField(20);
124 
125  JPanel plotPanel = new JPanel();
126  plotTypecb = new JComboBox(plotTypes);
127  plotTypecb.addActionListener(new ActionListener() {
128 
129  @Override
130  public void actionPerformed(ActionEvent ae) {
131  binslb.setVisible(isHistogram());
132  tfBins.setVisible(isHistogram());
133 
134  validate();
135  pack();
136  }
137  });
138  plotPanel.add(plotTypecb);
139  binslb = new JLabel("Bins");
140  binslb.setVisible(false);
141  tfBins = new JTextField(10);
142  tfBins.setText("50");
143  tfBins.setVisible(false);
144  plotPanel.add(binslb);
145  plotPanel.add(tfBins);
146  panelEntries = new JPanel(new GridBagLayout());
147  addPair("Title:", tfTitle, 0);
148  addPair("X label:", tfXLabel, 1);
149  addPair("Y label:", tfYLabel, 2);
150  addPair("Type:", plotPanel, 3);
151  jcbXAxis = new JComboBox();
152  jcbXAxis.addItem("");
153  for (ColumnInfo ci : rows)
154  jcbXAxis.addItem(ci.labelName);
155  addPair("X Axis:", jcbXAxis, 5);
156  jcbXAxis.addActionListener(new ActionListener() {
157 
158  @Override
159  public void actionPerformed(ActionEvent ae) {
160  tfXLabel.setText(jcbXAxis.getSelectedItem().toString());
161  }
162  });
163  }
xmipp.utils.XmippDialog.actionPerformed
void actionPerformed(ActionEvent evt)
Definition: XmippDialog.java:163
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◆ getBins()

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String xmipp.viewer.windows.PlotJDialog.getBins ()
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Definition at line 316 of file PlotJDialog.java.

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316  {
317  if(tfBins.isVisible())
318  return tfBins.getText();
319  return "";
320  }
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String xmipp.viewer.windows.PlotJDialog.getPlotTitle ()
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Definition at line 312 of file PlotJDialog.java.

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312  {
313  return tfTitle.getText();
314  }
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◆ getXColumn()

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String xmipp.viewer.windows.PlotJDialog.getXColumn ()
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Definition at line 298 of file PlotJDialog.java.

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299  {
300  if (jcbXAxis.getSelectedIndex() != 0)
301  return jcbXAxis.getSelectedItem().toString();
302  return "";
303  }
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String xmipp.viewer.windows.PlotJDialog.getXLabel ()
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Definition at line 305 of file PlotJDialog.java.

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306  {
307  return tfXLabel.getText().trim();
308  }
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◆ handleCancel()

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void xmipp.viewer.windows.PlotJDialog.handleCancel ()
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Definition at line 206 of file PlotJDialog.java.

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206  {
207  closeOnAction = true;
208  }
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void xmipp.viewer.windows.PlotJDialog.handleOk ()
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Definition at line 211 of file PlotJDialog.java.

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211  {
212 
213  if(plotTypecb.getSelectedItem().equals("Histogram") && tfBins.getText().isEmpty())
214  {
215  XmippDialog.showError((JFrame)parent, XmippMessage.getEmptyFieldMsg("Bins"));
216  return;
217  }
218 
219  String labels = "";
220  String colors = "";
221  String styles = "";
222  String markers = "";
223  Boolean checked = false;
224 
225  int plots = 0;
226  ColumnInfo plotci = null;
227  for (ColumnInfo ci: rows) {
228  ColumnInfo.ColumnExtraInfo cei = rowsExtra.get(ci);
229  if (cei.plot) {
230  plots ++;
231  labels += ci.labelName + " ";
232  colors += "#" + cei.color + " ";
233  styles += cei.linestyle + " ";
234  markers += cei.marker + " ";
235  checked = true;
236  plotci = ci;
237  }
238  }
239  String ylabel = tfYLabel.getText().trim();
240  if(plots == 1 && ylabel.isEmpty())
241  ylabel = plotci.labelName;
242 
243  if (!checked)
244  {
245  XmippDialog.showError((JFrame)parent, XmippMessage.getEmptyFieldMsg("Label"));
246  return;
247  }
248 
249  try {
250 
251  String[] argsBasic;
252  Params params = gallery.data.parameters;
253  GalleryData data = gallery.data;
254  String orderColumn = "id";
255  String orderDirection = "ASC";
256  String[] sortby = data.getSortBy();
257  if(sortby != null)
258  {
259  orderColumn = sortby[0];
260  orderDirection = sortby[1];
261  }
262  if(params.port != null)
263  {
264  String command = String.format("run function schedulePlot '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' '%s' %s %s",
265  data.getFileName(), data.getPreffix(), plotTypecb.getSelectedItem(),
266  labels, colors, styles, markers, getXColumn(), ylabel, getXLabel(), getPlotTitle(), getBins(), orderColumn, orderDirection);
267 
268  XmippWindowUtil.runCommand(command, params.port);
269  }
270  else
271  {
272  String pwplot = "python -m pyworkflow.apps.pw_plot";
273  String cmd = String.format("%s --file %s --type %s --columns \"%s\" --orderColumn %s --orderDir %s --colors \"%s\" --styles \"%s\" --markers \"%s\""
274  , pwplot, data.getFileName(), plotTypecb.getSelectedItem(), labels, orderColumn, orderDirection, colors, styles, markers);
275  if(!data.getPreffix().isEmpty())
276  cmd += " --block " + data.getPreffix();
277 
278  if(!getXColumn().isEmpty())
279  cmd += " --xcolumn " + getXColumn();
280  if(!data.getPreffix().isEmpty())
281  cmd += " --block " + data.getPreffix();
282  if(plotTypecb.getSelectedItem().equals("Histogram"))
283  cmd += " --bins " + getBins();
284  if(!getPlotTitle().isEmpty())
285  cmd += " --title " + getPlotTitle();
286  if(!getXLabel().isEmpty())
287  cmd += " --xtitle " + getXLabel();
288  if(!ylabel.isEmpty())
289  cmd += " --ytitle " + ylabel;
290  String output = XmippWindowUtil.executeCommand(cmd, false);
291  }
292 
293  } catch (Exception e) {
294  e.printStackTrace();
295  }
296  }
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xmipp.utils.XmippDialog.XmippDialog
XmippDialog(JFrame parent, String title, boolean modal)
Definition: XmippDialog.java:61
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◆ isHistogram()

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boolean xmipp.viewer.windows.PlotJDialog.isHistogram ()
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Definition at line 165 of file PlotJDialog.java.

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166  {
167  return plotTypecb.getSelectedIndex() == 1;
168  }
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The documentation for this class was generated from the following file: -
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-} diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog__coll__graph.md5 b/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog__coll__graph.md5 deleted file mode 100644 index 0624ae3e..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog__coll__graph.md5 +++ /dev/null @@ -1 +0,0 @@ -cfc1e68a89e745d8045c60d9ba78a563 \ No newline at end of file diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog__inherit__graph.dot b/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog__inherit__graph.dot deleted file mode 100644 index 707ca4ac..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1PlotJDialog__inherit__graph.dot +++ /dev/null @@ -1,12 +0,0 @@ -digraph "xmipp.viewer.windows.PlotJDialog" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - Node0 [label="xmipp.viewer.windows.Plot\lJDialog",height=0.2,width=0.4,color="black", fillcolor="grey75", style="filled", fontcolor="black"]; 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xmipp.viewer.windows.SaveImagesJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.SaveImagesJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
browseImgxmipp.viewer.windows.SaveJDialogprotected
browseMdxmipp.viewer.windows.SaveJDialogprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
cbExtensionxmipp.viewer.windows.SaveJDialogprotected
cbLabelxmipp.viewer.windows.SaveJDialogprotected
chbMdxmipp.viewer.windows.SaveJDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createBrowse(BrowseField browse)xmipp.viewer.windows.SaveJDialoginlineprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.SaveImagesJDialoginlineprotected
createMdOptions()xmipp.viewer.windows.SaveJDialoginlineprotected
dataxmipp.viewer.windows.SaveJDialogprotected
disposeOnClosexmipp.utils.XmippDialogprotected
doSaveImages()xmipp.viewer.windows.SaveJDialoginline
fcxmipp.viewer.windows.SaveJDialogprotected
fillMdOptions()xmipp.viewer.windows.SaveImagesJDialoginlineprotected
gbcxmipp.viewer.windows.SaveJDialogprotected
getImageLabel()xmipp.viewer.windows.SaveJDialoginline
getMdFilename()xmipp.viewer.windows.SaveJDialoginline
getOutput()xmipp.viewer.windows.SaveJDialoginline
groupxmipp.viewer.windows.SaveJDialogprotected
handleActionPerformed(ActionEvent evt)xmipp.viewer.windows.SaveJDialoginline
handleCancel()xmipp.viewer.windows.SaveImagesJDialoginline
handleOk()xmipp.viewer.windows.SaveImagesJDialoginline
initComponents()xmipp.viewer.windows.SaveImagesJDialoginlineprotected
isAppendMode()xmipp.viewer.windows.SaveJDialoginline
isOutputIndependent()xmipp.viewer.windows.SaveJDialoginline
isOverwrite()xmipp.viewer.windows.SaveJDialoginline
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
panelMdxmipp.viewer.windows.SaveJDialogprotected
parentxmipp.utils.XmippDialogprotected
rbIndependentxmipp.viewer.windows.SaveJDialogprotected
rbMdAppendxmipp.viewer.windows.SaveJDialogprotected
rbMdOverridexmipp.viewer.windows.SaveJDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
saveActiveMetadataOnly()xmipp.viewer.windows.SaveJDialoginline
SaveImagesJDialog(GalleryJFrame parent, String proposedFileName)xmipp.viewer.windows.SaveImagesJDialoginline
SaveJDialog(GalleryJFrame parent, String file, boolean isselection)xmipp.viewer.windows.SaveJDialoginline
SaveJDialog(GalleryJFrame parent)xmipp.viewer.windows.SaveJDialoginline
setAppendMode(boolean value)xmipp.viewer.windows.SaveJDialoginline
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
setInitialValues()xmipp.viewer.windows.SaveJDialoginline
setMdFilename(String file)xmipp.viewer.windows.SaveJDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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-Generated by   -doxygen - 1.8.13 -
- - diff --git a/html/classxmipp_1_1viewer_1_1windows_1_1SaveImagesJDialog.html b/html/classxmipp_1_1viewer_1_1windows_1_1SaveImagesJDialog.html deleted file mode 100644 index 01c6b054..00000000 --- a/html/classxmipp_1_1viewer_1_1windows_1_1SaveImagesJDialog.html +++ /dev/null @@ -1,467 +0,0 @@ - - - - - - - -Xmipp: xmipp.viewer.windows.SaveImagesJDialog Class Reference - - - - - - - - - -
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Xmipp -  v20.07 -
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-Public Member Functions | -Protected Member Functions | -List of all members
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xmipp.viewer.windows.SaveImagesJDialog Class Reference
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-Inheritance diagram for xmipp.viewer.windows.SaveImagesJDialog:
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-Public Member Functions

 SaveImagesJDialog (GalleryJFrame parent, String proposedFileName)
 
void handleOk ()
 
void handleCancel ()
 
- Public Member Functions inherited from xmipp.viewer.windows.SaveJDialog
 SaveJDialog (GalleryJFrame parent, String file, boolean isselection)
 
 SaveJDialog (GalleryJFrame parent)
 
boolean isOverwrite ()
 
void setInitialValues ()
 
void handleActionPerformed (ActionEvent evt)
 
String getMdFilename ()
 
void setMdFilename (String file)
 
boolean isAppendMode ()
 
void setAppendMode (boolean value)
 
boolean doSaveImages ()
 
boolean isOutputIndependent ()
 
String getOutput ()
 
int getImageLabel ()
 
boolean saveActiveMetadataOnly ()
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void initComponents ()
 
void createContent (JPanel panel)
 
void fillMdOptions ()
 
- Protected Member Functions inherited from xmipp.viewer.windows.SaveJDialog
void createContent (JPanel panel)
 
JPanel createBrowse (BrowseField browse)
 
void createMdOptions ()
 
void fillMdOptions ()
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
- Protected Attributes inherited from xmipp.viewer.windows.SaveJDialog
JPanel group
 
GridBagConstraints gbc
 
XmippFileChooser fc
 
JCheckBox chbMd
 
BrowseField browseMd
 
BrowseField browseImg
 
JComboBox cbExtension
 
JComboBox cbLabel
 
JRadioButton rbIndependent
 
JRadioButton rbMdOverride
 
JRadioButton rbMdAppend
 
JPanel panelMd
 
GalleryData data
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
- Static Protected Attributes inherited from xmipp.viewer.windows.SaveJDialog
static final long serialVersionUID = 1L
 
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Detailed Description

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Definition at line 35 of file SaveImagesJDialog.java.

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Constructor & Destructor Documentation

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◆ SaveImagesJDialog()

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xmipp.viewer.windows.SaveImagesJDialog.SaveImagesJDialog (GalleryJFrame parent,
String proposedFileName 
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Definition at line 42 of file SaveImagesJDialog.java.

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42  {
43  super(parent, proposedFileName, true);
44  }// constructor ColumnsJDialog
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Member Function Documentation

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◆ createContent()

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void xmipp.viewer.windows.SaveImagesJDialog.createContent (JPanel panel)
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Definition at line 54 of file SaveImagesJDialog.java.

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54  {
55  super.createContent(panel);
56 
57  imagesMd = gallery.data.getClassesImages(gallery.getSelection());
58  String text = String.format("<html>You are about to save <font color='red'>%d</font> images from <font color='red'>%d</font> classes.",
59  imagesMd.size(), gallery.getSelectionCount());
60  panel.add(new JLabel(text), XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
61  }// function initComponents
xmipp.viewer.models.GalleryData.getClassesImages
MetaData getClassesImages(boolean[] selection)
Definition: GalleryData.java:1098
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◆ fillMdOptions()

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void xmipp.viewer.windows.SaveImagesJDialog.fillMdOptions ()
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Definition at line 64 of file SaveImagesJDialog.java.

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64  {
65  // Just to avoid adding some metadata options.
66  // this dialog will override the existing file
67  }
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Definition at line 76 of file SaveImagesJDialog.java.

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76  {
77  imagesMd.destroy();
78  }
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synchronized native void destroy()
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void xmipp.viewer.windows.SaveImagesJDialog.handleOk ()
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Definition at line 70 of file SaveImagesJDialog.java.

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70  {
71  imagesMd.write(getMdFilename());
72  imagesMd.destroy();
73  }// function actionPerformed
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native void write(String filename)
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◆ initComponents()

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void xmipp.viewer.windows.SaveImagesJDialog.initComponents ()
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Definition at line 47 of file SaveImagesJDialog.java.

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47  {
48  this.gallery = ((GalleryJFrame)parent).gallery;
49  this.btnOkText = "Save Images";
50  super.initComponents();
51  }
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The documentation for this class was generated from the following file: -
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-Generated by   -doxygen - 1.8.13 -
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xmipp.viewer.windows.SaveJDialog Member List
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This is the complete list of members for xmipp.viewer.windows.SaveJDialog, including all inherited members.

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actionPerformed(ActionEvent evt)xmipp.utils.XmippDialoginline
addButton(String text)xmipp.utils.XmippDialoginlineprotected
addButton(String text, int keyStroke)xmipp.utils.XmippDialoginlineprotected
browseImgxmipp.viewer.windows.SaveJDialogprotected
browseMdxmipp.viewer.windows.SaveJDialogprotected
btnCancelxmipp.utils.XmippDialogprotected
btnCancelDisplayxmipp.utils.XmippDialogprotected
btnCancelTextxmipp.utils.XmippDialogprotected
btnOkxmipp.utils.XmippDialogprotected
btnOkTextxmipp.utils.XmippDialogprotected
cbExtensionxmipp.viewer.windows.SaveJDialogprotected
cbLabelxmipp.viewer.windows.SaveJDialogprotected
chbMdxmipp.viewer.windows.SaveJDialogprotected
close(boolean result)xmipp.utils.XmippDialoginlineprotected
closeOnActionxmipp.utils.XmippDialogprotected
createBrowse(BrowseField browse)xmipp.viewer.windows.SaveJDialoginlineprotected
createButtons()xmipp.utils.XmippDialoginlineprotected
createContent(JPanel panel)xmipp.viewer.windows.SaveJDialoginlineprotected
createMdOptions()xmipp.viewer.windows.SaveJDialoginlineprotected
dataxmipp.viewer.windows.SaveJDialogprotected
disposeOnClosexmipp.utils.XmippDialogprotected
doSaveImages()xmipp.viewer.windows.SaveJDialoginline
fcxmipp.viewer.windows.SaveJDialogprotected
fillMdOptions()xmipp.viewer.windows.SaveJDialoginlineprotected
gbcxmipp.viewer.windows.SaveJDialogprotected
getImageLabel()xmipp.viewer.windows.SaveJDialoginline
getMdFilename()xmipp.viewer.windows.SaveJDialoginline
getOutput()xmipp.viewer.windows.SaveJDialoginline
groupxmipp.viewer.windows.SaveJDialogprotected
handleActionPerformed(ActionEvent evt)xmipp.viewer.windows.SaveJDialoginline
handleCancel()xmipp.utils.XmippDialoginline
handleOk()xmipp.utils.XmippDialoginline
initComponents()xmipp.utils.XmippDialoginlineprotected
isAppendMode()xmipp.viewer.windows.SaveJDialoginline
isOutputIndependent()xmipp.viewer.windows.SaveJDialoginline
isOverwrite()xmipp.viewer.windows.SaveJDialoginline
panelxmipp.utils.XmippDialogprotected
panelBtnxmipp.utils.XmippDialogprotected
panelMdxmipp.viewer.windows.SaveJDialogprotected
parentxmipp.utils.XmippDialogprotected
rbIndependentxmipp.viewer.windows.SaveJDialogprotected
rbMdAppendxmipp.viewer.windows.SaveJDialogprotected
rbMdOverridexmipp.viewer.windows.SaveJDialogprotected
registerHotKeys(final JButton btn, int keyStroke)xmipp.utils.XmippDialoginlineprotected
removeColors(String message)xmipp.utils.XmippDialoginlinestatic
resultxmipp.utils.XmippDialogprotected
saveActiveMetadataOnly()xmipp.viewer.windows.SaveJDialoginline
SaveJDialog(GalleryJFrame parent, String file, boolean isselection)xmipp.viewer.windows.SaveJDialoginline
SaveJDialog(GalleryJFrame parent)xmipp.viewer.windows.SaveJDialoginline
serialVersionUIDxmipp.viewer.windows.SaveJDialogprotectedstatic
setAppendMode(boolean value)xmipp.viewer.windows.SaveJDialoginline
setCloseOnOk(boolean value)xmipp.utils.XmippDialoginline
setDisposeOnClose(boolean value)xmipp.utils.XmippDialoginline
setInitialValues()xmipp.viewer.windows.SaveJDialoginline
setMdFilename(String file)xmipp.viewer.windows.SaveJDialoginline
showDialog()xmipp.utils.XmippDialoginline
showError(String message)xmipp.utils.XmippDialoginline
showError(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showException(Exception e)xmipp.utils.XmippDialoginline
showException(JFrame parent, Exception e)xmipp.utils.XmippDialoginlinestatic
showInfo(String message)xmipp.utils.XmippDialoginline
showInfo(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestion(JDialog parent, String message)xmipp.utils.XmippDialoginlinestatic
showQuestionYesNoCancel(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showWarning(String message)xmipp.utils.XmippDialoginline
showWarning(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
showYesNoQuestion(JFrame parent, String message)xmipp.utils.XmippDialoginlinestatic
XmippDialog(JFrame parent, String title, boolean modal)xmipp.utils.XmippDialoginline
XmippDialog(Dialog parent, String title, boolean modal)xmipp.utils.XmippDialoginline
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Xmipp -  v20.07 -
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-Classes | -Public Member Functions | -Protected Member Functions | -Protected Attributes | -Static Protected Attributes | -List of all members
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xmipp.viewer.windows.SaveJDialog Class Reference
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-Classes

class  BrowseField
 
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-Public Member Functions

 SaveJDialog (GalleryJFrame parent, String file, boolean isselection)
 
 SaveJDialog (GalleryJFrame parent)
 
boolean isOverwrite ()
 
void setInitialValues ()
 
void handleActionPerformed (ActionEvent evt)
 
String getMdFilename ()
 
void setMdFilename (String file)
 
boolean isAppendMode ()
 
void setAppendMode (boolean value)
 
boolean doSaveImages ()
 
boolean isOutputIndependent ()
 
String getOutput ()
 
int getImageLabel ()
 
boolean saveActiveMetadataOnly ()
 
- Public Member Functions inherited from xmipp.utils.XmippDialog
 XmippDialog (JFrame parent, String title, boolean modal)
 
 XmippDialog (Dialog parent, String title, boolean modal)
 
boolean showDialog ()
 
void handleActionPerformed (ActionEvent evt)
 
void handleOk ()
 
void handleCancel ()
 
void actionPerformed (ActionEvent evt)
 
void setDisposeOnClose (boolean value)
 
void setCloseOnOk (boolean value)
 
boolean showInfo (String message)
 
boolean showWarning (String message)
 
boolean showError (String message)
 
boolean showException (Exception e)
 
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-Protected Member Functions

void createContent (JPanel panel)
 
JPanel createBrowse (BrowseField browse)
 
void createMdOptions ()
 
void fillMdOptions ()
 
- Protected Member Functions inherited from xmipp.utils.XmippDialog
void initComponents ()
 
void registerHotKeys (final JButton btn, int keyStroke)
 
JButton addButton (String text)
 
JButton addButton (String text, int keyStroke)
 
void createButtons ()
 
void createContent (JPanel panel)
 
void close (boolean result)
 
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-Protected Attributes

JPanel group
 
GridBagConstraints gbc
 
XmippFileChooser fc
 
JCheckBox chbMd
 
BrowseField browseMd
 
BrowseField browseImg
 
JComboBox cbExtension
 
JComboBox cbLabel
 
JRadioButton rbIndependent
 
JRadioButton rbMdOverride
 
JRadioButton rbMdAppend
 
JPanel panelMd
 
GalleryData data
 
- Protected Attributes inherited from xmipp.utils.XmippDialog
Window parent
 
boolean result
 
JPanel panel
 
JButton btnCancel
 
JButton btnOk
 
String btnOkText = "Ok"
 
String btnCancelText = "Cancel"
 
boolean btnCancelDisplay = true
 
JPanel panelBtn
 
boolean disposeOnClose = true
 
boolean closeOnAction = true
 
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-Static Protected Attributes

static final long serialVersionUID = 1L
 
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-Additional Inherited Members

- Static Public Member Functions inherited from xmipp.utils.XmippDialog
static boolean showInfo (JFrame parent, String message)
 
static boolean showWarning (JFrame parent, String message)
 
static boolean showError (JFrame parent, String message)
 
static boolean showException (JFrame parent, Exception e)
 
static boolean showQuestion (JFrame parent, String message)
 
static boolean showYesNoQuestion (JFrame parent, String message)
 
static boolean showQuestion (JDialog parent, String message)
 
static int showQuestionYesNoCancel (JFrame parent, String message)
 
static String removeColors (String message)
 
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Detailed Description

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Definition at line 53 of file SaveJDialog.java.

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Constructor & Destructor Documentation

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◆ SaveJDialog() [1/2]

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xmipp.viewer.windows.SaveJDialog.SaveJDialog (GalleryJFrame parent,
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boolean isselection 
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Definition at line 82 of file SaveJDialog.java.

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83  {
84  super(parent, "Save", true);
85  this.isselection = isselection;
86  this.filename = file;
87  initComponents();
88  setMdFilename(file);
89  }// constructor SaveJDialog
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xmipp.viewer.windows.SaveJDialog.SaveJDialog (GalleryJFrame parent)
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Definition at line 91 of file SaveJDialog.java.

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92  {
93  this(parent, null, false);
94  }// constructor SaveJDialog
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◆ createBrowse()

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JPanel xmipp.viewer.windows.SaveJDialog.createBrowse (BrowseField browse)
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Definition at line 145 of file SaveJDialog.java.

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146  {
147  JPanel panel = new JPanel();
148  browse.tb = new JTextField(30);
149  panel.add(browse.tb);
150  browse.btn = XmippWindowUtil.getIconButton("folderopen.gif", this);
151  panel.add(browse.btn);
152  return panel;
153  }
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void xmipp.viewer.windows.SaveJDialog.createContent (JPanel panel)
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Definition at line 97 of file SaveJDialog.java.

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98  {
99  this.data = ((GalleryJFrame) parent).getData();
100  //setMinimumSize(new Dimension(500, 300));
101  setResizable(false);
102  panel.setLayout(new GridBagLayout());
103  gbc = new GridBagConstraints();
104  gbc.ipadx = 5;
105  gbc.ipady = 5;
106  gbc.weightx = 1.0;
107  gbc.weighty = 1.0;
108  // gbc.insets = new Insets(5, 5, 5, 5);
109  // gbc.weightx = 1.0;
110  // gbc.weighty = 1.0;
111  gbc.anchor = GridBagConstraints.NORTHWEST;
112  File initial;
113  if (filename != null)
114  initial = new File(Filename.getFilename(filename));
115  else
116  initial = new File(System.getProperty("user.dir"));
117  fc = new XmippFileChooser(initial);
118 
119  group = new JPanel(new GridBagLayout());
120  group.setBorder(BorderFactory.createTitledBorder("Save options"));
121 
122  // Checkbox to save metadata
123  // chbMd = new JCheckBox("Save metadata", true);
124  // chbMd.addActionListener(this);
125  group.add(new JLabel("Metadata path:"), XmippWindowUtil.getConstraints(gbc, 0, 0));
126 
127  createMdOptions();
128  group.add(panelMd, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
129 
130  // Checkbox to save images
131 // chbImg = new JCheckBox("Save images", false);
132 // chbImg.addActionListener(this);
133 // group.add(chbImg, XmippWindowUtil.getConstraints(gbc, 0, 2));
134 
135  //createImageOptions();
136  //group.add(panelImg, XmippWindowUtil.getConstraints(gbc, 0, 3, 2));
137 
138  gbc.anchor = GridBagConstraints.PAGE_START;
139  panel.add(group, XmippWindowUtil.getConstraints(gbc, 0, 0, 2));
140  // Change default Ok text button
141  btnOkText = "Save";
142  pack();
143  }// function initComponents
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Definition at line 155 of file SaveJDialog.java.

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156  {
157  GridBagConstraints gbc = new GridBagConstraints();
158  // Metadata options panel
159  panelMd = new JPanel(new GridBagLayout());
160  // panelMd.setBackground(Color.blue);
161  browseMd = new BrowseField();
162  JPanel panelBrowse = createBrowse(browseMd);
163  panelMd.add(panelBrowse, XmippWindowUtil.getConstraints(gbc, 0, 0, 3));
164  fillMdOptions();
165  }
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JPanel createBrowse(BrowseField browse)
Definition: SaveJDialog.java:145
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Definition at line 293 of file SaveJDialog.java.

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294  {
295  return false;
296  //return chbImg.isSelected();
297  }
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Definition at line 167 of file SaveJDialog.java.

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167  {
168  chbDiscard = new JCheckBox("Save Active Metadata Only", false);
169  if(!isselection)
170  panelMd.add(chbDiscard, XmippWindowUtil.getConstraints(gbc, 0, 1, 2));
171  rbMdOverride = new JRadioButton("Overwrite file");
172  panelMd.add(rbMdOverride, XmippWindowUtil.getConstraints(gbc, 0, 2));
173  gbc.anchor = GridBagConstraints.WEST;
174  rbMdAppend = new JRadioButton("Replace/Append", true);
175  panelMd.add(rbMdAppend, XmippWindowUtil.getConstraints(gbc, 1, 2));
176  ButtonGroup group = new ButtonGroup();
177  group.add(rbMdOverride);
178  group.add(rbMdAppend);
179  }
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Definition at line 309 of file SaveJDialog.java.

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310  {
311  try
312  {
313  return MetaData.str2Label(cbLabel.getSelectedItem().toString());
314  }
315  catch (Exception e)
316  {
317  e.printStackTrace();
318  return MDLabel.MDL_UNDEFINED;
319  }
320  }
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Definition at line 262 of file SaveJDialog.java.

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263  {
264  return browseMd.tb.getText();
265  }
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Definition at line 304 of file SaveJDialog.java.

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305  {
306  return browseImg.tb.getText();
307  }
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Definition at line 228 of file SaveJDialog.java.

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229  {
230  Object obj = evt.getSource();
231  // Handle open button action.
232  if (obj == browseMd.btn)
233  browseFile(browseMd.tb);
234  else if (obj == browseImg.btn)
235  browseFile(browseImg.tb);
236 // else if (obj == chbImg)
237 // panelImg.setVisible(chbImg.isSelected());
238  else if (obj == chbMd)
239  panelMd.setVisible(chbMd.isSelected());
240 
241  }
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Definition at line 283 of file SaveJDialog.java.

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284  {
285  return rbMdAppend.isSelected();
286  }
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Definition at line 299 of file SaveJDialog.java.

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300  {
301  return rbIndependent.isSelected();
302  }
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Definition at line 181 of file SaveJDialog.java.

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182  {
183  return rbMdOverride.isSelected();
184  }
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Definition at line 322 of file SaveJDialog.java.

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323  {
324  return chbDiscard.isSelected();
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Definition at line 288 of file SaveJDialog.java.

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289  {
290  rbMdAppend.setSelected(value);
291  }
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Definition at line 217 of file SaveJDialog.java.

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218  {
219  browseMd.tb.setText("");
220 // browseImg.tb.setText("");
221  rbMdAppend.setSelected(true);
222 // chbImg.setSelected(false);
223 // rbStack.setSelected(true);
224 
225  }
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Definition at line 267 of file SaveJDialog.java.

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268  {
269  if (file != null)
270  {
271  if (file.contains("@"))
272  block = file.substring(0, file.lastIndexOf("@"));
273  browseMd.tb.setText(file);
274  }
275  else
276  {
277  block = null;
278  browseMd.tb.setText("");
279  }
280 
281  }
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◆ browseImg

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Definition at line 67 of file SaveJDialog.java.

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Definition at line 66 of file SaveJDialog.java.

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Definition at line 68 of file SaveJDialog.java.

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Definition at line 69 of file SaveJDialog.java.

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Definition at line 60 of file SaveJDialog.java.

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Definition at line 76 of file SaveJDialog.java.

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Definition at line 59 of file SaveJDialog.java.

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Definition at line 57 of file SaveJDialog.java.

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Definition at line 56 of file SaveJDialog.java.

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Definition at line 75 of file SaveJDialog.java.

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Definition at line 71 of file SaveJDialog.java.

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Definition at line 73 of file SaveJDialog.java.

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Definition at line 72 of file SaveJDialog.java.

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Definition at line 55 of file SaveJDialog.java.

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JTextField tb
 
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Definition at line 255 of file SaveJDialog.java.

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Definition at line 258 of file SaveJDialog.java.

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Definition at line 257 of file SaveJDialog.java.

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-Generated by   -doxygen - 1.8.13 -
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xmipp.viewer.windows.TextfileJFrame Member List
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This is the complete list of members for xmipp.viewer.windows.TextfileJFrame, including all inherited members.

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TextfileJFrame(String filename)xmipp.viewer.windows.TextfileJFrameinline
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xmipp.viewer.windows.TextfileJFrame Class Reference
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-Public Member Functions

 TextfileJFrame (String filename)
 
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Detailed Description

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Author
Juanjo Vega
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Definition at line 29 of file TextfileJFrame.java.

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Constructor & Destructor Documentation

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◆ TextfileJFrame()

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xmipp.viewer.windows.TextfileJFrame.TextfileJFrame (String filename)
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Creates new form JFrameTextFile

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Definition at line 32 of file TextfileJFrame.java.

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32  {
33  super(filename);
34  setPreferredSize(new Dimension(600, 400));
35  setDefaultCloseOperation(DISPOSE_ON_CLOSE);
36  initComponents();
37  loadFile(filename);
38  pack();
39  }
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The documentation for this class was generated from the following file: -
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xmipp.viewer.windows.Worker Member List
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This is the complete list of members for xmipp.viewer.windows.Worker, including all inherited members.

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FSCxmipp.viewer.windows.Workerstatic
fsc()xmipp.viewer.windows.Workerinline
getImagesMd(MetaData md, int idlabel)xmipp.viewer.windows.Workerinline
getMessage()xmipp.viewer.windows.Workerinline
messagexmipp.viewer.windows.Worker
pca()xmipp.viewer.windows.Workerinline
PCAxmipp.viewer.windows.Workerstatic
run()xmipp.viewer.windows.Workerinline
STATSxmipp.viewer.windows.Workerstatic
Worker(int operation, boolean selected, GalleryJFrame frame)xmipp.viewer.windows.Workerinline
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-Public Member Functions

 Worker (int operation, boolean selected, GalleryJFrame frame)
 
void run ()
 
String getMessage ()
 
void pca () throws Exception
 
void fsc () throws Exception
 
MDRow [] getImagesMd (MetaData md, int idlabel)
 
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String message
 
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-Static Public Attributes

static final int STATS = 0
 
static final int PCA = 1
 
static final int FSC = 2
 
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Detailed Description

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Author
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Definition at line 25 of file Worker.java.

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◆ Worker()

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xmipp.viewer.windows.Worker.Worker (int operation,
boolean selected,
GalleryJFrame frame 
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Definition at line 36 of file Worker.java.

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37  {
38  this.frame = frame;
39 
40  op = operation;
41  imagesmd = frame.data.getImagesMd(frame.gallery.getSelection(), selected);
42  if (imagesmd.size() == 0)
43  throw new IllegalArgumentException("No images available");
44  }
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◆ fsc()

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void xmipp.viewer.windows.Worker.fsc () throws Exception
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Definition at line 117 of file Worker.java.

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118  {
119  FSCJFrame fscframe = new FSCJFrame(frame.data, imagesmd, MDLabel.MDL_IMAGE);
120  XmippWindowUtil.centerWindows(fscframe, frame);
121  fscframe.setVisible(true);
122  }
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MDRow [] xmipp.viewer.windows.Worker.getImagesMd (MetaData md,
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Definition at line 127 of file Worker.java.

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127  {
128 
129  MDRow mdRow;
130  ArrayList<MDRow> imagesmd = new ArrayList<MDRow>();
131  int index = 0;
132  String imagepath;
133  for (long id : md.findObjects()) {
134  if (frame.data.isEnabled(index)) {
135  imagepath = md.getValueString(idlabel, id, true);
136  System.out.println(imagepath);
137  if (imagepath != null && ImageGeneric.exists(imagepath)) {
138  mdRow = new MDRow();
139  if (frame.data.useGeo())
140  md.getRow(mdRow, id);//copy geo info in mdRow
141  mdRow.setValueString(idlabel, imagepath);
142  imagesmd.add(mdRow);
143  }
144  }
145  index++;
146  }
147  return imagesmd.toArray(new MDRow[]{});
148  }
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Definition at line 73 of file Worker.java.

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74  {
75  switch (op)
76  {
77  case STATS:
78  return "Computing average and std images...";
79  case PCA:
80  return "Computing PCA...";
81  case FSC:
82  return "Computing FSC...";
83  }
84  return "";
85  }
xmipp.viewer.windows.Worker.FSC
static final int FSC
Definition: Worker.java:29
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xmipp.viewer.windows.Worker.STATS
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Definition at line 107 of file Worker.java.

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108  {
109  ImageGeneric image = new ImageGeneric();
110  imagesmd.getPCAbasis(image, MDLabel.MDL_IMAGE);
111  ImagePlus imp = XmippImageConverter.convertToImagePlus(image);
112  imp.setTitle("PCA: " + frame.data.getFileName());
113  ImagesWindowFactory.openXmippImageWindow(imp, frame.data.parameters);
114 
115  }
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Definition at line 46 of file Worker.java.

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47  {
48  try
49  {
50  switch (op)
51  {
52  case STATS:
53  computeStatsImages();
54  break;
55  case PCA:
56  pca();
57  break;
58  case FSC:
59  fsc();
60  break;
61  }
62  }
63  catch (Exception e)
64  {
65  XmippWindowUtil.releaseGUI(frame.getRootPane());
66  XmippDialog.showException(frame, e);
67  return;
68 
69  }
70  XmippWindowUtil.releaseGUI(frame.getRootPane());
71  }
xmipp.viewer.windows.Worker.FSC
static final int FSC
Definition: Worker.java:29
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xmipp.viewer.windows.Worker.STATS
static final int STATS
Definition: Worker.java:27
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xmipp.viewer.windows.Worker.PCA
static final int PCA
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◆ FSC

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Definition at line 29 of file Worker.java.

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Definition at line 30 of file Worker.java.

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Definition at line 28 of file Worker.java.

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Definition at line 27 of file Worker.java.

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file  FloatRenderer.java [code]
 
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getTool(String name)xmipp.ij.commons.Toolinlinestatic
getTool(Tool tool)xmipp.ij.commons.Toolinlinestatic
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VIEWER enum valuexmipp.ij.commons.Tool
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xmipp.ij.commons.Tool Enum Reference
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static Tool getTool (String name)
 
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Definition at line 3 of file Tool.java.

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Definition at line 8 of file Tool.java.

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9  {
10  if (name.equalsIgnoreCase("Particle Picker Tool"))
11  return Tool.PICKER;
12  else if(name.equalsIgnoreCase("Xmipp Micrograph Viewer Tool"))
13  return Tool.VIEWER;
14  return Tool.IMAGEJ;
15  }
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Definition at line 17 of file Tool.java.

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18  {
19  if(tool == Tool.PICKER)
20  return "Particle Picker Tool";
21  else if(tool == Tool.VIEWER)
22  return "Xmipp Micrograph Viewer Tool";
23  return null;
24  }
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Definition at line 5 of file Tool.java.

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Definition at line 5 of file Tool.java.

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X_AXISxmipp.utils.CompoundIcon.Axis
Y_AXISxmipp.utils.CompoundIcon.Axis
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Definition at line 23 of file CompoundIcon.java.

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Definition at line 26 of file CompoundIcon.java.

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GALLERY_MDxmipp.viewer.models.GalleryData.Mode
GALLERY_VOLxmipp.viewer.models.GalleryData.Mode
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Definition at line 211 of file GalleryData.java.

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Definition at line 213 of file GalleryData.java.

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Definition at line 213 of file GalleryData.java.

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Autoxmipp.viewer.particlepicker.Format
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xmipp.viewer.particlepicker.Format Enum Reference
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 Xmipp24
 
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Definition at line 3 of file Format.java.

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xmipp.viewer.particlepicker.Format.Auto
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Definition at line 3 of file Shape.java.

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Definition at line 3 of file Mode.java.

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Definition at line 13 of file Mode.java.

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14  {
15  if(s.equalsIgnoreCase(Mode.Manual.toString()))
16  return Mode.Manual;
17  else if(s.equalsIgnoreCase(Mode.Supervised.toString()))
18  return Mode.Supervised;
19  else if(s.equalsIgnoreCase(Mode.Review.toString()))
20  return Mode.Review;
21  else if(s.equalsIgnoreCase(Mode.Available.toString()))
22  return Mode.Available;
23  else if(s.equalsIgnoreCase(Mode.ReadOnly.toString()))
24  return Mode.ReadOnly;
25  else if(s.equalsIgnoreCase(Mode.Extract.toString()))
26  return Mode.Extract;
27  else if (s.equalsIgnoreCase(Mode.Automatic.toString()))
28  return Mode.Automatic;
29 
30  return null;
31  }
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Definition at line 5 of file Mode.java.

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class  HandleExtraFileTypes
 
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1 import ij.*;
2 import ij.plugin.*;
3 import java.io.*;
4 
5 // Plugin to handle file types which are not implemented
6 // directly in ImageJ through io.Opener
7 // NB: since there is no _ in the name it will not appear in Plugins menu
8 // -----
9 // Can be user modified so that your own specialised file types
10 // can be opened through File ... Open
11 // OR by drag and drop onto the ImageJ main panel
12 // OR by double clicking in the MacOS 9/X Finder
13 // -----
14 // Go to the point marked MODIFY HERE and modify to
15 // recognise and load your own file type
16 // -----
17 // Gregory Jefferis - 030629
18 // jefferis@stanford.edu
19 
24 public class HandleExtraFileTypes extends ImagePlus implements PlugIn {
25  static final int IMAGE_OPENED = -1;
26  static final int PLUGIN_NOT_FOUND = -2;
27 
29  public void run(String path) {
30  if (path.equals("")) return;
31  File theFile = new File(path);
32  String directory = theFile.getParent();
33  String fileName = theFile.getName();
34  if (directory == null) directory = "";
35 
36  // Try and recognise file type and load the file if recognised
37  ImagePlus imp = openImage(directory, fileName, path);
38  if (imp==null) {
39  IJ.showStatus("");
40  return; // failed to load file or plugin has opened and displayed it
41  }
42  ImageStack stack = imp.getStack();
43  // get the title from the stack (falling back to the fileName)
44  String title=imp.getTitle().equals("")?fileName:imp.getTitle();
45  // set the stack of this HandleExtraFileTypes object
46  // to that attached to the ImagePlus object returned by openImage()
47  setStack(title, stack);
48  // copy over the calibration info since it doesn't come with the ImageProcessor
49  setCalibration(imp.getCalibration());
50  // also copy the Show Info field over if it exists
51  if (imp.getProperty("Info") != null)
52  setProperty("Info", imp.getProperty("Info"));
53  // copy the FileInfo
54  setFileInfo(imp.getOriginalFileInfo());
55  // copy dimensions
56  if (IJ.getVersion().compareTo("1.38s")>=0)
57  setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
58  if (IJ.getVersion().compareTo("1.41o")>=0)
59  setOpenAsHyperStack(imp.getOpenAsHyperStack());
60  }
61 
62 
63  private Object tryOpen(String directory, String name, String path) {
64  // set up a stream to read in 132 bytes from the file header
65  // These can be checked for "magic" values which are diagnostic
66  // of some image types
67  InputStream is;
68  byte[] buf = new byte[132];
69  try {
70  if (0 == path.indexOf("http://"))
71  is = new java.net.URL(path).openStream();
72  else
73  is = new FileInputStream(path);
74  is.read(buf, 0, 132);
75  is.close();
76  }
77  catch (IOException e) {
78  // couldn't open the file for reading
79  return null;
80  }
81  name = name.toLowerCase();
82  width = PLUGIN_NOT_FOUND;
83 
84  // Temporarily suppress "plugin not found" errors if LOCI Bio-Formats plugin is installed
85  if (Menus.getCommands().get("Bio-Formats Importer")!=null && IJ.getVersion().compareTo("1.37u")>=0)
86  IJ.suppressPluginNotFoundError();
87 
88  // OK now we get to the interesting bit
89 
90  // GJ: added Biorad PIC confocal file handler
91  // ------------------------------------------
92  // These make 12345 if you read them as the right kind of short
93  // and should have this value in every Biorad PIC file
94  if (buf[54]==57 && buf[55]==48) {
95  return tryPlugIn("Biorad_Reader", path);
96  }
97  // GJ: added Gatan Digital Micrograph DM3 handler
98  // ----------------------------------------------
99  // check if the file ends in .DM3 or .dm3,
100  // and bytes make an int value of 3 which is the DM3 version number
101  if (name.endsWith(".dm3") && buf[0]==0 && buf[1]==0 && buf[2]==0 && buf[3]==3) {
102  return tryPlugIn("DM3_Reader", path);
103  }
104 
105  // IPLab file handler
106  // Little-endian IPLab files start with "iiii" or "mmmm".
107  if (name.endsWith(".ipl") ||
108  (buf[0]==105 && buf[1]==105 && buf[2]==105 && buf[3]==105) ||
109  (buf[0]==109 && buf[1]==109 && buf[2]==109 && buf[3]==109)) {
110  return tryPlugIn("IPLab_Reader", path);
111  }
112 
113  // Packard InstantImager format (.img) handler -> check HERE
114  // before Analyze check below!
115  // Check extension and signature bytes KAJ_
116  if (name.endsWith(".img") && buf[0]==75 && buf[1]==65 && buf[2]==74 && buf[3]==0) {
117  return tryPlugIn("InstantImager_Reader", path);
118  }
119 
120  // Analyze format (.img/.hdr) handler
121  // Opens the file using the Nifti_Reader if it is installed,
122  // otherwise the Analyze_Reader is used. Note that
123  // the Analyze_Reader plugin opens and displays the
124  // image and does not implement the ImagePlus class.
125  if (name.endsWith(".img") || name.endsWith(".hdr")) {
126  if (Menus.getCommands().get("NIfTI-Analyze")!=null)
127  return tryPlugIn("Nifti_Reader", path);
128  else
129  return tryPlugIn("Analyze_Reader", path);
130  }
131 
132  // NIFTI format (.nii) handler
133  if (name.endsWith(".nii") || name.endsWith( ".nii.gz" ) || name.endsWith( ".nii.z" ) ) {
134  return tryPlugIn("Nifti_Reader", path);
135  }
136 
137  // Image Cytometry Standard (.ics) handler
138  // http://valelab.ucsf.edu/~nico/IJplugins/Ics_Opener.html
139  if (name.endsWith(".ics")) {
140  return tryPlugIn("Ics_Opener", path);
141  }
142 
143  // Princeton Instruments SPE image file (.spe) handler
144  // http://rsb.info.nih.gov/ij/plugins/spe.html
145  if (name.endsWith(".spe")) {
146  return tryPlugIn("OpenSPE_", path);
147  }
148 
149  // Zeiss Confocal LSM 510 image file (.lsm) handler
150  // http://rsb.info.nih.gov/ij/plugins/lsm-reader.html
151  if (name.endsWith(".lsm")) {
152  Object obj = tryPlugIn("LSM_Reader", path);
153  if (obj==null && Menus.getCommands().get("Show LSMToolbox")!=null)
154  obj = tryPlugIn("LSM_Toolbox", "file="+path);
155  return obj;
156  }
157 
158  // BM: added Bruker file handler 29.07.04
159  if (name.equals("ser") || name.equals("fid") || name.equals("2rr") ||
160  name.equals("2ii") || name.equals("3rrr") || name.equals("3iii") ||
161  name.equals("2dseq")) {
162  ij.IJ.showStatus("Opening Bruker " + name + " File");
163  return tryPlugIn("BrukerOpener", name + "|" + path);
164  }
165 
166  // AVI: open AVI files using AVI_Reader plugin
167  if (name.endsWith(".avi")) {
168  return tryPlugIn("AVI_Reader", path);
169  }
170 
171  // QuickTime: open .mov and .pict files using QT_Movie_Opener plugin
172  if (name.endsWith(".mov") || name.endsWith(".pict")) {
173  return tryPlugIn("QT_Movie_Opener", path);
174  }
175 
176  // ZVI file handler
177  // Little-endian ZVI and Thumbs.db files start with d0 cf 11 e0
178  // so we can only look at the extension.
179  if (name.endsWith(".zvi")) {
180  return tryPlugIn("ZVI_Reader", path);
181  }
182 
183  // University of North Carolina (UNC) file format handler
184  // 'magic' numbers are (int) offsets to data structures and
185  // may change in future releases.
186  if (name.endsWith(".unc") || (buf[3]==117 && buf[7]==-127 && buf[11]==36 && buf[14]==32 && buf[15]==-127)) {
187  return tryPlugIn("UNC_Reader", path);
188  }
189 
190  // Amira file handler
191  // http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/amira-io.html
192  if (buf[0]==0x23 && buf[1]==0x20 && buf[2]==0x41
193  && buf[3]==0x6d && buf[4]==0x69 && buf[5]==0x72
194  && buf[6]==0x61 && buf[7]==0x4d && buf[8]==0x65
195  && buf[9]==0x73&&buf[10]==0x68 && buf[11]==0x20) {
196  return tryPlugIn("AmiraMeshReader_", path);
197  }
198 
199  // Deltavision file handler
200  // Open DV files generated on Applied Precision DeltaVision systems
201  if (name.endsWith(".dv") || name.endsWith(".r3d")) {
202  return tryPlugIn("Deltavision_Opener", path);
203  }
204 
205  // Albert Cardona: read .mrc files (little endian).
206  // Documentation at: http://ami.scripps.edu/prtl_data/mrc_specification.htm.
207  // The parsing of the header is a bare minimum of what could be done.
208  if (name.endsWith(".mrc")) {
209  return tryPlugIn("Open_MRC_Leginon", path);
210  }
211 
212  // Albert Cardona: read .dat files from the EMMENU software
213  if (name.endsWith(".dat") && 1 == buf[1] && 0 == buf[2]) { // 'new format' only
214  return tryPlugIn("Open_DAT_EMMENU", path);
215  }
216 
217  // Timo Rantalainen and Michael Doube: read Stratec pQCT files.
218  // File name is IDDDDDDD.MHH, where D is decimal and H is hex.
219  if (name.matches("[iI]\\d{7}\\.[mM]\\p{XDigit}{2}")) {
220  return tryPlugIn("org.doube.bonej.pqct.Read_Stratec_File", path);
221  }
222 
223  //Michael Doube: read Scanco ISQ files
224  //File name is ADDDDDDD.ISQ;D where D is a decimal and A is a letter
225  try {
226  String isqMagic=new String(buf,0,16,"UTF-8");
227  if (name.matches("[a-z]\\d{7}.isq;\\d+") || isqMagic.equals("CTDATA-HEADER_V1"))
228  return tryPlugIn("org.bonej.io.ISQReader", path);
229  }
230  catch (Exception e) {}
231 
232  // ****************** MODIFY HERE ******************
233  // do what ever you have to do to recognise your own file type
234  // and then call appropriate plugin using the above as models
235  // e.g.:
236 
237  /*
238  // A. Dent: Added XYZ handler
239  // ----------------------------------------------
240  // check if the file ends in .xyz, and bytes 0 and 1 equal 42
241  if (name.endsWith(".xyz") && buf[0]==42 && buf[1]==42) {
242  // Ok we've identified the file type - now load it
243  return tryPlugIn("XYZ_Reader", path);
244  }
245  */
246 
247  return null;
248  }
249 
250  private ImagePlus openImage(String directory, String name, String path) {
251  Object o = tryOpen(directory, name, path);
252  // if an image was returned, assume success
253  if (o instanceof ImagePlus) return (ImagePlus)o;
254 
255  // try opening the file with LOCI Bio-Formats plugin - always check this last!
256  // Do not call Bio-Formats if File>Import>Image Sequence is opening this file.
257  if (o==null && (IJ.getVersion().compareTo("1.38j")<0||!IJ.redirectingErrorMessages()) && (new File(path).exists())) {
258  Object loci = IJ.runPlugIn("loci.plugins.LociImporter", path);
259  if (loci!=null) {
260  // plugin exists and was launched
261  try {
262  // check whether plugin was successful
263  Class c = loci.getClass();
264  boolean success = c.getField("success").getBoolean(loci);
265  boolean canceled = c.getField("canceled").getBoolean(loci);
266  if (success || canceled) {
267  width = IMAGE_OPENED;
268  return null;
269  }
270  }
271  catch (Exception exc) { }
272  }
273  }
274 
275  return null;
276 
277  } // openImage
278 
286  private Object tryPlugIn(String className, String path) {
287  Object o = IJ.runPlugIn(className, path);
288  if (o instanceof ImagePlus) {
289  // plugin extends ImagePlus class
290  ImagePlus imp = (ImagePlus)o;
291  if (imp.getWidth()==0)
292  o = null; // invalid image
293  else
294  width = IMAGE_OPENED; // success
295  } else {
296  // plugin does not extend ImagePlus; assume success
297  width = IMAGE_OPENED;
298  }
299  return o;
300  }
301 
302 
303 }
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This page explains how to interpret the graphs that are generated by doxygen.

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Consider the following example:

/*! Invisible class because of truncation */
class Invisible { };
/*! Truncated class, inheritance relation is hidden */
class Truncated : public Invisible { };
/* Class not documented with doxygen comments */
class Undocumented { };
/*! Class that is inherited using public inheritance */
class PublicBase : public Truncated { };
/*! A template class */
template<class T> class Templ { };
/*! Class that is inherited using protected inheritance */
class ProtectedBase { };
/*! Class that is inherited using private inheritance */
class PrivateBase { };
/*! Class that is used by the Inherited class */
class Used { };
/*! Super class that inherits a number of other classes */
class Inherited : public PublicBase,
protected ProtectedBase,
private PrivateBase,
public Undocumented,
public Templ<int>
{
private:
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};

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[detail level 12345]
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 ►CApplet
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 Cxmipp.utils.DEBUG
 Cxmipp.jni.EllipseCTF
 Cxmipp.viewer.scipion.ScipionMetaData.EMObject
 Cxmipp.jni.Filename
 Cxmipp.test.FilenameTest
 ►CFileView
 Cxmipp.viewer.particlepicker.Format
 ►Cxmipp.viewer.models.GalleryData
 Cxmipp.ij.commons.Geometry
 Cxmipp.ij.plugins.maskstoolbar.ICONS
 ►Cxmipp.viewer.ctf.iCTFGUI
 Cxmipp.ij.commons.IJCommand
 Cxmipp.viewer.ImageDimension
 Cxmipp.jni.ImageGeneric
 Cxmipp.test.ImageGenericTest
 Cxmipp.viewer.models.ImageGalleryTableModel.ImageItem
 Cxmipp.ij.commons.ImagePlusLoader
 ►Cxmipp.ij.commons.ImagePlusReader
 Cxmipp.viewer.windows.ImagesWindowFactory
 Cxmipp.jni.ImageWriteMode
 Cxmipp.viewer.windows.iPollImageWindow
 ►Cxmipp.viewer.ctf.iTaskCompletionListener
 Cxmipp.viewer.JMetaDataIO
 Cxmipp.ij.plugins.maskstoolbar.LABELS
 Cxmipp.jni.LinearAlgebra
 Cxmipp.tomography.alignment.Matrix
 Cxmipp.jni.MDLabel
 Cxmipp.jni.MDRow
 ►Cxmipp.jni.MetaData
 Cxmipp.test.MetadataTest
 ►Cxmipp.viewer.particlepicker.Micrograph
 Cxmipp.viewer.particlepicker.extract.MicrographData
 Cxmipp.viewer.particlepicker.training.model.MicrographState
 Cxmipp.viewer.models.GalleryData.Mode
 Cxmipp.viewer.particlepicker.training.model.Mode
 Cxmipp.ij.plugins.maskstoolbar.Operations
 Cxmipp.jni.Classifier.Parameter
 ►Cxmipp.utils.Params
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 Cxmipp.viewer.particlepicker.ParticlePickerParams
 Cxmipp.jni.Program
 Cxmipp.jni.ProgTomographAlignment
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 ►CRunnable
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 Cxmipp.viewer.particlepicker.Shape
 Cxmipp.utils.SpringUtilities
 Cxmipp.utils.StopWatch
 Clibsvm.svm
 Clibsvm.svm_print_interface
 Cxmipp.utils.Task
 Cxmipp.jni.TiltPairAligner
 Cxmipp.tomography.alignment.Tomography
 Cxmipp.tomography.alignment.TomoSerieAligner
 Cxmipp.ij.commons.Tool
 ►Cxmipp.viewer.Viewer
 Cxmipp.ij.commons.XmippApplication
 Cxmipp.jni.XmippError
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 Cxmipp.ij.commons.XmippImageConverter
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 Cxmipp.utils.XmippResource
 Cxmipp.utils.XmippStringUtils
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 Cxmipp.ij.commons.XmippUtil
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 ►CAbstractBorder
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1 /*
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5 package xmipp.viewer.ctf;
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11 public interface iCTFGUI {
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interface  xmipp.viewer.windows.iPollImageWindow
 
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1 /*
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5 package xmipp.viewer.windows;
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11 public interface iPollImageWindow {
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13  public boolean isPoll();
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15  public void setPoll(boolean poll);
16 }
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interface  xmipp.viewer.ctf.iTaskCompletionListener
 
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Xmipp
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Welcome to Xmipp API Documentation. Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.

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-Generated by   -doxygen - 1.8.13 -
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- Node182 -> Node0 [dir="back",color="midnightblue",fontsize="10",style="solid",fontname="Helvetica"]; - Node0 [label="xmipp.utils.Cache\<\l K, T \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1Cache.html"]; -} diff --git a/html/inherit_graph_47.md5 b/html/inherit_graph_47.md5 deleted file mode 100644 index ca74810e..00000000 --- a/html/inherit_graph_47.md5 +++ /dev/null @@ -1 +0,0 @@ -f9f29dc43b16368e58d56fe7d79c4e2f \ No newline at end of file diff --git a/html/inherit_graph_48.dot b/html/inherit_graph_48.dot deleted file mode 100644 index a7805e2b..00000000 --- a/html/inherit_graph_48.dot +++ /dev/null @@ -1,7 +0,0 @@ -digraph "Graphical Class Hierarchy" -{ - edge [fontname="Helvetica",fontsize="10",labelfontname="Helvetica",labelfontsize="10"]; - node [fontname="Helvetica",fontsize="10",shape=record]; - rankdir="LR"; - Node0 [label="xmipp.utils.Cache\<\l String, xmipp.viewer.models.\lImageGalleryTableModel.ImageItem \>",height=0.2,width=0.4,color="black", fillcolor="white", style="filled",URL="$classxmipp_1_1utils_1_1Cache.html"]; 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print(String s)libsvm.svm_print_interface
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void print (String s)
 
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Definition at line 2 of file svm_print_interface.java.

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getCanvas()xmipp.ij.commons.XmippIJWindow
getImagePlusLoader()xmipp.ij.commons.XmippIJWindow
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isStack()xmipp.ij.commons.XmippIJWindow
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saveDataAs(String file)xmipp.ij.commons.XmippIJWindow
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void loadData ()
 
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setRowBusy(int row)xmipp.viewer.ctf.iCTFGUI
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Definition at line 11 of file iCTFGUI.java.

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boolean isPoll ()
 
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Definition at line 11 of file iPollImageWindow.java.

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1 
2 import ij.IJ;
3 import ij.ImagePlus;
4 import ij.ImageStack;
5 import ij.Prefs;
6 import ij.plugin.PlugIn;
7 import java.io.File;
8 import java.io.FileInputStream;
9 import java.io.IOException;
10 import java.io.InputStream;
11 import xmipp.utils.Params;
12 import xmipp.viewer.windows.ImagesWindowFactory;
13 
14 // Plugin to handle file types which are not implemented
15 // directly in ImageJ through io.Opener
16 // nb since there is no _ in the name it will not appear in Plugins menu
17 // -----
18 // Can be user modified so that your own specialised file types
19 // can be opened through File>Open
20 // or by drag and drop onto the ImageJ main window
21 // or by drag and drop onto the ImageJ icon
22 // or by double clicking on the file icon (requires that
23 // the file extension be associated with ImageJ).
24 // -----
25 // Go to the point marked MODIFY HERE and modify to
26 // recognise and load your own file type
27 // I have implemented two file types as examples:
28 // Biorad PIC and Gatan DM3
29 // -----
30 // Gregory Jefferis - 030629
31 // jefferis@stanford.edu
32 //
33 // Note that the File>Import>Image Sequence command and
34 // IJ.openImage() method will not work as expected unless the
35 // reader plugin extends the ImagePlus class.
42 public class HandleExtraFileTypes extends ImagePlus implements PlugIn {
43 
44  final static int IMAGE_OPENED = -1;
45  final static int PLUGIN_NOT_FOUND = -1;
46 
47  // Called from io/Opener.java
53  public void run(String path) {
54  if (IJ.versionLessThan("1.30u")) {
55  return;
56  }
57  if (path.equals("")) {
58  return;
59  }
60  File theFile = new File(path);
61  String directory = theFile.getParent();
62  String fileName = theFile.getName();
63  if (directory == null) {
64  directory = "";
65  }
66 
67  // Try and recognise file type and load the file if recognised
68  ImagePlus imp = openImage(directory, fileName);
69  if (imp == null) {
70  // failed to load file or plugin has opened and displayed it
71  IJ.showStatus("");
72  return;
73  // failed to load file or plugin has opened and displayed it
74  }
75  ImageStack stack = imp.getStack();
76  // Set the stack of this HandleExtraFileTypes object
77  // to that attached to the ImagePlus object returned by openImage()
78  setStack(fileName, stack);
79  // Copy over the calibration info since it doesn't come with the ImageProcessor
80  setCalibration(imp.getCalibration());
81  // Also copy the Show Info field over if it exists
82  if (imp.getProperty("Info") != null) {
83  setProperty("Info", imp.getProperty("Info"));
84  }
85  // Copy over the FileInfo
86  setFileInfo(imp.getOriginalFileInfo());
87  }
88 
96  private ImagePlus openImage(String directory, String name) {
97  ImagePlus imp;
98 
99  // Set out file name and path
100  if (directory.length() > 0 && !directory.endsWith(Prefs.separator)) {
101  directory += Prefs.separator;
102  }
103  String path = directory + name;
104 
105  // set up a stream to read in 132 bytes from the file header
106  // These can be checked for "magic" values which are diagnostic
107  // of some image types
108  InputStream is;
109  byte[] buf = new byte[132];
110  try {
111  is = new FileInputStream(path);
112  is.read(buf, 0, 132);
113  is.close();
114  } catch (IOException e) {
115  // Couldn't open the file for reading
116  return null;
117  }
118  name = name.toLowerCase();
119 
120  // OK now we get to the interesting bit
121 
122  // CTR: try opening the file with LOCI Bio-Formats
123  // http://www.loci.wisc.edu/ome/formats.html
124  /*
125  Object loci = IJ.runPlugIn("LociPlugin", path);
126  if (loci != null) {
127  plugin exists and was launched
128  try {
129  check whether plugin was successful
130  boolean ok = loci.getClass().getField("success").getBoolean(loci);
131  if (ok) {
132  width = IMAGE_OPENED;
133  return null;
134  }
135  }
136  catch (Exception exc) { }
137  }
138  */
139  // GJ: added Biorad PIC confocal file handler
140  // Note that the Biorad_Reader plugin extends the ImagePlus class,
141  // which is why the IJ.runPlugIn() call below returns an ImagePlus object.
142  // ------------------------------------------
143  // These make 12345 if you read them as the right kind of short
144  // and should have this value in every Biorad PIC file
145  if (buf[54] == 57 && buf[55] == 48) {
146  // Ok we've identified the file type
147  // Now load it using the relevant plugin
148  imp = (ImagePlus) IJ.runPlugIn("Biorad_Reader", path);
149  if (imp == null) {
150  width = PLUGIN_NOT_FOUND;
151  }
152  if (imp != null && imp.getWidth() == 0) {
153  imp = null;
154  }
155  return imp;
156  }
157 
158  // Analyze format (.img/.hdr) handler
159  // Note that the Analyze_Reader plugin opens and displays the
160  // image and does not implement the ImagePlus class.
161  if (name.endsWith(".img") || name.endsWith(".hdr")) {
162  // Open Analyze image and display it
163  IJ.runPlugIn("Analyze_Reader", path);
164  // Set flag so Opener.openImage() does not display error
165  width = IMAGE_OPENED;
166  return null;
167  }
168 
169  // IPLab file handler
170  // Note that the IPLab_Reader plugin extends the ImagePlus class.
171  // Little-endian IPLab files start with "iiii" or "mmmm".
172  if ((buf[0] == 105 && buf[1] == 105 && buf[2] == 105 && buf[3] == 105)
173  || (buf[0] == 109 && buf[1] == 109 && buf[2] == 109 && buf[3] == 109)) {
174  imp = (ImagePlus) IJ.runPlugIn("IPLab_Reader", path);
175  if (imp == null) {
176  width = PLUGIN_NOT_FOUND;
177  }
178  if (imp != null && imp.getWidth() == 0) {
179  imp = null;
180  }
181  return imp;
182  }
183 
184  // Packard InstantImager format (.img) handler -> check HERE before Analyze check below!
185  // Note that the InstantImager_Reader plugin extends the ImagePlus class.
186  // Check extension and signature bytes KAJ_
187  if (name.endsWith(".img") && buf[0] == 75 && buf[1] == 65 && buf[2] == 74 && buf[3] == 0) {
188  imp = (ImagePlus) IJ.runPlugIn("InstantImager_Reader", path);
189  if (imp == null) {
190  width = PLUGIN_NOT_FOUND;
191  }
192  if (imp != null && imp.getWidth() == 0) {
193  imp = null;
194  }
195  return imp;
196  }
197 
198  // Analyze format (.img/.hdr) handler
199  // Note that the Analyze_Reader plugin opens and displays the
200  // image and does not implement the ImagePlus class.
201  if (name.endsWith(".img") || name.endsWith(".hdr")) {
202  // Open Analyze image and display it
203  IJ.runPlugIn("Analyze_Reader", path);
204  // Set flag so Opener.openImage() does not display error
205  width = IMAGE_OPENED;
206  return null;
207  }
208 
209  // Image Cytometry Standard (.ics) handler
210  // http://valelab.ucsf.edu/~nico/IJplugins/Ics_Opener.html
211  if (name.endsWith(".ics")) {
212  // Open ICS image and display it
213  IJ.runPlugIn("Ics_Opener", path);
214  // Set flag so Opener.openImage() does not display error
215  width = IMAGE_OPENED;
216  return null;
217  }
218 
219  // Zeiss Confocal LSM 510 image file (.lsm) handler
220  // http://rsb.info.nih.gov/ij/plugins/lsm-reader.html
221  if (name.endsWith(".lsm")) {
222  IJ.runPlugIn("LSM_Reader", path);
223  width = IMAGE_OPENED;
224  return null;
225  }
226 
227  // BM: added Bruker file handler 29.07.04
228  if (name.equals("ser") || name.equals("fid") || name.equals("2rr") || name.equals("2ii") || name.equals("3rrr")
229  || name.equals("3iii") || name.equals("2dseq")) {
230  IJ.showStatus("Opening Bruker " + name + " File");
231  IJ.runPlugIn("BrukerOpener", name + "|" + path);
232  width = IMAGE_OPENED;
233  return null;
234  }
235 
236  // AVI: open AVI files using AVI_Reader plugin
237  if (name.endsWith(".avi")) {
238  IJ.runPlugIn("AVI_Reader", path);
239  width = IMAGE_OPENED;
240  return null;
241  }
242 
243  // QuickTime: open .mov files using QT_Movie_Opener plugin
244  if (name.endsWith(".mov")) {
245  IJ.runPlugIn("QT_Movie_Opener", path);
246  width = IMAGE_OPENED;
247  return null;
248  }
249 
250  // ZVI file handler
251  // Little-endian ZVI and Thumbs.db files start with d0 cf 11 e0
252  // so we can only look at the extension.
253  if (name.endsWith(".zvi")) {
254  IJ.runPlugIn("ZVI_Reader", path);
255  width = IMAGE_OPENED;
256  return null;
257  }
258 
259  //University of North Carolina (UNC) file format handler
260  // 'magic' numbers are (int) offsets to data structures and may change in future releases.
261  if (name.endsWith(".unc") || (buf[3] == 117 && buf[7] == -127 && buf[11] == 36 && buf[14] == 32 && buf[15] == -127)) {
262  IJ.runPlugIn("UNC_Reader", path);
263  width = IMAGE_OPENED;
264  return null;
265  }
266 
267  // Leica SP confocal .lei file handler
268  if (name.endsWith(".lei")) {
269  int dotIndex = name.lastIndexOf(".");
270  if (dotIndex >= 0) {
271  name = name.substring(0, dotIndex);
272  }
273  path = directory + name + ".txt";
274  File f = new File(path);
275  if (!f.exists()) {
276  IJ.error("Cannot find the Leica information file: " + path);
277  return null;
278  }
279  IJ.runPlugIn("Leica_TIFF_sequence", path);
280  width = IMAGE_OPENED;
281  return null;
282  }
283 
284  // Amira file handler
285  // http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/amira-io.html
286  if (buf[0] == 0x23 && buf[1] == 0x20 && buf[2] == 0x41
287  && buf[3] == 0x6d && buf[4] == 0x69 && buf[5] == 0x72
288  && buf[6] == 0x61 && buf[7] == 0x4d && buf[8] == 0x65
289  && buf[9] == 0x73 && buf[10] == 0x68 && buf[11] == 0x20) {
290  ImagePlus i = (ImagePlus) IJ.runPlugIn("AmiraMeshReader_", path);
291  width = (i == null) ? PLUGIN_NOT_FOUND : IMAGE_OPENED;
292  return null;
293  }
294  /* // Deltavision file handler
295  // Open DV files generated on Applied Precision DeltaVision systems
296  if (name.endsWith(".dv") || name.endsWith(".r3d")) {
297  return tryPlugIn("Deltavision_Opener", path);
298  }
299  // Albert Cardona: read .dat files from the EMMENU software
300  if (name.endsWith(".dat") && 1 == buf[1] && 0 == buf[2]) { // 'new format' only
301  return tryPlugIn("Open_DAT_EMMENU", path);
302  } */
303 
304  if (name.toLowerCase().endsWith(".sdf")) {
305  imp = (ImagePlus) IJ.runPlugIn("SDF_reader", path);
306  if (imp == null) {
307  width = PLUGIN_NOT_FOUND;
308  }
309  if (imp != null && imp.getWidth() == 0) {
310  imp = null;
311  }
312  return imp;
313  }
314  // ****************** MODIFY HERE ** ****************
315  // Do what ever you have to do to recognise your own file type
316  // and then call appropriate plugin
317  // using the above as models
318  // eg:
319 
320 
321  // Obviouslly, IJ.Opener needs a valid ImagePlus. If for some reason we don't return it,
322  // an alert will apear complaining something like "File is not supported format, a reader plugin
323  // is not available..."
324  try{
325  System.err.println(path);
326 
327  Params param = new Params();
328 
329  imp=ImagesWindowFactory.openFileAsImagePlus(path, param);
330  if (imp == null) {
331  width = PLUGIN_NOT_FOUND;
332  }
333 
334  if (imp != null){
335  if(imp.getWidth() == 0)
336  imp = null;
337  return imp;
338  }
339 
340  }catch (Exception ex){
341  ex.printStackTrace();
342  }
343 
344 
345  /*if (Filename.isMetadata(name)) {
346  imp = (ImagePlus) tryPlugIn(xmipp.io.readers.MetaDataReader.class.getCanonicalName(), path);
347 
348 
349  } else if (Filename.isXmippType(name)) {
350  imp = (ImagePlus) tryPlugIn(xmipp.io.readers.ImageReader.class.getCanonicalName(), path);
351 
352  if (imp == null) {
353  width = PLUGIN_NOT_FOUND;
354  }
355  if (imp != null && imp.getWidth() == 0) {
356  imp = null;
357  }
358 
359  return imp;
360  }*/
361 
362  /*
363  A. Dent: Added XYZ handler
364  ----------------------------------------------
365  Check if the file ends in .XYZ or .xyz
366  if (name.toUpperCase().endsWith(".XYZ")) {
367  Bytes 0 and 1 must equal 42 for this file type
368  if(buf[0]==42 && buf[1]==42) {
369  Ok we've identified the file type - now load it
370  imp = (ImagePlus)IJ.runPlugIn("XYZ_Reader", path);
371  if (imp==null) width = PLUGIN_NOT_FOUND;
372  if (imp!=null&&imp.getWidth()==0) imp = null;
373  return imp;
374  }
375  }
376  */
377  // If we got this far we didn't recognise the file type
378  return null;
379  }
380 
388  private Object tryPlugIn(String className, String path) {
389  Object o = IJ.runPlugIn(className, path);
390  if (o instanceof ImagePlus) {
391  // plugin extends ImagePlus class
392  ImagePlus imp = (ImagePlus) o;
393  if (imp.getWidth() == 0) {
394  o = null; // invalid image
395  } else {
396  width = IMAGE_OPENED; // success
397  }
398  } else {
399  // plugin does not extend ImagePlus; assume success
400  width = IMAGE_OPENED;
401  }
402  return o;
403  }
404 
405 
406 }
- - - - - - - -
xmipp.viewer.windows.ImagesWindowFactory.openFileAsImagePlus
static ImagePlus openFileAsImagePlus(String path, Params parameters)
Definition: ImagesWindowFactory.java:119
- -
- -
-Generated by   -doxygen - 1.8.13 -
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true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){e.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(f)&&this._mouseDelayMet(f)){this._mouseStarted=(this._mouseStart(f)!==false);if(!this._mouseStarted){f.preventDefault();return true}}if(true===b.data(f.target,this.widgetName+".preventClickEvent")){b.removeData(f.target,this.widgetName+".preventClickEvent")}this._mouseMoveDelegate=function(h){return e._mouseMove(h)};this._mouseUpDelegate=function(h){return e._mouseUp(h)};b(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);f.preventDefault();a=true;return true},_mouseMove:function(d){if(b.browser.msie&&!(document.documentMode>=9)&&!d.button){return this._mouseUp(d)}if(this._mouseStarted){this._mouseDrag(d);return d.preventDefault()}if(this._mouseDistanceMet(d)&&this._mouseDelayMet(d)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,d)!==false);(this._mouseStarted?this._mouseDrag(d):this._mouseUp(d))}return !this._mouseStarted},_mouseUp:function(d){b(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;if(d.target==this._mouseDownEvent.target){b.data(d.target,this.widgetName+".preventClickEvent",true)}this._mouseStop(d)}return false},_mouseDistanceMet:function(d){return(Math.max(Math.abs(this._mouseDownEvent.pageX-d.pageX),Math.abs(this._mouseDownEvent.pageY-d.pageY))>=this.options.distance)},_mouseDelayMet:function(d){return this.mouseDelayMet},_mouseStart:function(d){},_mouseDrag:function(d){},_mouseStop:function(d){},_mouseCapture:function(d){return true}})})(jQuery);(function(c,d){c.widget("ui.resizable",c.ui.mouse,{widgetEventPrefix:"resize",options:{alsoResize:false,animate:false,animateDuration:"slow",animateEasing:"swing",aspectRatio:false,autoHide:false,containment:false,ghost:false,grid:false,handles:"e,s,se",helper:false,maxHeight:null,maxWidth:null,minHeight:10,minWidth:10,zIndex:1000},_create:function(){var f=this,k=this.options;this.element.addClass("ui-resizable");c.extend(this,{_aspectRatio:!!(k.aspectRatio),aspectRatio:k.aspectRatio,originalElement:this.element,_proportionallyResizeElements:[],_helper:k.helper||k.ghost||k.animate?k.helper||"ui-resizable-helper":null});if(this.element[0].nodeName.match(/canvas|textarea|input|select|button|img/i)){this.element.wrap(c('
').css({position:this.element.css("position"),width:this.element.outerWidth(),height:this.element.outerHeight(),top:this.element.css("top"),left:this.element.css("left")}));this.element=this.element.parent().data("resizable",this.element.data("resizable"));this.elementIsWrapper=true;this.element.css({marginLeft:this.originalElement.css("marginLeft"),marginTop:this.originalElement.css("marginTop"),marginRight:this.originalElement.css("marginRight"),marginBottom:this.originalElement.css("marginBottom")});this.originalElement.css({marginLeft:0,marginTop:0,marginRight:0,marginBottom:0});this.originalResizeStyle=this.originalElement.css("resize");this.originalElement.css("resize","none");this._proportionallyResizeElements.push(this.originalElement.css({position:"static",zoom:1,display:"block"}));this.originalElement.css({margin:this.originalElement.css("margin")});this._proportionallyResize()}this.handles=k.handles||(!c(".ui-resizable-handle",this.element).length?"e,s,se":{n:".ui-resizable-n",e:".ui-resizable-e",s:".ui-resizable-s",w:".ui-resizable-w",se:".ui-resizable-se",sw:".ui-resizable-sw",ne:".ui-resizable-ne",nw:".ui-resizable-nw"});if(this.handles.constructor==String){if(this.handles=="all"){this.handles="n,e,s,w,se,sw,ne,nw"}var l=this.handles.split(",");this.handles={};for(var g=0;g
');if(/sw|se|ne|nw/.test(j)){h.css({zIndex:++k.zIndex})}if("se"==j){h.addClass("ui-icon ui-icon-gripsmall-diagonal-se")}this.handles[j]=".ui-resizable-"+j;this.element.append(h)}}this._renderAxis=function(q){q=q||this.element;for(var n in this.handles){if(this.handles[n].constructor==String){this.handles[n]=c(this.handles[n],this.element).show()}if(this.elementIsWrapper&&this.originalElement[0].nodeName.match(/textarea|input|select|button/i)){var o=c(this.handles[n],this.element),p=0;p=/sw|ne|nw|se|n|s/.test(n)?o.outerHeight():o.outerWidth();var m=["padding",/ne|nw|n/.test(n)?"Top":/se|sw|s/.test(n)?"Bottom":/^e$/.test(n)?"Right":"Left"].join("");q.css(m,p);this._proportionallyResize()}if(!c(this.handles[n]).length){continue}}};this._renderAxis(this.element);this._handles=c(".ui-resizable-handle",this.element).disableSelection();this._handles.mouseover(function(){if(!f.resizing){if(this.className){var i=this.className.match(/ui-resizable-(se|sw|ne|nw|n|e|s|w)/i)}f.axis=i&&i[1]?i[1]:"se"}});if(k.autoHide){this._handles.hide();c(this.element).addClass("ui-resizable-autohide").hover(function(){if(k.disabled){return}c(this).removeClass("ui-resizable-autohide");f._handles.show()},function(){if(k.disabled){return}if(!f.resizing){c(this).addClass("ui-resizable-autohide");f._handles.hide()}})}this._mouseInit()},destroy:function(){this._mouseDestroy();var e=function(g){c(g).removeClass("ui-resizable ui-resizable-disabled ui-resizable-resizing").removeData("resizable").unbind(".resizable").find(".ui-resizable-handle").remove()};if(this.elementIsWrapper){e(this.element);var f=this.element;f.after(this.originalElement.css({position:f.css("position"),width:f.outerWidth(),height:f.outerHeight(),top:f.css("top"),left:f.css("left")})).remove()}this.originalElement.css("resize",this.originalResizeStyle);e(this.originalElement);return this},_mouseCapture:function(f){var g=false;for(var e in this.handles){if(c(this.handles[e])[0]==f.target){g=true}}return !this.options.disabled&&g},_mouseStart:function(g){var j=this.options,f=this.element.position(),e=this.element;this.resizing=true;this.documentScroll={top:c(document).scrollTop(),left:c(document).scrollLeft()};if(e.is(".ui-draggable")||(/absolute/).test(e.css("position"))){e.css({position:"absolute",top:f.top,left:f.left})}this._renderProxy();var k=b(this.helper.css("left")),h=b(this.helper.css("top"));if(j.containment){k+=c(j.containment).scrollLeft()||0;h+=c(j.containment).scrollTop()||0}this.offset=this.helper.offset();this.position={left:k,top:h};this.size=this._helper?{width:e.outerWidth(),height:e.outerHeight()}:{width:e.width(),height:e.height()};this.originalSize=this._helper?{width:e.outerWidth(),height:e.outerHeight()}:{width:e.width(),height:e.height()};this.originalPosition={left:k,top:h};this.sizeDiff={width:e.outerWidth()-e.width(),height:e.outerHeight()-e.height()};this.originalMousePosition={left:g.pageX,top:g.pageY};this.aspectRatio=(typeof j.aspectRatio=="number")?j.aspectRatio:((this.originalSize.width/this.originalSize.height)||1);var i=c(".ui-resizable-"+this.axis).css("cursor");c("body").css("cursor",i=="auto"?this.axis+"-resize":i);e.addClass("ui-resizable-resizing");this._propagate("start",g);return true},_mouseDrag:function(e){var h=this.helper,g=this.options,m={},q=this,j=this.originalMousePosition,n=this.axis;var r=(e.pageX-j.left)||0,p=(e.pageY-j.top)||0;var i=this._change[n];if(!i){return false}var l=i.apply(this,[e,r,p]),k=c.browser.msie&&c.browser.version<7,f=this.sizeDiff;this._updateVirtualBoundaries(e.shiftKey);if(this._aspectRatio||e.shiftKey){l=this._updateRatio(l,e)}l=this._respectSize(l,e);this._propagate("resize",e);h.css({top:this.position.top+"px",left:this.position.left+"px",width:this.size.width+"px",height:this.size.height+"px"});if(!this._helper&&this._proportionallyResizeElements.length){this._proportionallyResize()}this._updateCache(l);this._trigger("resize",e,this.ui());return false},_mouseStop:function(h){this.resizing=false;var i=this.options,m=this;if(this._helper){var g=this._proportionallyResizeElements,e=g.length&&(/textarea/i).test(g[0].nodeName),f=e&&c.ui.hasScroll(g[0],"left")?0:m.sizeDiff.height,k=e?0:m.sizeDiff.width;var n={width:(m.helper.width()-k),height:(m.helper.height()-f)},j=(parseInt(m.element.css("left"),10)+(m.position.left-m.originalPosition.left))||null,l=(parseInt(m.element.css("top"),10)+(m.position.top-m.originalPosition.top))||null;if(!i.animate){this.element.css(c.extend(n,{top:l,left:j}))}m.helper.height(m.size.height);m.helper.width(m.size.width);if(this._helper&&!i.animate){this._proportionallyResize()}}c("body").css("cursor","auto");this.element.removeClass("ui-resizable-resizing");this._propagate("stop",h);if(this._helper){this.helper.remove()}return false},_updateVirtualBoundaries:function(g){var j=this.options,i,h,f,k,e;e={minWidth:a(j.minWidth)?j.minWidth:0,maxWidth:a(j.maxWidth)?j.maxWidth:Infinity,minHeight:a(j.minHeight)?j.minHeight:0,maxHeight:a(j.maxHeight)?j.maxHeight:Infinity};if(this._aspectRatio||g){i=e.minHeight*this.aspectRatio;f=e.minWidth/this.aspectRatio;h=e.maxHeight*this.aspectRatio;k=e.maxWidth/this.aspectRatio;if(i>e.minWidth){e.minWidth=i}if(f>e.minHeight){e.minHeight=f}if(hl.width),s=a(l.height)&&i.minHeight&&(i.minHeight>l.height);if(h){l.width=i.minWidth}if(s){l.height=i.minHeight}if(t){l.width=i.maxWidth}if(m){l.height=i.maxHeight}var f=this.originalPosition.left+this.originalSize.width,p=this.position.top+this.size.height;var k=/sw|nw|w/.test(q),e=/nw|ne|n/.test(q);if(h&&k){l.left=f-i.minWidth}if(t&&k){l.left=f-i.maxWidth}if(s&&e){l.top=p-i.minHeight}if(m&&e){l.top=p-i.maxHeight}var n=!l.width&&!l.height;if(n&&!l.left&&l.top){l.top=null}else{if(n&&!l.top&&l.left){l.left=null}}return l},_proportionallyResize:function(){var k=this.options;if(!this._proportionallyResizeElements.length){return}var g=this.helper||this.element;for(var f=0;f');var e=c.browser.msie&&c.browser.version<7,g=(e?1:0),h=(e?2:-1);this.helper.addClass(this._helper).css({width:this.element.outerWidth()+h,height:this.element.outerHeight()+h,position:"absolute",left:this.elementOffset.left-g+"px",top:this.elementOffset.top-g+"px",zIndex:++i.zIndex});this.helper.appendTo("body").disableSelection()}else{this.helper=this.element}},_change:{e:function(g,f,e){return{width:this.originalSize.width+f}},w:function(h,f,e){var j=this.options,g=this.originalSize,i=this.originalPosition;return{left:i.left+f,width:g.width-f}},n:function(h,f,e){var j=this.options,g=this.originalSize,i=this.originalPosition;return{top:i.top+e,height:g.height-e}},s:function(g,f,e){return{height:this.originalSize.height+e}},se:function(g,f,e){return c.extend(this._change.s.apply(this,arguments),this._change.e.apply(this,[g,f,e]))},sw:function(g,f,e){return c.extend(this._change.s.apply(this,arguments),this._change.w.apply(this,[g,f,e]))},ne:function(g,f,e){return c.extend(this._change.n.apply(this,arguments),this._change.e.apply(this,[g,f,e]))},nw:function(g,f,e){return c.extend(this._change.n.apply(this,arguments),this._change.w.apply(this,[g,f,e]))}},_propagate:function(f,e){c.ui.plugin.call(this,f,[e,this.ui()]);(f!="resize"&&this._trigger(f,e,this.ui()))},plugins:{},ui:function(){return{originalElement:this.originalElement,element:this.element,helper:this.helper,position:this.position,size:this.size,originalSize:this.originalSize,originalPosition:this.originalPosition}}});c.extend(c.ui.resizable,{version:"1.8.18"});c.ui.plugin.add("resizable","alsoResize",{start:function(f,g){var e=c(this).data("resizable"),i=e.options;var h=function(j){c(j).each(function(){var k=c(this);k.data("resizable-alsoresize",{width:parseInt(k.width(),10),height:parseInt(k.height(),10),left:parseInt(k.css("left"),10),top:parseInt(k.css("top"),10)})})};if(typeof(i.alsoResize)=="object"&&!i.alsoResize.parentNode){if(i.alsoResize.length){i.alsoResize=i.alsoResize[0];h(i.alsoResize)}else{c.each(i.alsoResize,function(j){h(j)})}}else{h(i.alsoResize)}},resize:function(g,i){var f=c(this).data("resizable"),j=f.options,h=f.originalSize,l=f.originalPosition;var k={height:(f.size.height-h.height)||0,width:(f.size.width-h.width)||0,top:(f.position.top-l.top)||0,left:(f.position.left-l.left)||0},e=function(m,n){c(m).each(function(){var q=c(this),r=c(this).data("resizable-alsoresize"),p={},o=n&&n.length?n:q.parents(i.originalElement[0]).length?["width","height"]:["width","height","top","left"];c.each(o,function(s,u){var t=(r[u]||0)+(k[u]||0);if(t&&t>=0){p[u]=t||null}});q.css(p)})};if(typeof(j.alsoResize)=="object"&&!j.alsoResize.nodeType){c.each(j.alsoResize,function(m,n){e(m,n)})}else{e(j.alsoResize)}},stop:function(e,f){c(this).removeData("resizable-alsoresize")}});c.ui.plugin.add("resizable","animate",{stop:function(i,n){var p=c(this).data("resizable"),j=p.options;var h=p._proportionallyResizeElements,e=h.length&&(/textarea/i).test(h[0].nodeName),f=e&&c.ui.hasScroll(h[0],"left")?0:p.sizeDiff.height,l=e?0:p.sizeDiff.width;var g={width:(p.size.width-l),height:(p.size.height-f)},k=(parseInt(p.element.css("left"),10)+(p.position.left-p.originalPosition.left))||null,m=(parseInt(p.element.css("top"),10)+(p.position.top-p.originalPosition.top))||null;p.element.animate(c.extend(g,m&&k?{top:m,left:k}:{}),{duration:j.animateDuration,easing:j.animateEasing,step:function(){var o={width:parseInt(p.element.css("width"),10),height:parseInt(p.element.css("height"),10),top:parseInt(p.element.css("top"),10),left:parseInt(p.element.css("left"),10)};if(h&&h.length){c(h[0]).css({width:o.width,height:o.height})}p._updateCache(o);p._propagate("resize",i)}})}});c.ui.plugin.add("resizable","containment",{start:function(f,r){var t=c(this).data("resizable"),j=t.options,l=t.element;var g=j.containment,k=(g instanceof c)?g.get(0):(/parent/.test(g))?l.parent().get(0):g;if(!k){return}t.containerElement=c(k);if(/document/.test(g)||g==document){t.containerOffset={left:0,top:0};t.containerPosition={left:0,top:0};t.parentData={element:c(document),left:0,top:0,width:c(document).width(),height:c(document).height()||document.body.parentNode.scrollHeight}}else{var n=c(k),i=[];c(["Top","Right","Left","Bottom"]).each(function(p,o){i[p]=b(n.css("padding"+o))});t.containerOffset=n.offset();t.containerPosition=n.position();t.containerSize={height:(n.innerHeight()-i[3]),width:(n.innerWidth()-i[1])};var q=t.containerOffset,e=t.containerSize.height,m=t.containerSize.width,h=(c.ui.hasScroll(k,"left")?k.scrollWidth:m),s=(c.ui.hasScroll(k)?k.scrollHeight:e);t.parentData={element:k,left:q.left,top:q.top,width:h,height:s}}},resize:function(g,q){var t=c(this).data("resizable"),i=t.options,f=t.containerSize,p=t.containerOffset,m=t.size,n=t.position,r=t._aspectRatio||g.shiftKey,e={top:0,left:0},h=t.containerElement;if(h[0]!=document&&(/static/).test(h.css("position"))){e=p}if(n.left<(t._helper?p.left:0)){t.size.width=t.size.width+(t._helper?(t.position.left-p.left):(t.position.left-e.left));if(r){t.size.height=t.size.width/i.aspectRatio}t.position.left=i.helper?p.left:0}if(n.top<(t._helper?p.top:0)){t.size.height=t.size.height+(t._helper?(t.position.top-p.top):t.position.top);if(r){t.size.width=t.size.height*i.aspectRatio}t.position.top=t._helper?p.top:0}t.offset.left=t.parentData.left+t.position.left;t.offset.top=t.parentData.top+t.position.top;var l=Math.abs((t._helper?t.offset.left-e.left:(t.offset.left-e.left))+t.sizeDiff.width),s=Math.abs((t._helper?t.offset.top-e.top:(t.offset.top-p.top))+t.sizeDiff.height);var k=t.containerElement.get(0)==t.element.parent().get(0),j=/relative|absolute/.test(t.containerElement.css("position"));if(k&&j){l-=t.parentData.left}if(l+t.size.width>=t.parentData.width){t.size.width=t.parentData.width-l;if(r){t.size.height=t.size.width/t.aspectRatio}}if(s+t.size.height>=t.parentData.height){t.size.height=t.parentData.height-s;if(r){t.size.width=t.size.height*t.aspectRatio}}},stop:function(f,n){var q=c(this).data("resizable"),g=q.options,l=q.position,m=q.containerOffset,e=q.containerPosition,i=q.containerElement;var j=c(q.helper),r=j.offset(),p=j.outerWidth()-q.sizeDiff.width,k=j.outerHeight()-q.sizeDiff.height;if(q._helper&&!g.animate&&(/relative/).test(i.css("position"))){c(this).css({left:r.left-e.left-m.left,width:p,height:k})}if(q._helper&&!g.animate&&(/static/).test(i.css("position"))){c(this).css({left:r.left-e.left-m.left,width:p,height:k})}}});c.ui.plugin.add("resizable","ghost",{start:function(g,h){var 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a(j){j=j||location.href;return"#"+j.replace(/^[^#]*#?(.*)$/,"$1")}$.fn[c]=function(j){return j?this.bind(c,j):this.trigger(c)};$.fn[c].delay=50;g[c]=$.extend(g[c],{setup:function(){if(d){return false}$(f.start)},teardown:function(){if(d){return false}$(f.stop)}});f=(function(){var j={},p,m=a(),k=function(q){return q},l=k,o=k;j.start=function(){p||n()};j.stop=function(){p&&clearTimeout(p);p=b};function n(){var r=a(),q=o(m);if(r!==m){l(m=r,q);$(e).trigger(c)}else{if(q!==m){location.href=location.href.replace(/#.*/,"")+q}}p=setTimeout(n,$.fn[c].delay)}$.browser.msie&&!d&&(function(){var q,r;j.start=function(){if(!q){r=$.fn[c].src;r=r&&r+a();q=$(' - - - -
-
-Classes
-
-
Package libsvm
-
-
-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

-Classes

class  Cache
 
class  Kernel
 
class  ONE_CLASS_Q
 
class  QMatrix
 
class  Solver
 
class  Solver_NU
 
class  SVC_Q
 
class  svm
 
class  svm_model
 
class  svm_node
 
class  svm_parameter
 
interface  svm_print_interface
 
class  svm_problem
 
class  SVR_Q
 
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Authors: J.M. de la Rosa Trevin (jmdel.nosp@m.aros.nosp@m.a@cnb.nosp@m..csi.nosp@m.c.es)

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Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC

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This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

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-

Detailed Description

-
-

Authors: J.M. de la Rosa Trevin (jmdel.nosp@m.aros.nosp@m.a@cnb.nosp@m..csi.nosp@m.c.es)

-

Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC

-

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

-

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

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All comments concerning this program package may be sent to the e-mail address 'xmipp.nosp@m.@cnb.nosp@m..csic.nosp@m..es'

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- height: 15em; -} - -#MSearchResultsWindow { - display: none; - position: absolute; - left: 0; top: 0; - border: 1px solid #000; - background-color: #EEF1F7; - z-index:10000; -} - -/* ----------------------------------- */ - - -#SRIndex { - clear:both; - padding-bottom: 15px; -} - -.SREntry { - font-size: 10pt; - padding-left: 1ex; -} - -.SRPage .SREntry { - font-size: 8pt; - padding: 1px 5px; -} - -body.SRPage { - margin: 5px 2px; -} - -.SRChildren { - padding-left: 3ex; padding-bottom: .5em -} - -.SRPage .SRChildren { - display: none; -} - -.SRSymbol { - font-weight: bold; - color: #425E97; - font-family: Arial, Verdana, sans-serif; - text-decoration: none; - outline: none; -} - -a.SRScope { - display: block; - color: #425E97; - font-family: Arial, Verdana, sans-serif; - text-decoration: none; - outline: none; -} - -a.SRSymbol:focus, a.SRSymbol:active, -a.SRScope:focus, a.SRScope:active { - text-decoration: underline; -} - -span.SRScope { - padding-left: 4px; -} - -.SRPage .SRStatus { - padding: 2px 5px; - font-size: 8pt; - font-style: italic; -} - -.SRResult { - display: none; -} - -DIV.searchresults { - margin-left: 10px; - margin-right: 10px; -} - -/*---------------- External search page results */ - -.searchresult { - background-color: #F0F3F8; -} - -.pages b { - color: white; - padding: 5px 5px 3px 5px; - background-image: url("../tab_a.png"); - background-repeat: repeat-x; - text-shadow: 0 1px 1px #000000; -} - -.pages { - line-height: 17px; - margin-left: 4px; - text-decoration: none; -} - -.hl { - font-weight: bold; -} - -#searchresults { - margin-bottom: 20px; -} - -.searchpages { - margin-top: 10px; -} - diff --git a/html/search/search.js b/html/search/search.js deleted file mode 100644 index dedce3bf..00000000 --- a/html/search/search.js +++ /dev/null @@ -1,791 +0,0 @@ -function convertToId(search) -{ - var result = ''; - for (i=0;i do a search - { - this.Search(); - } - } - - this.OnSearchSelectKey = function(evt) - { - var e = (evt) ? evt : window.event; // for IE - if (e.keyCode==40 && this.searchIndex0) // Up - { - this.searchIndex--; - this.OnSelectItem(this.searchIndex); - } - else if (e.keyCode==13 || e.keyCode==27) - { - this.OnSelectItem(this.searchIndex); - this.CloseSelectionWindow(); - this.DOMSearchField().focus(); - } - return false; - } - - // --------- Actions - - // Closes the results window. - this.CloseResultsWindow = function() - { - this.DOMPopupSearchResultsWindow().style.display = 'none'; - this.DOMSearchClose().style.display = 'none'; - this.Activate(false); - } - - this.CloseSelectionWindow = function() - { - this.DOMSearchSelectWindow().style.display = 'none'; - } - - // Performs a search. - this.Search = function() - { - this.keyTimeout = 0; - - // strip leading whitespace - var searchValue = this.DOMSearchField().value.replace(/^ +/, ""); - - var code = searchValue.toLowerCase().charCodeAt(0); - var idxChar = searchValue.substr(0, 1).toLowerCase(); - if ( 0xD800 <= code && code <= 0xDBFF && searchValue > 1) // surrogate pair - { - idxChar = searchValue.substr(0, 2); - } - - var resultsPage; - var resultsPageWithSearch; - var hasResultsPage; - - var idx = indexSectionsWithContent[this.searchIndex].indexOf(idxChar); - if (idx!=-1) - { - var hexCode=idx.toString(16); - resultsPage = this.resultsPath + '/' + indexSectionNames[this.searchIndex] + '_' + hexCode + '.html'; - resultsPageWithSearch = resultsPage+'?'+escape(searchValue); - hasResultsPage = true; - } - else // nothing available for this search term - { - resultsPage = this.resultsPath + '/nomatches.html'; - resultsPageWithSearch = resultsPage; - hasResultsPage = false; - } - - window.frames.MSearchResults.location = resultsPageWithSearch; - var domPopupSearchResultsWindow = this.DOMPopupSearchResultsWindow(); - - if (domPopupSearchResultsWindow.style.display!='block') - { - var domSearchBox = this.DOMSearchBox(); - this.DOMSearchClose().style.display = 'inline'; - if (this.insideFrame) - { - var domPopupSearchResults = this.DOMPopupSearchResults(); - domPopupSearchResultsWindow.style.position = 'relative'; - domPopupSearchResultsWindow.style.display = 'block'; - var width = document.body.clientWidth - 8; // the -8 is for IE :-( - domPopupSearchResultsWindow.style.width = width + 'px'; - domPopupSearchResults.style.width = width + 'px'; - } - else - { - var domPopupSearchResults = this.DOMPopupSearchResults(); - var left = getXPos(domSearchBox) + 150; // domSearchBox.offsetWidth; - var top = getYPos(domSearchBox) + 20; // domSearchBox.offsetHeight + 1; - domPopupSearchResultsWindow.style.display = 'block'; - left -= domPopupSearchResults.offsetWidth; - domPopupSearchResultsWindow.style.top = top + 'px'; - domPopupSearchResultsWindow.style.left = left + 'px'; - } - } - - this.lastSearchValue = searchValue; - this.lastResultsPage = resultsPage; - } - - // -------- Activation Functions - - // Activates or deactivates the search panel, resetting things to - // their default values if necessary. - this.Activate = function(isActive) - { - if (isActive || // open it - this.DOMPopupSearchResultsWindow().style.display == 'block' - ) - { - this.DOMSearchBox().className = 'MSearchBoxActive'; - - var searchField = this.DOMSearchField(); - - if (searchField.value == this.searchLabel) // clear "Search" term upon entry - { - searchField.value = ''; - this.searchActive = true; - } - } - else if (!isActive) // directly remove the panel - { - this.DOMSearchBox().className = 'MSearchBoxInactive'; - this.DOMSearchField().value = this.searchLabel; - this.searchActive = false; - this.lastSearchValue = '' - this.lastResultsPage = ''; - } - } -} - -// ----------------------------------------------------------------------- - -// The class that handles everything on the search results page. -function SearchResults(name) -{ - // The number of matches from the last run of . - this.lastMatchCount = 0; - this.lastKey = 0; - this.repeatOn = false; - - // Toggles the visibility of the passed element ID. - this.FindChildElement = function(id) - { - var parentElement = document.getElementById(id); - var element = parentElement.firstChild; - - while (element && element!=parentElement) - { - if (element.nodeName == 'DIV' && element.className == 'SRChildren') - { - return element; - } - - if (element.nodeName == 'DIV' && element.hasChildNodes()) - { - element = element.firstChild; - } - else if (element.nextSibling) - { - element = element.nextSibling; - } - else - { - do - { - element = element.parentNode; - } - while (element && element!=parentElement && !element.nextSibling); - - if (element && element!=parentElement) - { - element = element.nextSibling; - } - } - } - } - - this.Toggle = function(id) - { - var element = this.FindChildElement(id); - if (element) - { - if (element.style.display == 'block') - { - element.style.display = 'none'; - } - else - { - element.style.display = 'block'; - } - } - } - - // Searches for the passed string. If there is no parameter, - // it takes it from the URL query. - // - // Always returns true, since other documents may try to call it - // and that may or may not be possible. - this.Search = function(search) - { - if (!search) // get search word from URL - { - search = window.location.search; - search = search.substring(1); // Remove the leading '?' - search = unescape(search); - } - - search = search.replace(/^ +/, ""); // strip leading spaces - search = search.replace(/ +$/, ""); // strip trailing spaces - search = search.toLowerCase(); - search = convertToId(search); - - var resultRows = document.getElementsByTagName("div"); - var matches = 0; - - var i = 0; - while (i < resultRows.length) - { - var row = resultRows.item(i); - if (row.className == "SRResult") - { - var rowMatchName = row.id.toLowerCase(); - rowMatchName = rowMatchName.replace(/^sr\d*_/, ''); // strip 'sr123_' - - if (search.length<=rowMatchName.length && - rowMatchName.substr(0, search.length)==search) - { - row.style.display = 'block'; - matches++; - } - else - { - row.style.display = 'none'; - } - } - i++; - } - document.getElementById("Searching").style.display='none'; - if (matches == 0) // no results - { - document.getElementById("NoMatches").style.display='block'; - } - else // at least one result - { - document.getElementById("NoMatches").style.display='none'; - } - this.lastMatchCount = matches; - return true; - } - - // return the first item with index index or higher that is visible - this.NavNext = function(index) - { - var focusItem; - while (1) - { - var focusName = 'Item'+index; - focusItem = document.getElementById(focusName); - if (focusItem && focusItem.parentNode.parentNode.style.display=='block') - { - break; - } - else if (!focusItem) // last element - { - break; - } - focusItem=null; - index++; - } - return focusItem; - } - - this.NavPrev = function(index) - { - var focusItem; - while (1) - { - var focusName = 'Item'+index; - focusItem = document.getElementById(focusName); - if (focusItem && focusItem.parentNode.parentNode.style.display=='block') - { - break; - } - else if (!focusItem) // last element - { - break; - } - focusItem=null; - index--; - } - return focusItem; - } - - this.ProcessKeys = function(e) - { - if (e.type == "keydown") - { - this.repeatOn = false; - this.lastKey = e.keyCode; - } - else if (e.type == "keypress") - { - if (!this.repeatOn) - { - if (this.lastKey) this.repeatOn = true; - return false; // ignore first keypress after keydown - } - } - else if (e.type == "keyup") - { - this.lastKey = 0; - this.repeatOn = false; - } - return this.lastKey!=0; - } - - this.Nav = function(evt,itemIndex) - { - var e = (evt) ? evt : window.event; // for IE - if (e.keyCode==13) return true; - if (!this.ProcessKeys(e)) return false; - - if (this.lastKey==38) // Up - { - var newIndex = itemIndex-1; - var focusItem = this.NavPrev(newIndex); - if (focusItem) - { - var child = this.FindChildElement(focusItem.parentNode.parentNode.id); - if (child && child.style.display == 'block') // children visible - { - var n=0; - var tmpElem; - while (1) // search for last child - { - tmpElem = document.getElementById('Item'+newIndex+'_c'+n); - if (tmpElem) - { - focusItem = tmpElem; - } - else // found it! - { - break; - } - n++; - } - } - } - if (focusItem) - { - focusItem.focus(); - } - else // return focus to search field - { - parent.document.getElementById("MSearchField").focus(); - } - } - else if (this.lastKey==40) // Down - { - var newIndex = itemIndex+1; - var focusItem; - var item = document.getElementById('Item'+itemIndex); - var elem = this.FindChildElement(item.parentNode.parentNode.id); - if (elem && elem.style.display == 'block') // children visible - { - focusItem = document.getElementById('Item'+itemIndex+'_c0'); - } - if (!focusItem) focusItem = this.NavNext(newIndex); - if (focusItem) focusItem.focus(); - } - else if (this.lastKey==39) // Right - { - var item = document.getElementById('Item'+itemIndex); - var elem = this.FindChildElement(item.parentNode.parentNode.id); - if (elem) elem.style.display = 'block'; - } - else if (this.lastKey==37) // Left - { - var item = document.getElementById('Item'+itemIndex); - var elem = this.FindChildElement(item.parentNode.parentNode.id); - if (elem) elem.style.display = 'none'; - } - else if (this.lastKey==27) // Escape - { - parent.searchBox.CloseResultsWindow(); - parent.document.getElementById("MSearchField").focus(); - } - else if (this.lastKey==13) // Enter - { - return true; - } - return false; - } - - this.NavChild = function(evt,itemIndex,childIndex) - { - var e = (evt) ? evt : window.event; // for IE - if (e.keyCode==13) return true; - if (!this.ProcessKeys(e)) return false; - - if (this.lastKey==38) // Up - { - if (childIndex>0) - { - var newIndex = childIndex-1; - document.getElementById('Item'+itemIndex+'_c'+newIndex).focus(); - } - else // already at first child, jump to parent - { - document.getElementById('Item'+itemIndex).focus(); - } - } - else if (this.lastKey==40) // Down - { - var newIndex = childIndex+1; - var elem = document.getElementById('Item'+itemIndex+'_c'+newIndex); - if (!elem) // last child, jump to parent next parent - { - elem = this.NavNext(itemIndex+1); - } - if (elem) - { - elem.focus(); - } - } - else if (this.lastKey==27) // Escape - { - parent.searchBox.CloseResultsWindow(); - parent.document.getElementById("MSearchField").focus(); - } - else if (this.lastKey==13) // Enter - { - return true; - } - return false; - } -} - -function setKeyActions(elem,action) -{ - elem.setAttribute('onkeydown',action); - elem.setAttribute('onkeypress',action); - elem.setAttribute('onkeyup',action); -} - -function setClassAttr(elem,attr) -{ - elem.setAttribute('class',attr); - elem.setAttribute('className',attr); -} - -function createResults() -{ - var results = document.getElementById("SRResults"); - for (var e=0; ek7RCwB~R6VQOP#AvB$vH7i{6H{96zot$7cZT<7246EF5Np6N}+$IbiG6W zg#87A+NFaX+=_^xM1#gCtshC=E{%9^uQX_%?YwXvo{#q&MnpJ8uh(O?ZRc&~_1%^SsPxG@rfElJg-?U zm!Cz-IOn(qJP3kDp-^~qt+FGbl=5jNli^Wj_xIBG{Rc0en{!oFvyoNC7{V~T8}b>| z=jL2WIReZzX(YN(_9fV;BBD$VXQIxNasAL8ATvEu822WQ%mvv4FO#qs` BFGc_W diff --git a/html/search/search_r.png b/html/search/search_r.png deleted file mode 100644 index 97ee8b439687084201b79c6f776a41f495c6392a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 612 zcmV-q0-ODbP)PbXFRCwB?)W514K@j&X?z2*SxFI6-@HT2E2K=9X9%Pb zEK*!TBw&g(DMC;|A)uGlRkOS9vd-?zNs%bR4d$w+ox_iFnE8fvIvv7^5<(>Te12Li z7C)9srCzmK{ZcNM{YIl9j{DePFgOWiS%xG@5CnnnJa4nvY<^glbz7^|-ZY!dUkAwd z{gaTC@_>b5h~;ug#R0wRL0>o5!hxm*s0VW?8dr}O#zXTRTnrQm_Z7z1Mrnx>&p zD4qifUjzLvbVVWi?l?rUzwt^sdb~d!f_LEhsRVIXZtQ=qSxuxqm zEX#tf>$?M_Y1-LSDT)HqG?`%-%ZpY!#{N!rcNIiL;G7F0`l?)mNGTD9;f9F5Up3Kg zw}a<-JylhG&;=!>B+fZaCX+?C+kHYrP%c?X2!Zu_olK|GcS4A70HEy;vn)I0>0kLH z`jc(WIaaHc7!HS@f*^R^Znx8W=_jIl2oWJoQ*h1^$FX!>*PqR1J8k|fw}w_y}TpE>7m8DqDO<3z`OzXt$ccSejbEZCg@0000 - - - - - - - - -
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class  libsvm.Cache
 
class  libsvm.QMatrix
 
class  libsvm.Kernel
 
class  libsvm.Solver
 
class  libsvm.Solver.SolutionInfo
 
class  libsvm.Solver_NU
 
class  libsvm.SVC_Q
 
class  libsvm.ONE_CLASS_Q
 
class  libsvm.SVR_Q
 
class  libsvm.svm
 
class  libsvm.svm.decision_function
 
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package  libsvm
 
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svm.java
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1 
2 
3 
4 
5 
6 package libsvm;
7 import java.io.*;
8 import java.util.*;
9 
10 //
11 // Kernel Cache
12 //
13 // l is the number of total data items
14 // size is the cache size limit in bytes
15 //
16 class Cache {
17  private final int l;
18  private long size;
19  private final class head_t
20  {
21  head_t prev, next; // a cicular list
22  float[] data;
23  int len; // data[0,len) is cached in this entry
24  }
25  private final head_t[] head;
26  private head_t lru_head;
27 
28  Cache(int l_, long size_)
29  {
30  l = l_;
31  size = size_;
32  head = new head_t[l];
33  for(int i=0;i<l;i++) head[i] = new head_t();
34  size /= 4;
35  size -= l * (16/4); // sizeof(head_t) == 16
36  size = Math.max(size, 2* (long) l); // cache must be large enough for two columns
37  lru_head = new head_t();
38  lru_head.next = lru_head.prev = lru_head;
39  }
40 
41  private void lru_delete(head_t h)
42  {
43  // delete from current location
44  h.prev.next = h.next;
45  h.next.prev = h.prev;
46  }
47 
48  private void lru_insert(head_t h)
49  {
50  // insert to last position
51  h.next = lru_head;
52  h.prev = lru_head.prev;
53  h.prev.next = h;
54  h.next.prev = h;
55  }
56 
57  // request data [0,len)
58  // return some position p where [p,len) need to be filled
59  // (p >= len if nothing needs to be filled)
60  // java: simulate pointer using single-element array
61  int get_data(int index, float[][] data, int len)
62  {
63  head_t h = head[index];
64  if(h.len > 0) lru_delete(h);
65  int more = len - h.len;
66 
67  if(more > 0)
68  {
69  // free old space
70  while(size < more)
71  {
72  head_t old = lru_head.next;
73  lru_delete(old);
74  size += old.len;
75  old.data = null;
76  old.len = 0;
77  }
78 
79  // allocate new space
80  float[] new_data = new float[len];
81  if(h.data != null) System.arraycopy(h.data,0,new_data,0,h.len);
82  h.data = new_data;
83  size -= more;
84  do {int tmp=h.len; h.len=len; len=tmp;} while(false);
85  }
86 
87  lru_insert(h);
88  data[0] = h.data;
89  return len;
90  }
91 
92  void swap_index(int i, int j)
93  {
94  if(i==j) return;
95 
96  if(head[i].len > 0) lru_delete(head[i]);
97  if(head[j].len > 0) lru_delete(head[j]);
98  do {float[] tmp=head[i].data; head[i].data=head[j].data; head[j].data=tmp;} while(false);
99  do {int tmp=head[i].len; head[i].len=head[j].len; head[j].len=tmp;} while(false);
100  if(head[i].len > 0) lru_insert(head[i]);
101  if(head[j].len > 0) lru_insert(head[j]);
102 
103  if(i>j) do {int tmp=i; i=j; j=tmp;} while(false);
104  for(head_t h = lru_head.next; h!=lru_head; h=h.next)
105  {
106  if(h.len > i)
107  {
108  if(h.len > j)
109  do {float tmp=h.data[i]; h.data[i]=h.data[j]; h.data[j]=tmp;} while(false);
110  else
111  {
112  // give up
113  lru_delete(h);
114  size += h.len;
115  h.data = null;
116  h.len = 0;
117  }
118  }
119  }
120  }
121 }
122 
123 //
124 // Kernel evaluation
125 //
126 // the static method k_function is for doing single kernel evaluation
127 // the constructor of Kernel prepares to calculate the l*l kernel matrix
128 // the member function get_Q is for getting one column from the Q Matrix
129 //
130 abstract class QMatrix {
131  abstract float[] get_Q(int column, int len);
132  abstract double[] get_QD();
133  abstract void swap_index(int i, int j);
134 };
135 
136 abstract class Kernel extends QMatrix {
137  private svm_node[][] x;
138  private final double[] x_square;
139 
140  // svm_parameter
141  private final int kernel_type;
142  private final int degree;
143  private final double gamma;
144  private final double coef0;
145 
146  abstract float[] get_Q(int column, int len);
147  abstract double[] get_QD();
148 
149  void swap_index(int i, int j)
150  {
151  do {svm_node[] tmp=x[i]; x[i]=x[j]; x[j]=tmp;} while(false);
152  if(x_square != null) do {double tmp=x_square[i]; x_square[i]=x_square[j]; x_square[j]=tmp;} while(false);
153  }
154 
155  private static double powi(double base, int times)
156  {
157  double tmp = base, ret = 1.0;
158 
159  for(int t=times; t>0; t/=2)
160  {
161  if(t%2==1) ret*=tmp;
162  tmp = tmp * tmp;
163  }
164  return ret;
165  }
166 
167  double kernel_function(int i, int j)
168  {
169  switch(kernel_type)
170  {
171  case svm_parameter.LINEAR:
172  return dot(x[i],x[j]);
173  case svm_parameter.POLY:
174  return powi(gamma*dot(x[i],x[j])+coef0,degree);
175  case svm_parameter.RBF:
176  return Math.exp(-gamma*(x_square[i]+x_square[j]-2*dot(x[i],x[j])));
177  case svm_parameter.SIGMOID:
178  return Math.tanh(gamma*dot(x[i],x[j])+coef0);
179  case svm_parameter.PRECOMPUTED:
180  return x[i][(int)(x[j][0].value)].value;
181  default:
182  return 0; // Unreachable
183  }
184  }
185 
186  Kernel(int l, svm_node[][] x_, svm_parameter param)
187  {
188  this.kernel_type = param.kernel_type;
189  this.degree = param.degree;
190  this.gamma = param.gamma;
191  this.coef0 = param.coef0;
192 
193  x = (svm_node[][])x_.clone();
194 
195  if(kernel_type == svm_parameter.RBF)
196  {
197  x_square = new double[l];
198  for(int i=0;i<l;i++)
199  x_square[i] = dot(x[i],x[i]);
200  }
201  else
202  x_square = null;
203  }
204 
205  static double dot(svm_node[] x, svm_node[] y)
206  {
207  double sum = 0;
208  int xlen = x.length;
209  int ylen = y.length;
210  int i = 0;
211  int j = 0;
212  while(i < xlen && j < ylen)
213  {
214  if(x[i].index == y[j].index)
215  sum += x[i++].value * y[j++].value;
216  else
217  {
218  if(x[i].index > y[j].index)
219  ++j;
220  else
221  ++i;
222  }
223  }
224  return sum;
225  }
226 
227  static double k_function(svm_node[] x, svm_node[] y,
228  svm_parameter param)
229  {
230  switch(param.kernel_type)
231  {
232  case svm_parameter.LINEAR:
233  return dot(x,y);
234  case svm_parameter.POLY:
235  return powi(param.gamma*dot(x,y)+param.coef0,param.degree);
236  case svm_parameter.RBF:
237  {
238  double sum = 0;
239  int xlen = x.length;
240  int ylen = y.length;
241  int i = 0;
242  int j = 0;
243  while(i < xlen && j < ylen)
244  {
245  if(x[i].index == y[j].index)
246  {
247  double d = x[i++].value - y[j++].value;
248  sum += d*d;
249  }
250  else if(x[i].index > y[j].index)
251  {
252  sum += y[j].value * y[j].value;
253  ++j;
254  }
255  else
256  {
257  sum += x[i].value * x[i].value;
258  ++i;
259  }
260  }
261 
262  while(i < xlen)
263  {
264  sum += x[i].value * x[i].value;
265  ++i;
266  }
267 
268  while(j < ylen)
269  {
270  sum += y[j].value * y[j].value;
271  ++j;
272  }
273 
274  return Math.exp(-param.gamma*sum);
275  }
276  case svm_parameter.SIGMOID:
277  return Math.tanh(param.gamma*dot(x,y)+param.coef0);
278  case svm_parameter.PRECOMPUTED: //x: test (validation), y: SV
279  return x[(int)(y[0].value)].value;
280  default:
281  return 0; // Unreachable
282  }
283  }
284 }
285 
286 // An SMO algorithm in Fan et al., JMLR 6(2005), p. 1889--1918
287 // Solves:
288 //
289 // min 0.5(\alpha^T Q \alpha) + p^T \alpha
290 //
291 // y^T \alpha = \delta
292 // y_i = +1 or -1
293 // 0 <= alpha_i <= Cp for y_i = 1
294 // 0 <= alpha_i <= Cn for y_i = -1
295 //
296 // Given:
297 //
298 // Q, p, y, Cp, Cn, and an initial feasible point \alpha
299 // l is the size of vectors and matrices
300 // eps is the stopping tolerance
301 //
302 // solution will be put in \alpha, objective value will be put in obj
303 //
304 class Solver {
305  int active_size;
306  byte[] y;
307  double[] G; // gradient of objective function
308  static final byte LOWER_BOUND = 0;
309  static final byte UPPER_BOUND = 1;
310  static final byte FREE = 2;
311  byte[] alpha_status; // LOWER_BOUND, UPPER_BOUND, FREE
312  double[] alpha;
313  QMatrix Q;
314  double[] QD;
315  double eps;
316  double Cp,Cn;
317  double[] p;
318  int[] active_set;
319  double[] G_bar; // gradient, if we treat free variables as 0
320  int l;
321  boolean unshrink; // XXX
322 
323  static final double INF = java.lang.Double.POSITIVE_INFINITY;
324 
325  double get_C(int i)
326  {
327  return (y[i] > 0)? Cp : Cn;
328  }
329  void update_alpha_status(int i)
330  {
331  if(alpha[i] >= get_C(i))
332  alpha_status[i] = UPPER_BOUND;
333  else if(alpha[i] <= 0)
334  alpha_status[i] = LOWER_BOUND;
335  else alpha_status[i] = FREE;
336  }
337  boolean is_upper_bound(int i) { return alpha_status[i] == UPPER_BOUND; }
338  boolean is_lower_bound(int i) { return alpha_status[i] == LOWER_BOUND; }
339  boolean is_free(int i) { return alpha_status[i] == FREE; }
340 
341  // java: information about solution except alpha,
342  // because we cannot return multiple values otherwise...
343  static class SolutionInfo {
344  double obj;
345  double rho;
346  double upper_bound_p;
347  double upper_bound_n;
348  double r; // for Solver_NU
349  }
350 
351  void swap_index(int i, int j)
352  {
353  Q.swap_index(i,j);
354  do {byte tmp=y[i]; y[i]=y[j]; y[j]=tmp;} while(false);
355  do {double tmp=G[i]; G[i]=G[j]; G[j]=tmp;} while(false);
356  do {byte tmp=alpha_status[i]; alpha_status[i]=alpha_status[j]; alpha_status[j]=tmp;} while(false);
357  do {double tmp=alpha[i]; alpha[i]=alpha[j]; alpha[j]=tmp;} while(false);
358  do {double tmp=p[i]; p[i]=p[j]; p[j]=tmp;} while(false);
359  do {int tmp=active_set[i]; active_set[i]=active_set[j]; active_set[j]=tmp;} while(false);
360  do {double tmp=G_bar[i]; G_bar[i]=G_bar[j]; G_bar[j]=tmp;} while(false);
361  }
362 
363  void reconstruct_gradient()
364  {
365  // reconstruct inactive elements of G from G_bar and free variables
366 
367  if(active_size == l) return;
368 
369  int i,j;
370  int nr_free = 0;
371 
372  for(j=active_size;j<l;j++)
373  G[j] = G_bar[j] + p[j];
374 
375  for(j=0;j<active_size;j++)
376  if(is_free(j))
377  nr_free++;
378 
379  if(2*nr_free < active_size)
380  svm.info("\nWARNING: using -h 0 may be faster\n");
381 
382  if (nr_free*l > 2*active_size*(l-active_size))
383  {
384  for(i=active_size;i<l;i++)
385  {
386  float[] Q_i = Q.get_Q(i,active_size);
387  for(j=0;j<active_size;j++)
388  if(is_free(j))
389  G[i] += alpha[j] * Q_i[j];
390  }
391  }
392  else
393  {
394  for(i=0;i<active_size;i++)
395  if(is_free(i))
396  {
397  float[] Q_i = Q.get_Q(i,l);
398  double alpha_i = alpha[i];
399  for(j=active_size;j<l;j++)
400  G[j] += alpha_i * Q_i[j];
401  }
402  }
403  }
404 
405  void Solve(int l, QMatrix Q, double[] p_, byte[] y_,
406  double[] alpha_, double Cp, double Cn, double eps, SolutionInfo si, int shrinking)
407  {
408  this.l = l;
409  this.Q = Q;
410  QD = Q.get_QD();
411  p = (double[])p_.clone();
412  y = (byte[])y_.clone();
413  alpha = (double[])alpha_.clone();
414  this.Cp = Cp;
415  this.Cn = Cn;
416  this.eps = eps;
417  this.unshrink = false;
418 
419  // initialize alpha_status
420  {
421  alpha_status = new byte[l];
422  for(int i=0;i<l;i++)
423  update_alpha_status(i);
424  }
425 
426  // initialize active set (for shrinking)
427  {
428  active_set = new int[l];
429  for(int i=0;i<l;i++)
430  active_set[i] = i;
431  active_size = l;
432  }
433 
434  // initialize gradient
435  {
436  G = new double[l];
437  G_bar = new double[l];
438  int i;
439  for(i=0;i<l;i++)
440  {
441  G[i] = p[i];
442  G_bar[i] = 0;
443  }
444  for(i=0;i<l;i++)
445  if(!is_lower_bound(i))
446  {
447  float[] Q_i = Q.get_Q(i,l);
448  double alpha_i = alpha[i];
449  int j;
450  for(j=0;j<l;j++)
451  G[j] += alpha_i*Q_i[j];
452  if(is_upper_bound(i))
453  for(j=0;j<l;j++)
454  G_bar[j] += get_C(i) * Q_i[j];
455  }
456  }
457 
458  // optimization step
459 
460  int iter = 0;
461  int max_iter = Math.max(10000000, l>Integer.MAX_VALUE/100 ? Integer.MAX_VALUE : 100*l);
462  int counter = Math.min(l,1000)+1;
463  int[] working_set = new int[2];
464 
465  while(iter < max_iter)
466  {
467  // show progress and do shrinking
468 
469  if(--counter == 0)
470  {
471  counter = Math.min(l,1000);
472  if(shrinking!=0) do_shrinking();
473  svm.info(".");
474  }
475 
476  if(select_working_set(working_set)!=0)
477  {
478  // reconstruct the whole gradient
479  reconstruct_gradient();
480  // reset active set size and check
481  active_size = l;
482  svm.info("*");
483  if(select_working_set(working_set)!=0)
484  break;
485  else
486  counter = 1; // do shrinking next iteration
487  }
488 
489  int i = working_set[0];
490  int j = working_set[1];
491 
492  ++iter;
493 
494  // update alpha[i] and alpha[j], handle bounds carefully
495 
496  float[] Q_i = Q.get_Q(i,active_size);
497  float[] Q_j = Q.get_Q(j,active_size);
498 
499  double C_i = get_C(i);
500  double C_j = get_C(j);
501 
502  double old_alpha_i = alpha[i];
503  double old_alpha_j = alpha[j];
504 
505  if(y[i]!=y[j])
506  {
507  double quad_coef = QD[i]+QD[j]+2*Q_i[j];
508  if (quad_coef <= 0)
509  quad_coef = 1e-12;
510  double delta = (-G[i]-G[j])/quad_coef;
511  double diff = alpha[i] - alpha[j];
512  alpha[i] += delta;
513  alpha[j] += delta;
514 
515  if(diff > 0)
516  {
517  if(alpha[j] < 0)
518  {
519  alpha[j] = 0;
520  alpha[i] = diff;
521  }
522  }
523  else
524  {
525  if(alpha[i] < 0)
526  {
527  alpha[i] = 0;
528  alpha[j] = -diff;
529  }
530  }
531  if(diff > C_i - C_j)
532  {
533  if(alpha[i] > C_i)
534  {
535  alpha[i] = C_i;
536  alpha[j] = C_i - diff;
537  }
538  }
539  else
540  {
541  if(alpha[j] > C_j)
542  {
543  alpha[j] = C_j;
544  alpha[i] = C_j + diff;
545  }
546  }
547  }
548  else
549  {
550  double quad_coef = QD[i]+QD[j]-2*Q_i[j];
551  if (quad_coef <= 0)
552  quad_coef = 1e-12;
553  double delta = (G[i]-G[j])/quad_coef;
554  double sum = alpha[i] + alpha[j];
555  alpha[i] -= delta;
556  alpha[j] += delta;
557 
558  if(sum > C_i)
559  {
560  if(alpha[i] > C_i)
561  {
562  alpha[i] = C_i;
563  alpha[j] = sum - C_i;
564  }
565  }
566  else
567  {
568  if(alpha[j] < 0)
569  {
570  alpha[j] = 0;
571  alpha[i] = sum;
572  }
573  }
574  if(sum > C_j)
575  {
576  if(alpha[j] > C_j)
577  {
578  alpha[j] = C_j;
579  alpha[i] = sum - C_j;
580  }
581  }
582  else
583  {
584  if(alpha[i] < 0)
585  {
586  alpha[i] = 0;
587  alpha[j] = sum;
588  }
589  }
590  }
591 
592  // update G
593 
594  double delta_alpha_i = alpha[i] - old_alpha_i;
595  double delta_alpha_j = alpha[j] - old_alpha_j;
596 
597  for(int k=0;k<active_size;k++)
598  {
599  G[k] += Q_i[k]*delta_alpha_i + Q_j[k]*delta_alpha_j;
600  }
601 
602  // update alpha_status and G_bar
603 
604  {
605  boolean ui = is_upper_bound(i);
606  boolean uj = is_upper_bound(j);
607  update_alpha_status(i);
608  update_alpha_status(j);
609  int k;
610  if(ui != is_upper_bound(i))
611  {
612  Q_i = Q.get_Q(i,l);
613  if(ui)
614  for(k=0;k<l;k++)
615  G_bar[k] -= C_i * Q_i[k];
616  else
617  for(k=0;k<l;k++)
618  G_bar[k] += C_i * Q_i[k];
619  }
620 
621  if(uj != is_upper_bound(j))
622  {
623  Q_j = Q.get_Q(j,l);
624  if(uj)
625  for(k=0;k<l;k++)
626  G_bar[k] -= C_j * Q_j[k];
627  else
628  for(k=0;k<l;k++)
629  G_bar[k] += C_j * Q_j[k];
630  }
631  }
632 
633  }
634 
635  if(iter >= max_iter)
636  {
637  if(active_size < l)
638  {
639  // reconstruct the whole gradient to calculate objective value
640  reconstruct_gradient();
641  active_size = l;
642  svm.info("*");
643  }
644  System.err.print("\nWARNING: reaching max number of iterations\n");
645  }
646 
647  // calculate rho
648 
649  si.rho = calculate_rho();
650 
651  // calculate objective value
652  {
653  double v = 0;
654  int i;
655  for(i=0;i<l;i++)
656  v += alpha[i] * (G[i] + p[i]);
657 
658  si.obj = v/2;
659  }
660 
661  // put back the solution
662  {
663  for(int i=0;i<l;i++)
664  alpha_[active_set[i]] = alpha[i];
665  }
666 
667  si.upper_bound_p = Cp;
668  si.upper_bound_n = Cn;
669 
670  svm.info("\noptimization finished, #iter = "+iter+"\n");
671  }
672 
673  // return 1 if already optimal, return 0 otherwise
674  int select_working_set(int[] working_set)
675  {
676  // return i,j such that
677  // i: maximizes -y_i * grad(f)_i, i in I_up(\alpha)
678  // j: minimizes the decrease of obj value
679  // (if quadratic coefficeint <= 0, replace it with tau)
680  // -y_j*grad(f)_j < -y_i*grad(f)_i, j in I_low(\alpha)
681 
682  double Gmax = -INF;
683  double Gmax2 = -INF;
684  int Gmax_idx = -1;
685  int Gmin_idx = -1;
686  double obj_diff_min = INF;
687 
688  for(int t=0;t<active_size;t++)
689  if(y[t]==+1)
690  {
691  if(!is_upper_bound(t))
692  if(-G[t] >= Gmax)
693  {
694  Gmax = -G[t];
695  Gmax_idx = t;
696  }
697  }
698  else
699  {
700  if(!is_lower_bound(t))
701  if(G[t] >= Gmax)
702  {
703  Gmax = G[t];
704  Gmax_idx = t;
705  }
706  }
707 
708  int i = Gmax_idx;
709  float[] Q_i = null;
710  if(i != -1) // null Q_i not accessed: Gmax=-INF if i=-1
711  Q_i = Q.get_Q(i,active_size);
712 
713  for(int j=0;j<active_size;j++)
714  {
715  if(y[j]==+1)
716  {
717  if (!is_lower_bound(j))
718  {
719  double grad_diff=Gmax+G[j];
720  if (G[j] >= Gmax2)
721  Gmax2 = G[j];
722  if (grad_diff > 0)
723  {
724  double obj_diff;
725  double quad_coef = QD[i]+QD[j]-2.0*y[i]*Q_i[j];
726  if (quad_coef > 0)
727  obj_diff = -(grad_diff*grad_diff)/quad_coef;
728  else
729  obj_diff = -(grad_diff*grad_diff)/1e-12;
730 
731  if (obj_diff <= obj_diff_min)
732  {
733  Gmin_idx=j;
734  obj_diff_min = obj_diff;
735  }
736  }
737  }
738  }
739  else
740  {
741  if (!is_upper_bound(j))
742  {
743  double grad_diff= Gmax-G[j];
744  if (-G[j] >= Gmax2)
745  Gmax2 = -G[j];
746  if (grad_diff > 0)
747  {
748  double obj_diff;
749  double quad_coef = QD[i]+QD[j]+2.0*y[i]*Q_i[j];
750  if (quad_coef > 0)
751  obj_diff = -(grad_diff*grad_diff)/quad_coef;
752  else
753  obj_diff = -(grad_diff*grad_diff)/1e-12;
754 
755  if (obj_diff <= obj_diff_min)
756  {
757  Gmin_idx=j;
758  obj_diff_min = obj_diff;
759  }
760  }
761  }
762  }
763  }
764 
765  if(Gmax+Gmax2 < eps || Gmin_idx == -1)
766  return 1;
767 
768  working_set[0] = Gmax_idx;
769  working_set[1] = Gmin_idx;
770  return 0;
771  }
772 
773  private boolean be_shrunk(int i, double Gmax1, double Gmax2)
774  {
775  if(is_upper_bound(i))
776  {
777  if(y[i]==+1)
778  return(-G[i] > Gmax1);
779  else
780  return(-G[i] > Gmax2);
781  }
782  else if(is_lower_bound(i))
783  {
784  if(y[i]==+1)
785  return(G[i] > Gmax2);
786  else
787  return(G[i] > Gmax1);
788  }
789  else
790  return(false);
791  }
792 
793  void do_shrinking()
794  {
795  int i;
796  double Gmax1 = -INF; // max { -y_i * grad(f)_i | i in I_up(\alpha) }
797  double Gmax2 = -INF; // max { y_i * grad(f)_i | i in I_low(\alpha) }
798 
799  // find maximal violating pair first
800  for(i=0;i<active_size;i++)
801  {
802  if(y[i]==+1)
803  {
804  if(!is_upper_bound(i))
805  {
806  if(-G[i] >= Gmax1)
807  Gmax1 = -G[i];
808  }
809  if(!is_lower_bound(i))
810  {
811  if(G[i] >= Gmax2)
812  Gmax2 = G[i];
813  }
814  }
815  else
816  {
817  if(!is_upper_bound(i))
818  {
819  if(-G[i] >= Gmax2)
820  Gmax2 = -G[i];
821  }
822  if(!is_lower_bound(i))
823  {
824  if(G[i] >= Gmax1)
825  Gmax1 = G[i];
826  }
827  }
828  }
829 
830  if(unshrink == false && Gmax1 + Gmax2 <= eps*10)
831  {
832  unshrink = true;
833  reconstruct_gradient();
834  active_size = l;
835  svm.info("*");
836  }
837 
838  for(i=0;i<active_size;i++)
839  if (be_shrunk(i, Gmax1, Gmax2))
840  {
841  active_size--;
842  while (active_size > i)
843  {
844  if (!be_shrunk(active_size, Gmax1, Gmax2))
845  {
846  swap_index(i,active_size);
847  break;
848  }
849  active_size--;
850  }
851  }
852  }
853 
854  double calculate_rho()
855  {
856  double r;
857  int nr_free = 0;
858  double ub = INF, lb = -INF, sum_free = 0;
859  for(int i=0;i<active_size;i++)
860  {
861  double yG = y[i]*G[i];
862 
863  if(is_upper_bound(i))
864  {
865  if(y[i] < 0)
866  ub = Math.min(ub,yG);
867  else
868  lb = Math.max(lb,yG);
869  }
870  else if(is_lower_bound(i))
871  {
872  if(y[i] > 0)
873  ub = Math.min(ub,yG);
874  else
875  lb = Math.max(lb,yG);
876  }
877  else
878  {
879  ++nr_free;
880  sum_free += yG;
881  }
882  }
883 
884  if(nr_free>0)
885  r = sum_free/nr_free;
886  else
887  r = (ub+lb)/2;
888 
889  return r;
890  }
891 
892 }
893 
894 //
895 // Solver for nu-svm classification and regression
896 //
897 // additional constraint: e^T \alpha = constant
898 //
899 final class Solver_NU extends Solver
900 {
901  private SolutionInfo si;
902 
903  void Solve(int l, QMatrix Q, double[] p, byte[] y,
904  double[] alpha, double Cp, double Cn, double eps,
905  SolutionInfo si, int shrinking)
906  {
907  this.si = si;
908  super.Solve(l,Q,p,y,alpha,Cp,Cn,eps,si,shrinking);
909  }
910 
911  // return 1 if already optimal, return 0 otherwise
912  int select_working_set(int[] working_set)
913  {
914  // return i,j such that y_i = y_j and
915  // i: maximizes -y_i * grad(f)_i, i in I_up(\alpha)
916  // j: minimizes the decrease of obj value
917  // (if quadratic coefficeint <= 0, replace it with tau)
918  // -y_j*grad(f)_j < -y_i*grad(f)_i, j in I_low(\alpha)
919 
920  double Gmaxp = -INF;
921  double Gmaxp2 = -INF;
922  int Gmaxp_idx = -1;
923 
924  double Gmaxn = -INF;
925  double Gmaxn2 = -INF;
926  int Gmaxn_idx = -1;
927 
928  int Gmin_idx = -1;
929  double obj_diff_min = INF;
930 
931  for(int t=0;t<active_size;t++)
932  if(y[t]==+1)
933  {
934  if(!is_upper_bound(t))
935  if(-G[t] >= Gmaxp)
936  {
937  Gmaxp = -G[t];
938  Gmaxp_idx = t;
939  }
940  }
941  else
942  {
943  if(!is_lower_bound(t))
944  if(G[t] >= Gmaxn)
945  {
946  Gmaxn = G[t];
947  Gmaxn_idx = t;
948  }
949  }
950 
951  int ip = Gmaxp_idx;
952  int in = Gmaxn_idx;
953  float[] Q_ip = null;
954  float[] Q_in = null;
955  if(ip != -1) // null Q_ip not accessed: Gmaxp=-INF if ip=-1
956  Q_ip = Q.get_Q(ip,active_size);
957  if(in != -1)
958  Q_in = Q.get_Q(in,active_size);
959 
960  for(int j=0;j<active_size;j++)
961  {
962  if(y[j]==+1)
963  {
964  if (!is_lower_bound(j))
965  {
966  double grad_diff=Gmaxp+G[j];
967  if (G[j] >= Gmaxp2)
968  Gmaxp2 = G[j];
969  if (grad_diff > 0)
970  {
971  double obj_diff;
972  double quad_coef = QD[ip]+QD[j]-2*Q_ip[j];
973  if (quad_coef > 0)
974  obj_diff = -(grad_diff*grad_diff)/quad_coef;
975  else
976  obj_diff = -(grad_diff*grad_diff)/1e-12;
977 
978  if (obj_diff <= obj_diff_min)
979  {
980  Gmin_idx=j;
981  obj_diff_min = obj_diff;
982  }
983  }
984  }
985  }
986  else
987  {
988  if (!is_upper_bound(j))
989  {
990  double grad_diff=Gmaxn-G[j];
991  if (-G[j] >= Gmaxn2)
992  Gmaxn2 = -G[j];
993  if (grad_diff > 0)
994  {
995  double obj_diff;
996  double quad_coef = QD[in]+QD[j]-2*Q_in[j];
997  if (quad_coef > 0)
998  obj_diff = -(grad_diff*grad_diff)/quad_coef;
999  else
1000  obj_diff = -(grad_diff*grad_diff)/1e-12;
1001 
1002  if (obj_diff <= obj_diff_min)
1003  {
1004  Gmin_idx=j;
1005  obj_diff_min = obj_diff;
1006  }
1007  }
1008  }
1009  }
1010  }
1011 
1012  if(Math.max(Gmaxp+Gmaxp2,Gmaxn+Gmaxn2) < eps || Gmin_idx == -1)
1013  return 1;
1014 
1015  if(y[Gmin_idx] == +1)
1016  working_set[0] = Gmaxp_idx;
1017  else
1018  working_set[0] = Gmaxn_idx;
1019  working_set[1] = Gmin_idx;
1020 
1021  return 0;
1022  }
1023 
1024  private boolean be_shrunk(int i, double Gmax1, double Gmax2, double Gmax3, double Gmax4)
1025  {
1026  if(is_upper_bound(i))
1027  {
1028  if(y[i]==+1)
1029  return(-G[i] > Gmax1);
1030  else
1031  return(-G[i] > Gmax4);
1032  }
1033  else if(is_lower_bound(i))
1034  {
1035  if(y[i]==+1)
1036  return(G[i] > Gmax2);
1037  else
1038  return(G[i] > Gmax3);
1039  }
1040  else
1041  return(false);
1042  }
1043 
1044  void do_shrinking()
1045  {
1046  double Gmax1 = -INF; // max { -y_i * grad(f)_i | y_i = +1, i in I_up(\alpha) }
1047  double Gmax2 = -INF; // max { y_i * grad(f)_i | y_i = +1, i in I_low(\alpha) }
1048  double Gmax3 = -INF; // max { -y_i * grad(f)_i | y_i = -1, i in I_up(\alpha) }
1049  double Gmax4 = -INF; // max { y_i * grad(f)_i | y_i = -1, i in I_low(\alpha) }
1050 
1051  // find maximal violating pair first
1052  int i;
1053  for(i=0;i<active_size;i++)
1054  {
1055  if(!is_upper_bound(i))
1056  {
1057  if(y[i]==+1)
1058  {
1059  if(-G[i] > Gmax1) Gmax1 = -G[i];
1060  }
1061  else if(-G[i] > Gmax4) Gmax4 = -G[i];
1062  }
1063  if(!is_lower_bound(i))
1064  {
1065  if(y[i]==+1)
1066  {
1067  if(G[i] > Gmax2) Gmax2 = G[i];
1068  }
1069  else if(G[i] > Gmax3) Gmax3 = G[i];
1070  }
1071  }
1072 
1073  if(unshrink == false && Math.max(Gmax1+Gmax2,Gmax3+Gmax4) <= eps*10)
1074  {
1075  unshrink = true;
1076  reconstruct_gradient();
1077  active_size = l;
1078  }
1079 
1080  for(i=0;i<active_size;i++)
1081  if (be_shrunk(i, Gmax1, Gmax2, Gmax3, Gmax4))
1082  {
1083  active_size--;
1084  while (active_size > i)
1085  {
1086  if (!be_shrunk(active_size, Gmax1, Gmax2, Gmax3, Gmax4))
1087  {
1088  swap_index(i,active_size);
1089  break;
1090  }
1091  active_size--;
1092  }
1093  }
1094  }
1095 
1096  double calculate_rho()
1097  {
1098  int nr_free1 = 0,nr_free2 = 0;
1099  double ub1 = INF, ub2 = INF;
1100  double lb1 = -INF, lb2 = -INF;
1101  double sum_free1 = 0, sum_free2 = 0;
1102 
1103  for(int i=0;i<active_size;i++)
1104  {
1105  if(y[i]==+1)
1106  {
1107  if(is_upper_bound(i))
1108  lb1 = Math.max(lb1,G[i]);
1109  else if(is_lower_bound(i))
1110  ub1 = Math.min(ub1,G[i]);
1111  else
1112  {
1113  ++nr_free1;
1114  sum_free1 += G[i];
1115  }
1116  }
1117  else
1118  {
1119  if(is_upper_bound(i))
1120  lb2 = Math.max(lb2,G[i]);
1121  else if(is_lower_bound(i))
1122  ub2 = Math.min(ub2,G[i]);
1123  else
1124  {
1125  ++nr_free2;
1126  sum_free2 += G[i];
1127  }
1128  }
1129  }
1130 
1131  double r1,r2;
1132  if(nr_free1 > 0)
1133  r1 = sum_free1/nr_free1;
1134  else
1135  r1 = (ub1+lb1)/2;
1136 
1137  if(nr_free2 > 0)
1138  r2 = sum_free2/nr_free2;
1139  else
1140  r2 = (ub2+lb2)/2;
1141 
1142  si.r = (r1+r2)/2;
1143  return (r1-r2)/2;
1144  }
1145 }
1146 
1147 //
1148 // Q matrices for various formulations
1149 //
1150 class SVC_Q extends Kernel
1151 {
1152  private final byte[] y;
1153  private final Cache cache;
1154  private final double[] QD;
1155 
1156  SVC_Q(svm_problem prob, svm_parameter param, byte[] y_)
1157  {
1158  super(prob.l, prob.x, param);
1159  y = (byte[])y_.clone();
1160  cache = new Cache(prob.l,(long)(param.cache_size*(1<<20)));
1161  QD = new double[prob.l];
1162  for(int i=0;i<prob.l;i++)
1163  QD[i] = kernel_function(i,i);
1164  }
1165 
1166  float[] get_Q(int i, int len)
1167  {
1168  float[][] data = new float[1][];
1169  int start, j;
1170  if((start = cache.get_data(i,data,len)) < len)
1171  {
1172  for(j=start;j<len;j++)
1173  data[0][j] = (float)(y[i]*y[j]*kernel_function(i,j));
1174  }
1175  return data[0];
1176  }
1177 
1178  double[] get_QD()
1179  {
1180  return QD;
1181  }
1182 
1183  void swap_index(int i, int j)
1184  {
1185  cache.swap_index(i,j);
1186  super.swap_index(i,j);
1187  do {byte tmp=y[i]; y[i]=y[j]; y[j]=tmp;} while(false);
1188  do {double tmp=QD[i]; QD[i]=QD[j]; QD[j]=tmp;} while(false);
1189  }
1190 }
1191 
1192 class ONE_CLASS_Q extends Kernel
1193 {
1194  private final Cache cache;
1195  private final double[] QD;
1196 
1197  ONE_CLASS_Q(svm_problem prob, svm_parameter param)
1198  {
1199  super(prob.l, prob.x, param);
1200  cache = new Cache(prob.l,(long)(param.cache_size*(1<<20)));
1201  QD = new double[prob.l];
1202  for(int i=0;i<prob.l;i++)
1203  QD[i] = kernel_function(i,i);
1204  }
1205 
1206  float[] get_Q(int i, int len)
1207  {
1208  float[][] data = new float[1][];
1209  int start, j;
1210  if((start = cache.get_data(i,data,len)) < len)
1211  {
1212  for(j=start;j<len;j++)
1213  data[0][j] = (float)kernel_function(i,j);
1214  }
1215  return data[0];
1216  }
1217 
1218  double[] get_QD()
1219  {
1220  return QD;
1221  }
1222 
1223  void swap_index(int i, int j)
1224  {
1225  cache.swap_index(i,j);
1226  super.swap_index(i,j);
1227  do {double tmp=QD[i]; QD[i]=QD[j]; QD[j]=tmp;} while(false);
1228  }
1229 }
1230 
1231 class SVR_Q extends Kernel
1232 {
1233  private final int l;
1234  private final Cache cache;
1235  private final byte[] sign;
1236  private final int[] index;
1237  private int next_buffer;
1238  private float[][] buffer;
1239  private final double[] QD;
1240 
1241  SVR_Q(svm_problem prob, svm_parameter param)
1242  {
1243  super(prob.l, prob.x, param);
1244  l = prob.l;
1245  cache = new Cache(l,(long)(param.cache_size*(1<<20)));
1246  QD = new double[2*l];
1247  sign = new byte[2*l];
1248  index = new int[2*l];
1249  for(int k=0;k<l;k++)
1250  {
1251  sign[k] = 1;
1252  sign[k+l] = -1;
1253  index[k] = k;
1254  index[k+l] = k;
1255  QD[k] = kernel_function(k,k);
1256  QD[k+l] = QD[k];
1257  }
1258  buffer = new float[2][2*l];
1259  next_buffer = 0;
1260  }
1261 
1262  void swap_index(int i, int j)
1263  {
1264  do {byte tmp=sign[i]; sign[i]=sign[j]; sign[j]=tmp;} while(false);
1265  do {int tmp=index[i]; index[i]=index[j]; index[j]=tmp;} while(false);
1266  do {double tmp=QD[i]; QD[i]=QD[j]; QD[j]=tmp;} while(false);
1267  }
1268 
1269  float[] get_Q(int i, int len)
1270  {
1271  float[][] data = new float[1][];
1272  int j, real_i = index[i];
1273  if(cache.get_data(real_i,data,l) < l)
1274  {
1275  for(j=0;j<l;j++)
1276  data[0][j] = (float)kernel_function(real_i,j);
1277  }
1278 
1279  // reorder and copy
1280  float buf[] = buffer[next_buffer];
1281  next_buffer = 1 - next_buffer;
1282  byte si = sign[i];
1283  for(j=0;j<len;j++)
1284  buf[j] = (float) si * sign[j] * data[0][index[j]];
1285  return buf;
1286  }
1287 
1288  double[] get_QD()
1289  {
1290  return QD;
1291  }
1292 }
1293 
1294 public class svm {
1295  //
1296  // construct and solve various formulations
1297  //
1298  public static final int LIBSVM_VERSION=325;
1299  public static final Random rand = new Random();
1300 
1301  private static svm_print_interface svm_print_stdout = new svm_print_interface()
1302  {
1303  public void print(String s)
1304  {
1305  System.out.print(s);
1306  System.out.flush();
1307  }
1308  };
1309 
1310  private static svm_print_interface svm_print_string = svm_print_stdout;
1311 
1312  static void info(String s)
1313  {
1314  svm_print_string.print(s);
1315  }
1316 
1317  private static void solve_c_svc(svm_problem prob, svm_parameter param,
1318  double[] alpha, Solver.SolutionInfo si,
1319  double Cp, double Cn)
1320  {
1321  int l = prob.l;
1322  double[] minus_ones = new double[l];
1323  byte[] y = new byte[l];
1324 
1325  int i;
1326 
1327  for(i=0;i<l;i++)
1328  {
1329  alpha[i] = 0;
1330  minus_ones[i] = -1;
1331  if(prob.y[i] > 0) y[i] = +1; else y[i] = -1;
1332  }
1333 
1334  Solver s = new Solver();
1335  s.Solve(l, new SVC_Q(prob,param,y), minus_ones, y,
1336  alpha, Cp, Cn, param.eps, si, param.shrinking);
1337 
1338  double sum_alpha=0;
1339  for(i=0;i<l;i++)
1340  sum_alpha += alpha[i];
1341 
1342  if (Cp==Cn)
1343  svm.info("nu = "+sum_alpha/(Cp*prob.l)+"\n");
1344 
1345  for(i=0;i<l;i++)
1346  alpha[i] *= y[i];
1347  }
1348 
1349  private static void solve_nu_svc(svm_problem prob, svm_parameter param,
1350  double[] alpha, Solver.SolutionInfo si)
1351  {
1352  int i;
1353  int l = prob.l;
1354  double nu = param.nu;
1355 
1356  byte[] y = new byte[l];
1357 
1358  for(i=0;i<l;i++)
1359  if(prob.y[i]>0)
1360  y[i] = +1;
1361  else
1362  y[i] = -1;
1363 
1364  double sum_pos = nu*l/2;
1365  double sum_neg = nu*l/2;
1366 
1367  for(i=0;i<l;i++)
1368  if(y[i] == +1)
1369  {
1370  alpha[i] = Math.min(1.0,sum_pos);
1371  sum_pos -= alpha[i];
1372  }
1373  else
1374  {
1375  alpha[i] = Math.min(1.0,sum_neg);
1376  sum_neg -= alpha[i];
1377  }
1378 
1379  double[] zeros = new double[l];
1380 
1381  for(i=0;i<l;i++)
1382  zeros[i] = 0;
1383 
1384  Solver_NU s = new Solver_NU();
1385  s.Solve(l, new SVC_Q(prob,param,y), zeros, y,
1386  alpha, 1.0, 1.0, param.eps, si, param.shrinking);
1387  double r = si.r;
1388 
1389  svm.info("C = "+1/r+"\n");
1390 
1391  for(i=0;i<l;i++)
1392  alpha[i] *= y[i]/r;
1393 
1394  si.rho /= r;
1395  si.obj /= (r*r);
1396  si.upper_bound_p = 1/r;
1397  si.upper_bound_n = 1/r;
1398  }
1399 
1400  private static void solve_one_class(svm_problem prob, svm_parameter param,
1401  double[] alpha, Solver.SolutionInfo si)
1402  {
1403  int l = prob.l;
1404  double[] zeros = new double[l];
1405  byte[] ones = new byte[l];
1406  int i;
1407 
1408  int n = (int)(param.nu*prob.l); // # of alpha's at upper bound
1409 
1410  for(i=0;i<n;i++)
1411  alpha[i] = 1;
1412  if(n<prob.l)
1413  alpha[n] = param.nu * prob.l - n;
1414  for(i=n+1;i<l;i++)
1415  alpha[i] = 0;
1416 
1417  for(i=0;i<l;i++)
1418  {
1419  zeros[i] = 0;
1420  ones[i] = 1;
1421  }
1422 
1423  Solver s = new Solver();
1424  s.Solve(l, new ONE_CLASS_Q(prob,param), zeros, ones,
1425  alpha, 1.0, 1.0, param.eps, si, param.shrinking);
1426  }
1427 
1428  private static void solve_epsilon_svr(svm_problem prob, svm_parameter param,
1429  double[] alpha, Solver.SolutionInfo si)
1430  {
1431  int l = prob.l;
1432  double[] alpha2 = new double[2*l];
1433  double[] linear_term = new double[2*l];
1434  byte[] y = new byte[2*l];
1435  int i;
1436 
1437  for(i=0;i<l;i++)
1438  {
1439  alpha2[i] = 0;
1440  linear_term[i] = param.p - prob.y[i];
1441  y[i] = 1;
1442 
1443  alpha2[i+l] = 0;
1444  linear_term[i+l] = param.p + prob.y[i];
1445  y[i+l] = -1;
1446  }
1447 
1448  Solver s = new Solver();
1449  s.Solve(2*l, new SVR_Q(prob,param), linear_term, y,
1450  alpha2, param.C, param.C, param.eps, si, param.shrinking);
1451 
1452  double sum_alpha = 0;
1453  for(i=0;i<l;i++)
1454  {
1455  alpha[i] = alpha2[i] - alpha2[i+l];
1456  sum_alpha += Math.abs(alpha[i]);
1457  }
1458  svm.info("nu = "+sum_alpha/(param.C*l)+"\n");
1459  }
1460 
1461  private static void solve_nu_svr(svm_problem prob, svm_parameter param,
1462  double[] alpha, Solver.SolutionInfo si)
1463  {
1464  int l = prob.l;
1465  double C = param.C;
1466  double[] alpha2 = new double[2*l];
1467  double[] linear_term = new double[2*l];
1468  byte[] y = new byte[2*l];
1469  int i;
1470 
1471  double sum = C * param.nu * l / 2;
1472  for(i=0;i<l;i++)
1473  {
1474  alpha2[i] = alpha2[i+l] = Math.min(sum,C);
1475  sum -= alpha2[i];
1476 
1477  linear_term[i] = - prob.y[i];
1478  y[i] = 1;
1479 
1480  linear_term[i+l] = prob.y[i];
1481  y[i+l] = -1;
1482  }
1483 
1484  Solver_NU s = new Solver_NU();
1485  s.Solve(2*l, new SVR_Q(prob,param), linear_term, y,
1486  alpha2, C, C, param.eps, si, param.shrinking);
1487 
1488  svm.info("epsilon = "+(-si.r)+"\n");
1489 
1490  for(i=0;i<l;i++)
1491  alpha[i] = alpha2[i] - alpha2[i+l];
1492  }
1493 
1494  //
1495  // decision_function
1496  //
1497  static class decision_function
1498  {
1499  double[] alpha;
1500  double rho;
1501  };
1502 
1503  static decision_function svm_train_one(
1504  svm_problem prob, svm_parameter param,
1505  double Cp, double Cn)
1506  {
1507  double[] alpha = new double[prob.l];
1508  Solver.SolutionInfo si = new Solver.SolutionInfo();
1509  switch(param.svm_type)
1510  {
1511  case svm_parameter.C_SVC:
1512  solve_c_svc(prob,param,alpha,si,Cp,Cn);
1513  break;
1514  case svm_parameter.NU_SVC:
1515  solve_nu_svc(prob,param,alpha,si);
1516  break;
1517  case svm_parameter.ONE_CLASS:
1518  solve_one_class(prob,param,alpha,si);
1519  break;
1520  case svm_parameter.EPSILON_SVR:
1521  solve_epsilon_svr(prob,param,alpha,si);
1522  break;
1523  case svm_parameter.NU_SVR:
1524  solve_nu_svr(prob,param,alpha,si);
1525  break;
1526  }
1527 
1528  svm.info("obj = "+si.obj+", rho = "+si.rho+"\n");
1529 
1530  // output SVs
1531 
1532  int nSV = 0;
1533  int nBSV = 0;
1534  for(int i=0;i<prob.l;i++)
1535  {
1536  if(Math.abs(alpha[i]) > 0)
1537  {
1538  ++nSV;
1539  if(prob.y[i] > 0)
1540  {
1541  if(Math.abs(alpha[i]) >= si.upper_bound_p)
1542  ++nBSV;
1543  }
1544  else
1545  {
1546  if(Math.abs(alpha[i]) >= si.upper_bound_n)
1547  ++nBSV;
1548  }
1549  }
1550  }
1551 
1552  svm.info("nSV = "+nSV+", nBSV = "+nBSV+"\n");
1553 
1554  decision_function f = new decision_function();
1555  f.alpha = alpha;
1556  f.rho = si.rho;
1557  return f;
1558  }
1559 
1560  // Platt's binary SVM Probablistic Output: an improvement from Lin et al.
1561  private static void sigmoid_train(int l, double[] dec_values, double[] labels,
1562  double[] probAB)
1563  {
1564  double A, B;
1565  double prior1=0, prior0 = 0;
1566  int i;
1567 
1568  for (i=0;i<l;i++)
1569  if (labels[i] > 0) prior1+=1;
1570  else prior0+=1;
1571 
1572  int max_iter=100; // Maximal number of iterations
1573  double min_step=1e-10; // Minimal step taken in line search
1574  double sigma=1e-12; // For numerically strict PD of Hessian
1575  double eps=1e-5;
1576  double hiTarget=(prior1+1.0)/(prior1+2.0);
1577  double loTarget=1/(prior0+2.0);
1578  double[] t= new double[l];
1579  double fApB,p,q,h11,h22,h21,g1,g2,det,dA,dB,gd,stepsize;
1580  double newA,newB,newf,d1,d2;
1581  int iter;
1582 
1583  // Initial Point and Initial Fun Value
1584  A=0.0; B=Math.log((prior0+1.0)/(prior1+1.0));
1585  double fval = 0.0;
1586 
1587  for (i=0;i<l;i++)
1588  {
1589  if (labels[i]>0) t[i]=hiTarget;
1590  else t[i]=loTarget;
1591  fApB = dec_values[i]*A+B;
1592  if (fApB>=0)
1593  fval += t[i]*fApB + Math.log(1+Math.exp(-fApB));
1594  else
1595  fval += (t[i] - 1)*fApB +Math.log(1+Math.exp(fApB));
1596  }
1597  for (iter=0;iter<max_iter;iter++)
1598  {
1599  // Update Gradient and Hessian (use H' = H + sigma I)
1600  h11=sigma; // numerically ensures strict PD
1601  h22=sigma;
1602  h21=0.0;g1=0.0;g2=0.0;
1603  for (i=0;i<l;i++)
1604  {
1605  fApB = dec_values[i]*A+B;
1606  if (fApB >= 0)
1607  {
1608  p=Math.exp(-fApB)/(1.0+Math.exp(-fApB));
1609  q=1.0/(1.0+Math.exp(-fApB));
1610  }
1611  else
1612  {
1613  p=1.0/(1.0+Math.exp(fApB));
1614  q=Math.exp(fApB)/(1.0+Math.exp(fApB));
1615  }
1616  d2=p*q;
1617  h11+=dec_values[i]*dec_values[i]*d2;
1618  h22+=d2;
1619  h21+=dec_values[i]*d2;
1620  d1=t[i]-p;
1621  g1+=dec_values[i]*d1;
1622  g2+=d1;
1623  }
1624 
1625  // Stopping Criteria
1626  if (Math.abs(g1)<eps && Math.abs(g2)<eps)
1627  break;
1628 
1629  // Finding Newton direction: -inv(H') * g
1630  det=h11*h22-h21*h21;
1631  dA=-(h22*g1 - h21 * g2) / det;
1632  dB=-(-h21*g1+ h11 * g2) / det;
1633  gd=g1*dA+g2*dB;
1634 
1635 
1636  stepsize = 1; // Line Search
1637  while (stepsize >= min_step)
1638  {
1639  newA = A + stepsize * dA;
1640  newB = B + stepsize * dB;
1641 
1642  // New function value
1643  newf = 0.0;
1644  for (i=0;i<l;i++)
1645  {
1646  fApB = dec_values[i]*newA+newB;
1647  if (fApB >= 0)
1648  newf += t[i]*fApB + Math.log(1+Math.exp(-fApB));
1649  else
1650  newf += (t[i] - 1)*fApB +Math.log(1+Math.exp(fApB));
1651  }
1652  // Check sufficient decrease
1653  if (newf<fval+0.0001*stepsize*gd)
1654  {
1655  A=newA;B=newB;fval=newf;
1656  break;
1657  }
1658  else
1659  stepsize = stepsize / 2.0;
1660  }
1661 
1662  if (stepsize < min_step)
1663  {
1664  svm.info("Line search fails in two-class probability estimates\n");
1665  break;
1666  }
1667  }
1668 
1669  if (iter>=max_iter)
1670  svm.info("Reaching maximal iterations in two-class probability estimates\n");
1671  probAB[0]=A;probAB[1]=B;
1672  }
1673 
1674  private static double sigmoid_predict(double decision_value, double A, double B)
1675  {
1676  double fApB = decision_value*A+B;
1677  // 1-p used later; avoid catastrophic cancellation
1678  if (fApB >= 0)
1679  return Math.exp(-fApB)/(1.0+Math.exp(-fApB));
1680  else
1681  return 1.0/(1+Math.exp(fApB)) ;
1682  }
1683 
1684  // Method 2 from the multiclass_prob paper by Wu, Lin, and Weng
1685  private static void multiclass_probability(int k, double[][] r, double[] p)
1686  {
1687  int t,j;
1688  int iter = 0, max_iter=Math.max(100,k);
1689  double[][] Q=new double[k][k];
1690  double[] Qp=new double[k];
1691  double pQp, eps=0.005/k;
1692 
1693  for (t=0;t<k;t++)
1694  {
1695  p[t]=1.0/k; // Valid if k = 1
1696  Q[t][t]=0;
1697  for (j=0;j<t;j++)
1698  {
1699  Q[t][t]+=r[j][t]*r[j][t];
1700  Q[t][j]=Q[j][t];
1701  }
1702  for (j=t+1;j<k;j++)
1703  {
1704  Q[t][t]+=r[j][t]*r[j][t];
1705  Q[t][j]=-r[j][t]*r[t][j];
1706  }
1707  }
1708  for (iter=0;iter<max_iter;iter++)
1709  {
1710  // stopping condition, recalculate QP,pQP for numerical accuracy
1711  pQp=0;
1712  for (t=0;t<k;t++)
1713  {
1714  Qp[t]=0;
1715  for (j=0;j<k;j++)
1716  Qp[t]+=Q[t][j]*p[j];
1717  pQp+=p[t]*Qp[t];
1718  }
1719  double max_error=0;
1720  for (t=0;t<k;t++)
1721  {
1722  double error=Math.abs(Qp[t]-pQp);
1723  if (error>max_error)
1724  max_error=error;
1725  }
1726  if (max_error<eps) break;
1727 
1728  for (t=0;t<k;t++)
1729  {
1730  double diff=(-Qp[t]+pQp)/Q[t][t];
1731  p[t]+=diff;
1732  pQp=(pQp+diff*(diff*Q[t][t]+2*Qp[t]))/(1+diff)/(1+diff);
1733  for (j=0;j<k;j++)
1734  {
1735  Qp[j]=(Qp[j]+diff*Q[t][j])/(1+diff);
1736  p[j]/=(1+diff);
1737  }
1738  }
1739  }
1740  if (iter>=max_iter)
1741  svm.info("Exceeds max_iter in multiclass_prob\n");
1742  }
1743 
1744  // Cross-validation decision values for probability estimates
1745  private static void svm_binary_svc_probability(svm_problem prob, svm_parameter param, double Cp, double Cn, double[] probAB)
1746  {
1747  int i;
1748  int nr_fold = 5;
1749  int[] perm = new int[prob.l];
1750  double[] dec_values = new double[prob.l];
1751 
1752  // random shuffle
1753  for(i=0;i<prob.l;i++) perm[i]=i;
1754  for(i=0;i<prob.l;i++)
1755  {
1756  int j = i+rand.nextInt(prob.l-i);
1757  do {int tmp=perm[i]; perm[i]=perm[j]; perm[j]=tmp;} while(false);
1758  }
1759  for(i=0;i<nr_fold;i++)
1760  {
1761  int begin = i*prob.l/nr_fold;
1762  int end = (i+1)*prob.l/nr_fold;
1763  int j,k;
1764  svm_problem subprob = new svm_problem();
1765 
1766  subprob.l = prob.l-(end-begin);
1767  subprob.x = new svm_node[subprob.l][];
1768  subprob.y = new double[subprob.l];
1769 
1770  k=0;
1771  for(j=0;j<begin;j++)
1772  {
1773  subprob.x[k] = prob.x[perm[j]];
1774  subprob.y[k] = prob.y[perm[j]];
1775  ++k;
1776  }
1777  for(j=end;j<prob.l;j++)
1778  {
1779  subprob.x[k] = prob.x[perm[j]];
1780  subprob.y[k] = prob.y[perm[j]];
1781  ++k;
1782  }
1783  int p_count=0,n_count=0;
1784  for(j=0;j<k;j++)
1785  if(subprob.y[j]>0)
1786  p_count++;
1787  else
1788  n_count++;
1789 
1790  if(p_count==0 && n_count==0)
1791  for(j=begin;j<end;j++)
1792  dec_values[perm[j]] = 0;
1793  else if(p_count > 0 && n_count == 0)
1794  for(j=begin;j<end;j++)
1795  dec_values[perm[j]] = 1;
1796  else if(p_count == 0 && n_count > 0)
1797  for(j=begin;j<end;j++)
1798  dec_values[perm[j]] = -1;
1799  else
1800  {
1801  svm_parameter subparam = (svm_parameter)param.clone();
1802  subparam.probability=0;
1803  subparam.C=1.0;
1804  subparam.nr_weight=2;
1805  subparam.weight_label = new int[2];
1806  subparam.weight = new double[2];
1807  subparam.weight_label[0]=+1;
1808  subparam.weight_label[1]=-1;
1809  subparam.weight[0]=Cp;
1810  subparam.weight[1]=Cn;
1811  svm_model submodel = svm_train(subprob,subparam);
1812  for(j=begin;j<end;j++)
1813  {
1814  double[] dec_value=new double[1];
1815  svm_predict_values(submodel,prob.x[perm[j]],dec_value);
1816  dec_values[perm[j]]=dec_value[0];
1817  // ensure +1 -1 order; reason not using CV subroutine
1818  dec_values[perm[j]] *= submodel.label[0];
1819  }
1820  }
1821  }
1822  sigmoid_train(prob.l,dec_values,prob.y,probAB);
1823  }
1824 
1825  // Return parameter of a Laplace distribution
1826  private static double svm_svr_probability(svm_problem prob, svm_parameter param)
1827  {
1828  int i;
1829  int nr_fold = 5;
1830  double[] ymv = new double[prob.l];
1831  double mae = 0;
1832 
1833  svm_parameter newparam = (svm_parameter)param.clone();
1834  newparam.probability = 0;
1835  svm_cross_validation(prob,newparam,nr_fold,ymv);
1836  for(i=0;i<prob.l;i++)
1837  {
1838  ymv[i]=prob.y[i]-ymv[i];
1839  mae += Math.abs(ymv[i]);
1840  }
1841  mae /= prob.l;
1842  double std=Math.sqrt(2*mae*mae);
1843  int count=0;
1844  mae=0;
1845  for(i=0;i<prob.l;i++)
1846  if (Math.abs(ymv[i]) > 5*std)
1847  count=count+1;
1848  else
1849  mae+=Math.abs(ymv[i]);
1850  mae /= (prob.l-count);
1851  svm.info("Prob. model for test data: target value = predicted value + z,\nz: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma="+mae+"\n");
1852  return mae;
1853  }
1854 
1855  // label: label name, start: begin of each class, count: #data of classes, perm: indices to the original data
1856  // perm, length l, must be allocated before calling this subroutine
1857  private static void svm_group_classes(svm_problem prob, int[] nr_class_ret, int[][] label_ret, int[][] start_ret, int[][] count_ret, int[] perm)
1858  {
1859  int l = prob.l;
1860  int max_nr_class = 16;
1861  int nr_class = 0;
1862  int[] label = new int[max_nr_class];
1863  int[] count = new int[max_nr_class];
1864  int[] data_label = new int[l];
1865  int i;
1866 
1867  for(i=0;i<l;i++)
1868  {
1869  int this_label = (int)(prob.y[i]);
1870  int j;
1871  for(j=0;j<nr_class;j++)
1872  {
1873  if(this_label == label[j])
1874  {
1875  ++count[j];
1876  break;
1877  }
1878  }
1879  data_label[i] = j;
1880  if(j == nr_class)
1881  {
1882  if(nr_class == max_nr_class)
1883  {
1884  max_nr_class *= 2;
1885  int[] new_data = new int[max_nr_class];
1886  System.arraycopy(label,0,new_data,0,label.length);
1887  label = new_data;
1888  new_data = new int[max_nr_class];
1889  System.arraycopy(count,0,new_data,0,count.length);
1890  count = new_data;
1891  }
1892  label[nr_class] = this_label;
1893  count[nr_class] = 1;
1894  ++nr_class;
1895  }
1896  }
1897 
1898  //
1899  // Labels are ordered by their first occurrence in the training set.
1900  // However, for two-class sets with -1/+1 labels and -1 appears first,
1901  // we swap labels to ensure that internally the binary SVM has positive data corresponding to the +1 instances.
1902  //
1903  if (nr_class == 2 && label[0] == -1 && label[1] == +1)
1904  {
1905  do {int tmp=label[0]; label[0]=label[1]; label[1]=tmp;} while(false);
1906  do {int tmp=count[0]; count[0]=count[1]; count[1]=tmp;} while(false);
1907  for(i=0;i<l;i++)
1908  {
1909  if(data_label[i] == 0)
1910  data_label[i] = 1;
1911  else
1912  data_label[i] = 0;
1913  }
1914  }
1915 
1916  int[] start = new int[nr_class];
1917  start[0] = 0;
1918  for(i=1;i<nr_class;i++)
1919  start[i] = start[i-1]+count[i-1];
1920  for(i=0;i<l;i++)
1921  {
1922  perm[start[data_label[i]]] = i;
1923  ++start[data_label[i]];
1924  }
1925  start[0] = 0;
1926  for(i=1;i<nr_class;i++)
1927  start[i] = start[i-1]+count[i-1];
1928 
1929  nr_class_ret[0] = nr_class;
1930  label_ret[0] = label;
1931  start_ret[0] = start;
1932  count_ret[0] = count;
1933  }
1934 
1935  //
1936  // Interface functions
1937  //
1938  public static svm_model svm_train(svm_problem prob, svm_parameter param)
1939  {
1940  svm_model model = new svm_model();
1941  model.param = param;
1942 
1943  if(param.svm_type == svm_parameter.ONE_CLASS ||
1944  param.svm_type == svm_parameter.EPSILON_SVR ||
1945  param.svm_type == svm_parameter.NU_SVR)
1946  {
1947  // regression or one-class-svm
1948  model.nr_class = 2;
1949  model.label = null;
1950  model.nSV = null;
1951  model.probA = null; model.probB = null;
1952  model.sv_coef = new double[1][];
1953 
1954  if(param.probability == 1 &&
1955  (param.svm_type == svm_parameter.EPSILON_SVR ||
1956  param.svm_type == svm_parameter.NU_SVR))
1957  {
1958  model.probA = new double[1];
1959  model.probA[0] = svm_svr_probability(prob,param);
1960  }
1961 
1962  decision_function f = svm_train_one(prob,param,0,0);
1963  model.rho = new double[1];
1964  model.rho[0] = f.rho;
1965 
1966  int nSV = 0;
1967  int i;
1968  for(i=0;i<prob.l;i++)
1969  if(Math.abs(f.alpha[i]) > 0) ++nSV;
1970  model.l = nSV;
1971  model.SV = new svm_node[nSV][];
1972  model.sv_coef[0] = new double[nSV];
1973  model.sv_indices = new int[nSV];
1974  int j = 0;
1975  for(i=0;i<prob.l;i++)
1976  if(Math.abs(f.alpha[i]) > 0)
1977  {
1978  model.SV[j] = prob.x[i];
1979  model.sv_coef[0][j] = f.alpha[i];
1980  model.sv_indices[j] = i+1;
1981  ++j;
1982  }
1983  }
1984  else
1985  {
1986  // classification
1987  int l = prob.l;
1988  int[] tmp_nr_class = new int[1];
1989  int[][] tmp_label = new int[1][];
1990  int[][] tmp_start = new int[1][];
1991  int[][] tmp_count = new int[1][];
1992  int[] perm = new int[l];
1993 
1994  // group training data of the same class
1995  svm_group_classes(prob,tmp_nr_class,tmp_label,tmp_start,tmp_count,perm);
1996  int nr_class = tmp_nr_class[0];
1997  int[] label = tmp_label[0];
1998  int[] start = tmp_start[0];
1999  int[] count = tmp_count[0];
2000 
2001  if(nr_class == 1)
2002  svm.info("WARNING: training data in only one class. See README for details.\n");
2003 
2004  svm_node[][] x = new svm_node[l][];
2005  int i;
2006  for(i=0;i<l;i++)
2007  x[i] = prob.x[perm[i]];
2008 
2009  // calculate weighted C
2010 
2011  double[] weighted_C = new double[nr_class];
2012  for(i=0;i<nr_class;i++)
2013  weighted_C[i] = param.C;
2014  for(i=0;i<param.nr_weight;i++)
2015  {
2016  int j;
2017  for(j=0;j<nr_class;j++)
2018  if(param.weight_label[i] == label[j])
2019  break;
2020  if(j == nr_class)
2021  System.err.print("WARNING: class label "+param.weight_label[i]+" specified in weight is not found\n");
2022  else
2023  weighted_C[j] *= param.weight[i];
2024  }
2025 
2026  // train k*(k-1)/2 models
2027 
2028  boolean[] nonzero = new boolean[l];
2029  for(i=0;i<l;i++)
2030  nonzero[i] = false;
2031  decision_function[] f = new decision_function[nr_class*(nr_class-1)/2];
2032 
2033  double[] probA=null,probB=null;
2034  if (param.probability == 1)
2035  {
2036  probA=new double[nr_class*(nr_class-1)/2];
2037  probB=new double[nr_class*(nr_class-1)/2];
2038  }
2039 
2040  int p = 0;
2041  for(i=0;i<nr_class;i++)
2042  for(int j=i+1;j<nr_class;j++)
2043  {
2044  svm_problem sub_prob = new svm_problem();
2045  int si = start[i], sj = start[j];
2046  int ci = count[i], cj = count[j];
2047  sub_prob.l = ci+cj;
2048  sub_prob.x = new svm_node[sub_prob.l][];
2049  sub_prob.y = new double[sub_prob.l];
2050  int k;
2051  for(k=0;k<ci;k++)
2052  {
2053  sub_prob.x[k] = x[si+k];
2054  sub_prob.y[k] = +1;
2055  }
2056  for(k=0;k<cj;k++)
2057  {
2058  sub_prob.x[ci+k] = x[sj+k];
2059  sub_prob.y[ci+k] = -1;
2060  }
2061 
2062  if(param.probability == 1)
2063  {
2064  double[] probAB=new double[2];
2065  svm_binary_svc_probability(sub_prob,param,weighted_C[i],weighted_C[j],probAB);
2066  probA[p]=probAB[0];
2067  probB[p]=probAB[1];
2068  }
2069 
2070  f[p] = svm_train_one(sub_prob,param,weighted_C[i],weighted_C[j]);
2071  for(k=0;k<ci;k++)
2072  if(!nonzero[si+k] && Math.abs(f[p].alpha[k]) > 0)
2073  nonzero[si+k] = true;
2074  for(k=0;k<cj;k++)
2075  if(!nonzero[sj+k] && Math.abs(f[p].alpha[ci+k]) > 0)
2076  nonzero[sj+k] = true;
2077  ++p;
2078  }
2079 
2080  // build output
2081 
2082  model.nr_class = nr_class;
2083 
2084  model.label = new int[nr_class];
2085  for(i=0;i<nr_class;i++)
2086  model.label[i] = label[i];
2087 
2088  model.rho = new double[nr_class*(nr_class-1)/2];
2089  for(i=0;i<nr_class*(nr_class-1)/2;i++)
2090  model.rho[i] = f[i].rho;
2091 
2092  if(param.probability == 1)
2093  {
2094  model.probA = new double[nr_class*(nr_class-1)/2];
2095  model.probB = new double[nr_class*(nr_class-1)/2];
2096  for(i=0;i<nr_class*(nr_class-1)/2;i++)
2097  {
2098  model.probA[i] = probA[i];
2099  model.probB[i] = probB[i];
2100  }
2101  }
2102  else
2103  {
2104  model.probA=null;
2105  model.probB=null;
2106  }
2107 
2108  int total_sv = 0;
2109  int[] nz_count = new int[nr_class];
2110  model.nSV = new int[nr_class];
2111  for(i=0;i<nr_class;i++)
2112  {
2113  int nSV = 0;
2114  for(int j=0;j<count[i];j++)
2115  if(nonzero[start[i]+j])
2116  {
2117  ++nSV;
2118  ++total_sv;
2119  }
2120  model.nSV[i] = nSV;
2121  nz_count[i] = nSV;
2122  }
2123 
2124  svm.info("Total nSV = "+total_sv+"\n");
2125 
2126  model.l = total_sv;
2127  model.SV = new svm_node[total_sv][];
2128  model.sv_indices = new int[total_sv];
2129  p = 0;
2130  for(i=0;i<l;i++)
2131  if(nonzero[i])
2132  {
2133  model.SV[p] = x[i];
2134  model.sv_indices[p++] = perm[i] + 1;
2135  }
2136 
2137  int[] nz_start = new int[nr_class];
2138  nz_start[0] = 0;
2139  for(i=1;i<nr_class;i++)
2140  nz_start[i] = nz_start[i-1]+nz_count[i-1];
2141 
2142  model.sv_coef = new double[nr_class-1][];
2143  for(i=0;i<nr_class-1;i++)
2144  model.sv_coef[i] = new double[total_sv];
2145 
2146  p = 0;
2147  for(i=0;i<nr_class;i++)
2148  for(int j=i+1;j<nr_class;j++)
2149  {
2150  // classifier (i,j): coefficients with
2151  // i are in sv_coef[j-1][nz_start[i]...],
2152  // j are in sv_coef[i][nz_start[j]...]
2153 
2154  int si = start[i];
2155  int sj = start[j];
2156  int ci = count[i];
2157  int cj = count[j];
2158 
2159  int q = nz_start[i];
2160  int k;
2161  for(k=0;k<ci;k++)
2162  if(nonzero[si+k])
2163  model.sv_coef[j-1][q++] = f[p].alpha[k];
2164  q = nz_start[j];
2165  for(k=0;k<cj;k++)
2166  if(nonzero[sj+k])
2167  model.sv_coef[i][q++] = f[p].alpha[ci+k];
2168  ++p;
2169  }
2170  }
2171  return model;
2172  }
2173 
2174  // Stratified cross validation
2175  public static void svm_cross_validation(svm_problem prob, svm_parameter param, int nr_fold, double[] target)
2176  {
2177  int i;
2178  int[] fold_start = new int[nr_fold+1];
2179  int l = prob.l;
2180  int[] perm = new int[l];
2181 
2182  // stratified cv may not give leave-one-out rate
2183  // Each class to l folds -> some folds may have zero elements
2184  if((param.svm_type == svm_parameter.C_SVC ||
2185  param.svm_type == svm_parameter.NU_SVC) && nr_fold < l)
2186  {
2187  int[] tmp_nr_class = new int[1];
2188  int[][] tmp_label = new int[1][];
2189  int[][] tmp_start = new int[1][];
2190  int[][] tmp_count = new int[1][];
2191 
2192  svm_group_classes(prob,tmp_nr_class,tmp_label,tmp_start,tmp_count,perm);
2193 
2194  int nr_class = tmp_nr_class[0];
2195  int[] start = tmp_start[0];
2196  int[] count = tmp_count[0];
2197 
2198  // random shuffle and then data grouped by fold using the array perm
2199  int[] fold_count = new int[nr_fold];
2200  int c;
2201  int[] index = new int[l];
2202  for(i=0;i<l;i++)
2203  index[i]=perm[i];
2204  for (c=0; c<nr_class; c++)
2205  for(i=0;i<count[c];i++)
2206  {
2207  int j = i+rand.nextInt(count[c]-i);
2208  do {int tmp=index[start[c]+j]; index[start[c]+j]=index[start[c]+i]; index[start[c]+i]=tmp;} while(false);
2209  }
2210  for(i=0;i<nr_fold;i++)
2211  {
2212  fold_count[i] = 0;
2213  for (c=0; c<nr_class;c++)
2214  fold_count[i]+=(i+1)*count[c]/nr_fold-i*count[c]/nr_fold;
2215  }
2216  fold_start[0]=0;
2217  for (i=1;i<=nr_fold;i++)
2218  fold_start[i] = fold_start[i-1]+fold_count[i-1];
2219  for (c=0; c<nr_class;c++)
2220  for(i=0;i<nr_fold;i++)
2221  {
2222  int begin = start[c]+i*count[c]/nr_fold;
2223  int end = start[c]+(i+1)*count[c]/nr_fold;
2224  for(int j=begin;j<end;j++)
2225  {
2226  perm[fold_start[i]] = index[j];
2227  fold_start[i]++;
2228  }
2229  }
2230  fold_start[0]=0;
2231  for (i=1;i<=nr_fold;i++)
2232  fold_start[i] = fold_start[i-1]+fold_count[i-1];
2233  }
2234  else
2235  {
2236  for(i=0;i<l;i++) perm[i]=i;
2237  for(i=0;i<l;i++)
2238  {
2239  int j = i+rand.nextInt(l-i);
2240  do {int tmp=perm[i]; perm[i]=perm[j]; perm[j]=tmp;} while(false);
2241  }
2242  for(i=0;i<=nr_fold;i++)
2243  fold_start[i]=i*l/nr_fold;
2244  }
2245 
2246  for(i=0;i<nr_fold;i++)
2247  {
2248  int begin = fold_start[i];
2249  int end = fold_start[i+1];
2250  int j,k;
2251  svm_problem subprob = new svm_problem();
2252 
2253  subprob.l = l-(end-begin);
2254  subprob.x = new svm_node[subprob.l][];
2255  subprob.y = new double[subprob.l];
2256 
2257  k=0;
2258  for(j=0;j<begin;j++)
2259  {
2260  subprob.x[k] = prob.x[perm[j]];
2261  subprob.y[k] = prob.y[perm[j]];
2262  ++k;
2263  }
2264  for(j=end;j<l;j++)
2265  {
2266  subprob.x[k] = prob.x[perm[j]];
2267  subprob.y[k] = prob.y[perm[j]];
2268  ++k;
2269  }
2270  svm_model submodel = svm_train(subprob,param);
2271  if(param.probability==1 &&
2272  (param.svm_type == svm_parameter.C_SVC ||
2273  param.svm_type == svm_parameter.NU_SVC))
2274  {
2275  double[] prob_estimates= new double[svm_get_nr_class(submodel)];
2276  for(j=begin;j<end;j++)
2277  target[perm[j]] = svm_predict_probability(submodel,prob.x[perm[j]],prob_estimates);
2278  }
2279  else
2280  for(j=begin;j<end;j++)
2281  target[perm[j]] = svm_predict(submodel,prob.x[perm[j]]);
2282  }
2283  }
2284 
2285  public static int svm_get_svm_type(svm_model model)
2286  {
2287  return model.param.svm_type;
2288  }
2289 
2290  public static int svm_get_nr_class(svm_model model)
2291  {
2292  return model.nr_class;
2293  }
2294 
2295  public static void svm_get_labels(svm_model model, int[] label)
2296  {
2297  if (model.label != null)
2298  for(int i=0;i<model.nr_class;i++)
2299  label[i] = model.label[i];
2300  }
2301 
2302  public static void svm_get_sv_indices(svm_model model, int[] indices)
2303  {
2304  if (model.sv_indices != null)
2305  for(int i=0;i<model.l;i++)
2306  indices[i] = model.sv_indices[i];
2307  }
2308 
2309  public static int svm_get_nr_sv(svm_model model)
2310  {
2311  return model.l;
2312  }
2313 
2314  public static double svm_get_svr_probability(svm_model model)
2315  {
2316  if ((model.param.svm_type == svm_parameter.EPSILON_SVR || model.param.svm_type == svm_parameter.NU_SVR) &&
2317  model.probA!=null)
2318  return model.probA[0];
2319  else
2320  {
2321  System.err.print("Model doesn't contain information for SVR probability inference\n");
2322  return 0;
2323  }
2324  }
2325 
2326  public static double svm_predict_values(svm_model model, svm_node[] x, double[] dec_values)
2327  {
2328  int i;
2329  if(model.param.svm_type == svm_parameter.ONE_CLASS ||
2330  model.param.svm_type == svm_parameter.EPSILON_SVR ||
2331  model.param.svm_type == svm_parameter.NU_SVR)
2332  {
2333  double[] sv_coef = model.sv_coef[0];
2334  double sum = 0;
2335  for(i=0;i<model.l;i++)
2336  sum += sv_coef[i] * Kernel.k_function(x,model.SV[i],model.param);
2337  sum -= model.rho[0];
2338  dec_values[0] = sum;
2339 
2340  if(model.param.svm_type == svm_parameter.ONE_CLASS)
2341  return (sum>0)?1:-1;
2342  else
2343  return sum;
2344  }
2345  else
2346  {
2347  int nr_class = model.nr_class;
2348  int l = model.l;
2349 
2350  double[] kvalue = new double[l];
2351  for(i=0;i<l;i++)
2352  kvalue[i] = Kernel.k_function(x,model.SV[i],model.param);
2353 
2354  int[] start = new int[nr_class];
2355  start[0] = 0;
2356  for(i=1;i<nr_class;i++)
2357  start[i] = start[i-1]+model.nSV[i-1];
2358 
2359  int[] vote = new int[nr_class];
2360  for(i=0;i<nr_class;i++)
2361  vote[i] = 0;
2362 
2363  int p=0;
2364  for(i=0;i<nr_class;i++)
2365  for(int j=i+1;j<nr_class;j++)
2366  {
2367  double sum = 0;
2368  int si = start[i];
2369  int sj = start[j];
2370  int ci = model.nSV[i];
2371  int cj = model.nSV[j];
2372 
2373  int k;
2374  double[] coef1 = model.sv_coef[j-1];
2375  double[] coef2 = model.sv_coef[i];
2376  for(k=0;k<ci;k++)
2377  sum += coef1[si+k] * kvalue[si+k];
2378  for(k=0;k<cj;k++)
2379  sum += coef2[sj+k] * kvalue[sj+k];
2380  sum -= model.rho[p];
2381  dec_values[p] = sum;
2382 
2383  if(dec_values[p] > 0)
2384  ++vote[i];
2385  else
2386  ++vote[j];
2387  p++;
2388  }
2389 
2390  int vote_max_idx = 0;
2391  for(i=1;i<nr_class;i++)
2392  if(vote[i] > vote[vote_max_idx])
2393  vote_max_idx = i;
2394 
2395  return model.label[vote_max_idx];
2396  }
2397  }
2398 
2399  public static double svm_predict(svm_model model, svm_node[] x)
2400  {
2401  int nr_class = model.nr_class;
2402  double[] dec_values;
2403  if(model.param.svm_type == svm_parameter.ONE_CLASS ||
2404  model.param.svm_type == svm_parameter.EPSILON_SVR ||
2405  model.param.svm_type == svm_parameter.NU_SVR)
2406  dec_values = new double[1];
2407  else
2408  dec_values = new double[nr_class*(nr_class-1)/2];
2409  double pred_result = svm_predict_values(model, x, dec_values);
2410  return pred_result;
2411  }
2412 
2413  public static double svm_predict_probability(svm_model model, svm_node[] x, double[] prob_estimates)
2414  {
2415  if ((model.param.svm_type == svm_parameter.C_SVC || model.param.svm_type == svm_parameter.NU_SVC) &&
2416  model.probA!=null && model.probB!=null)
2417  {
2418  int i;
2419  int nr_class = model.nr_class;
2420  double[] dec_values = new double[nr_class*(nr_class-1)/2];
2421  svm_predict_values(model, x, dec_values);
2422 
2423  double min_prob=1e-7;
2424  double[][] pairwise_prob=new double[nr_class][nr_class];
2425 
2426  int k=0;
2427  for(i=0;i<nr_class;i++)
2428  for(int j=i+1;j<nr_class;j++)
2429  {
2430  pairwise_prob[i][j]=Math.min(Math.max(sigmoid_predict(dec_values[k],model.probA[k],model.probB[k]),min_prob),1-min_prob);
2431  pairwise_prob[j][i]=1-pairwise_prob[i][j];
2432  k++;
2433  }
2434  if (nr_class == 2)
2435  {
2436  prob_estimates[0] = pairwise_prob[0][1];
2437  prob_estimates[1] = pairwise_prob[1][0];
2438  }
2439  else
2440  multiclass_probability(nr_class,pairwise_prob,prob_estimates);
2441 
2442  int prob_max_idx = 0;
2443  for(i=1;i<nr_class;i++)
2444  if(prob_estimates[i] > prob_estimates[prob_max_idx])
2445  prob_max_idx = i;
2446  return model.label[prob_max_idx];
2447  }
2448  else
2449  return svm_predict(model, x);
2450  }
2451 
2452  static final String svm_type_table[] =
2453  {
2454  "c_svc","nu_svc","one_class","epsilon_svr","nu_svr",
2455  };
2456 
2457  static final String kernel_type_table[]=
2458  {
2459  "linear","polynomial","rbf","sigmoid","precomputed"
2460  };
2461 
2462  public static void svm_save_model(String model_file_name, svm_model model) throws IOException
2463  {
2464  DataOutputStream fp = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(model_file_name)));
2465 
2466  svm_parameter param = model.param;
2467 
2468  fp.writeBytes("svm_type "+svm_type_table[param.svm_type]+"\n");
2469  fp.writeBytes("kernel_type "+kernel_type_table[param.kernel_type]+"\n");
2470 
2471  if(param.kernel_type == svm_parameter.POLY)
2472  fp.writeBytes("degree "+param.degree+"\n");
2473 
2474  if(param.kernel_type == svm_parameter.POLY ||
2475  param.kernel_type == svm_parameter.RBF ||
2476  param.kernel_type == svm_parameter.SIGMOID)
2477  fp.writeBytes("gamma "+param.gamma+"\n");
2478 
2479  if(param.kernel_type == svm_parameter.POLY ||
2480  param.kernel_type == svm_parameter.SIGMOID)
2481  fp.writeBytes("coef0 "+param.coef0+"\n");
2482 
2483  int nr_class = model.nr_class;
2484  int l = model.l;
2485  fp.writeBytes("nr_class "+nr_class+"\n");
2486  fp.writeBytes("total_sv "+l+"\n");
2487 
2488  {
2489  fp.writeBytes("rho");
2490  for(int i=0;i<nr_class*(nr_class-1)/2;i++)
2491  fp.writeBytes(" "+model.rho[i]);
2492  fp.writeBytes("\n");
2493  }
2494 
2495  if(model.label != null)
2496  {
2497  fp.writeBytes("label");
2498  for(int i=0;i<nr_class;i++)
2499  fp.writeBytes(" "+model.label[i]);
2500  fp.writeBytes("\n");
2501  }
2502 
2503  if(model.probA != null) // regression has probA only
2504  {
2505  fp.writeBytes("probA");
2506  for(int i=0;i<nr_class*(nr_class-1)/2;i++)
2507  fp.writeBytes(" "+model.probA[i]);
2508  fp.writeBytes("\n");
2509  }
2510  if(model.probB != null)
2511  {
2512  fp.writeBytes("probB");
2513  for(int i=0;i<nr_class*(nr_class-1)/2;i++)
2514  fp.writeBytes(" "+model.probB[i]);
2515  fp.writeBytes("\n");
2516  }
2517 
2518  if(model.nSV != null)
2519  {
2520  fp.writeBytes("nr_sv");
2521  for(int i=0;i<nr_class;i++)
2522  fp.writeBytes(" "+model.nSV[i]);
2523  fp.writeBytes("\n");
2524  }
2525 
2526  fp.writeBytes("SV\n");
2527  double[][] sv_coef = model.sv_coef;
2528  svm_node[][] SV = model.SV;
2529 
2530  for(int i=0;i<l;i++)
2531  {
2532  for(int j=0;j<nr_class-1;j++)
2533  fp.writeBytes(sv_coef[j][i]+" ");
2534 
2535  svm_node[] p = SV[i];
2536  if(param.kernel_type == svm_parameter.PRECOMPUTED)
2537  fp.writeBytes("0:"+(int)(p[0].value));
2538  else
2539  for(int j=0;j<p.length;j++)
2540  fp.writeBytes(p[j].index+":"+p[j].value+" ");
2541  fp.writeBytes("\n");
2542  }
2543 
2544  fp.close();
2545  }
2546 
2547  private static double atof(String s)
2548  {
2549  return Double.valueOf(s).doubleValue();
2550  }
2551 
2552  private static int atoi(String s)
2553  {
2554  return Integer.parseInt(s);
2555  }
2556 
2557  private static boolean read_model_header(BufferedReader fp, svm_model model)
2558  {
2559  svm_parameter param = new svm_parameter();
2560  model.param = param;
2561  // parameters for training only won't be assigned, but arrays are assigned as null for safety
2562  param.nr_weight = 0;
2563  param.weight_label = null;
2564  param.weight = null;
2565 
2566  try
2567  {
2568  while(true)
2569  {
2570  String cmd = fp.readLine();
2571  String arg = cmd.substring(cmd.indexOf(' ')+1);
2572 
2573  if(cmd.startsWith("svm_type"))
2574  {
2575  int i;
2576  for(i=0;i<svm_type_table.length;i++)
2577  {
2578  if(arg.indexOf(svm_type_table[i])!=-1)
2579  {
2580  param.svm_type=i;
2581  break;
2582  }
2583  }
2584  if(i == svm_type_table.length)
2585  {
2586  System.err.print("unknown svm type.\n");
2587  return false;
2588  }
2589  }
2590  else if(cmd.startsWith("kernel_type"))
2591  {
2592  int i;
2593  for(i=0;i<kernel_type_table.length;i++)
2594  {
2595  if(arg.indexOf(kernel_type_table[i])!=-1)
2596  {
2597  param.kernel_type=i;
2598  break;
2599  }
2600  }
2601  if(i == kernel_type_table.length)
2602  {
2603  System.err.print("unknown kernel function.\n");
2604  return false;
2605  }
2606  }
2607  else if(cmd.startsWith("degree"))
2608  param.degree = atoi(arg);
2609  else if(cmd.startsWith("gamma"))
2610  param.gamma = atof(arg);
2611  else if(cmd.startsWith("coef0"))
2612  param.coef0 = atof(arg);
2613  else if(cmd.startsWith("nr_class"))
2614  model.nr_class = atoi(arg);
2615  else if(cmd.startsWith("total_sv"))
2616  model.l = atoi(arg);
2617  else if(cmd.startsWith("rho"))
2618  {
2619  int n = model.nr_class * (model.nr_class-1)/2;
2620  model.rho = new double[n];
2621  StringTokenizer st = new StringTokenizer(arg);
2622  for(int i=0;i<n;i++)
2623  model.rho[i] = atof(st.nextToken());
2624  }
2625  else if(cmd.startsWith("label"))
2626  {
2627  int n = model.nr_class;
2628  model.label = new int[n];
2629  StringTokenizer st = new StringTokenizer(arg);
2630  for(int i=0;i<n;i++)
2631  model.label[i] = atoi(st.nextToken());
2632  }
2633  else if(cmd.startsWith("probA"))
2634  {
2635  int n = model.nr_class*(model.nr_class-1)/2;
2636  model.probA = new double[n];
2637  StringTokenizer st = new StringTokenizer(arg);
2638  for(int i=0;i<n;i++)
2639  model.probA[i] = atof(st.nextToken());
2640  }
2641  else if(cmd.startsWith("probB"))
2642  {
2643  int n = model.nr_class*(model.nr_class-1)/2;
2644  model.probB = new double[n];
2645  StringTokenizer st = new StringTokenizer(arg);
2646  for(int i=0;i<n;i++)
2647  model.probB[i] = atof(st.nextToken());
2648  }
2649  else if(cmd.startsWith("nr_sv"))
2650  {
2651  int n = model.nr_class;
2652  model.nSV = new int[n];
2653  StringTokenizer st = new StringTokenizer(arg);
2654  for(int i=0;i<n;i++)
2655  model.nSV[i] = atoi(st.nextToken());
2656  }
2657  else if(cmd.startsWith("SV"))
2658  {
2659  break;
2660  }
2661  else
2662  {
2663  System.err.print("unknown text in model file: ["+cmd+"]\n");
2664  return false;
2665  }
2666  }
2667  }
2668  catch(Exception e)
2669  {
2670  return false;
2671  }
2672  return true;
2673  }
2674 
2675  public static svm_model svm_load_model(String model_file_name) throws IOException
2676  {
2677  return svm_load_model(new BufferedReader(new FileReader(model_file_name)));
2678  }
2679 
2680  public static svm_model svm_load_model(BufferedReader fp) throws IOException
2681  {
2682  // read parameters
2683 
2684  svm_model model = new svm_model();
2685  model.rho = null;
2686  model.probA = null;
2687  model.probB = null;
2688  model.label = null;
2689  model.nSV = null;
2690 
2691  // read header
2692  if (!read_model_header(fp, model))
2693  {
2694  System.err.print("ERROR: failed to read model\n");
2695  return null;
2696  }
2697 
2698  // read sv_coef and SV
2699 
2700  int m = model.nr_class - 1;
2701  int l = model.l;
2702  model.sv_coef = new double[m][l];
2703  model.SV = new svm_node[l][];
2704 
2705  for(int i=0;i<l;i++)
2706  {
2707  String line = fp.readLine();
2708  StringTokenizer st = new StringTokenizer(line," \t\n\r\f:");
2709 
2710  for(int k=0;k<m;k++)
2711  model.sv_coef[k][i] = atof(st.nextToken());
2712  int n = st.countTokens()/2;
2713  model.SV[i] = new svm_node[n];
2714  for(int j=0;j<n;j++)
2715  {
2716  model.SV[i][j] = new svm_node();
2717  model.SV[i][j].index = atoi(st.nextToken());
2718  model.SV[i][j].value = atof(st.nextToken());
2719  }
2720  }
2721 
2722  fp.close();
2723  return model;
2724  }
2725 
2726  public static String svm_check_parameter(svm_problem prob, svm_parameter param)
2727  {
2728  // svm_type
2729 
2730  int svm_type = param.svm_type;
2731  if(svm_type != svm_parameter.C_SVC &&
2732  svm_type != svm_parameter.NU_SVC &&
2733  svm_type != svm_parameter.ONE_CLASS &&
2734  svm_type != svm_parameter.EPSILON_SVR &&
2735  svm_type != svm_parameter.NU_SVR)
2736  return "unknown svm type";
2737 
2738  // kernel_type, degree
2739 
2740  int kernel_type = param.kernel_type;
2741  if(kernel_type != svm_parameter.LINEAR &&
2742  kernel_type != svm_parameter.POLY &&
2743  kernel_type != svm_parameter.RBF &&
2744  kernel_type != svm_parameter.SIGMOID &&
2745  kernel_type != svm_parameter.PRECOMPUTED)
2746  return "unknown kernel type";
2747 
2748  if((kernel_type == svm_parameter.POLY ||
2749  kernel_type == svm_parameter.RBF ||
2750  kernel_type == svm_parameter.SIGMOID) &&
2751  param.gamma < 0)
2752  return "gamma < 0";
2753 
2754  if(kernel_type == svm_parameter.POLY && param.degree < 0)
2755  return "degree of polynomial kernel < 0";
2756 
2757  // cache_size,eps,C,nu,p,shrinking
2758 
2759  if(param.cache_size <= 0)
2760  return "cache_size <= 0";
2761 
2762  if(param.eps <= 0)
2763  return "eps <= 0";
2764 
2765  if(svm_type == svm_parameter.C_SVC ||
2766  svm_type == svm_parameter.EPSILON_SVR ||
2767  svm_type == svm_parameter.NU_SVR)
2768  if(param.C <= 0)
2769  return "C <= 0";
2770 
2771  if(svm_type == svm_parameter.NU_SVC ||
2772  svm_type == svm_parameter.ONE_CLASS ||
2773  svm_type == svm_parameter.NU_SVR)
2774  if(param.nu <= 0 || param.nu > 1)
2775  return "nu <= 0 or nu > 1";
2776 
2777  if(svm_type == svm_parameter.EPSILON_SVR)
2778  if(param.p < 0)
2779  return "p < 0";
2780 
2781  if(param.shrinking != 0 &&
2782  param.shrinking != 1)
2783  return "shrinking != 0 and shrinking != 1";
2784 
2785  if(param.probability != 0 &&
2786  param.probability != 1)
2787  return "probability != 0 and probability != 1";
2788 
2789  if(param.probability == 1 &&
2790  svm_type == svm_parameter.ONE_CLASS)
2791  return "one-class SVM probability output not supported yet";
2792 
2793  // check whether nu-svc is feasible
2794 
2795  if(svm_type == svm_parameter.NU_SVC)
2796  {
2797  int l = prob.l;
2798  int max_nr_class = 16;
2799  int nr_class = 0;
2800  int[] label = new int[max_nr_class];
2801  int[] count = new int[max_nr_class];
2802 
2803  int i;
2804  for(i=0;i<l;i++)
2805  {
2806  int this_label = (int)prob.y[i];
2807  int j;
2808  for(j=0;j<nr_class;j++)
2809  if(this_label == label[j])
2810  {
2811  ++count[j];
2812  break;
2813  }
2814 
2815  if(j == nr_class)
2816  {
2817  if(nr_class == max_nr_class)
2818  {
2819  max_nr_class *= 2;
2820  int[] new_data = new int[max_nr_class];
2821  System.arraycopy(label,0,new_data,0,label.length);
2822  label = new_data;
2823 
2824  new_data = new int[max_nr_class];
2825  System.arraycopy(count,0,new_data,0,count.length);
2826  count = new_data;
2827  }
2828  label[nr_class] = this_label;
2829  count[nr_class] = 1;
2830  ++nr_class;
2831  }
2832  }
2833 
2834  for(i=0;i<nr_class;i++)
2835  {
2836  int n1 = count[i];
2837  for(int j=i+1;j<nr_class;j++)
2838  {
2839  int n2 = count[j];
2840  if(param.nu*(n1+n2)/2 > Math.min(n1,n2))
2841  return "specified nu is infeasible";
2842  }
2843  }
2844  }
2845 
2846  return null;
2847  }
2848 
2849  public static int svm_check_probability_model(svm_model model)
2850  {
2851  if (((model.param.svm_type == svm_parameter.C_SVC || model.param.svm_type == svm_parameter.NU_SVC) &&
2852  model.probA!=null && model.probB!=null) ||
2853  ((model.param.svm_type == svm_parameter.EPSILON_SVR || model.param.svm_type == svm_parameter.NU_SVR) &&
2854  model.probA!=null))
2855  return 1;
2856  else
2857  return 0;
2858  }
2859 
2860  public static void svm_set_print_string_function(svm_print_interface print_func)
2861  {
2862  if (print_func == null)
2863  svm_print_string = svm_print_stdout;
2864  else
2865  svm_print_string = print_func;
2866  }
2867 }
libsvm.svm_parameter.C_SVC
static final int C_SVC
Definition: svm_parameter.java:5
-
libsvm.svm_parameter.degree
int degree
Definition: svm_parameter.java:20
-
libsvm.svm_model.param
svm_parameter param
Definition: svm_model.java:7
-
libsvm.svm.svm_load_model
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Definition: svm.java:2413
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1 //
2 // svm_model
3 //
4 package libsvm;
5 public class svm_model implements java.io.Serializable
6 {
7  public svm_parameter param; // parameter
8  public int nr_class; // number of classes, = 2 in regression/one class svm
9  public int l; // total #SV
10  public svm_node[][] SV; // SVs (SV[l])
11  public double[][] sv_coef; // coefficients for SVs in decision functions (sv_coef[k-1][l])
12  public double[] rho; // constants in decision functions (rho[k*(k-1)/2])
13  public double[] probA; // pariwise probability information
14  public double[] probB;
15  public int[] sv_indices; // sv_indices[0,...,nSV-1] are values in [1,...,num_traning_data] to indicate SVs in the training set
16 
17  // for classification only
18 
19  public int[] label; // label of each class (label[k])
20  public int[] nSV; // number of SVs for each class (nSV[k])
21  // nSV[0] + nSV[1] + ... + nSV[k-1] = l
22 };
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1 package libsvm;
2 public class svm_node implements java.io.Serializable
3 {
4  public int index;
5  public double value;
6 }
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1 package libsvm;
2 public class svm_parameter implements Cloneable,java.io.Serializable
3 {
4  /* svm_type */
5  public static final int C_SVC = 0;
6  public static final int NU_SVC = 1;
7  public static final int ONE_CLASS = 2;
8  public static final int EPSILON_SVR = 3;
9  public static final int NU_SVR = 4;
10 
11  /* kernel_type */
12  public static final int LINEAR = 0;
13  public static final int POLY = 1;
14  public static final int RBF = 2;
15  public static final int SIGMOID = 3;
16  public static final int PRECOMPUTED = 4;
17 
18  public int svm_type;
19  public int kernel_type;
20  public int degree; // for poly
21  public double gamma; // for poly/rbf/sigmoid
22  public double coef0; // for poly/sigmoid
23 
24  // these are for training only
25  public double cache_size; // in MB
26  public double eps; // stopping criteria
27  public double C; // for C_SVC, EPSILON_SVR and NU_SVR
28  public int nr_weight; // for C_SVC
29  public int[] weight_label; // for C_SVC
30  public double[] weight; // for C_SVC
31  public double nu; // for NU_SVC, ONE_CLASS, and NU_SVR
32  public double p; // for EPSILON_SVR
33  public int shrinking; // use the shrinking heuristics
34  public int probability; // do probability estimates
35 
36  public Object clone()
37  {
38  try
39  {
40  return super.clone();
41  } catch (CloneNotSupportedException e)
42  {
43  return null;
44  }
45  }
46 
47 }
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1 import libsvm.*;
2 import java.io.*;
3 import java.util.*;
4 
5 class svm_predict {
6  private static svm_print_interface svm_print_null = new svm_print_interface()
7  {
8  public void print(String s) {}
9  };
10 
11  private static svm_print_interface svm_print_stdout = new svm_print_interface()
12  {
13  public void print(String s)
14  {
15  System.out.print(s);
16  }
17  };
18 
19  private static svm_print_interface svm_print_string = svm_print_stdout;
20 
21  static void info(String s)
22  {
23  svm_print_string.print(s);
24  }
25 
26  private static double atof(String s)
27  {
28  return Double.valueOf(s).doubleValue();
29  }
30 
31  private static int atoi(String s)
32  {
33  return Integer.parseInt(s);
34  }
35 
36  private static void predict(BufferedReader input, DataOutputStream output, svm_model model, int predict_probability) throws IOException
37  {
38  int correct = 0;
39  int total = 0;
40  double error = 0;
41  double sump = 0, sumt = 0, sumpp = 0, sumtt = 0, sumpt = 0;
42 
43  int svm_type=svm.svm_get_svm_type(model);
44  int nr_class=svm.svm_get_nr_class(model);
45  double[] prob_estimates=null;
46 
47  if(predict_probability == 1)
48  {
49  if(svm_type == svm_parameter.EPSILON_SVR ||
50  svm_type == svm_parameter.NU_SVR)
51  {
52  svm_predict.info("Prob. model for test data: target value = predicted value + z,\nz: Laplace distribution e^(-|z|/sigma)/(2sigma),sigma="+svm.svm_get_svr_probability(model)+"\n");
53  }
54  else
55  {
56  int[] labels=new int[nr_class];
57  svm.svm_get_labels(model,labels);
58  prob_estimates = new double[nr_class];
59  output.writeBytes("labels");
60  for(int j=0;j<nr_class;j++)
61  output.writeBytes(" "+labels[j]);
62  output.writeBytes("\n");
63  }
64  }
65  while(true)
66  {
67  String line = input.readLine();
68  if(line == null) break;
69 
70  StringTokenizer st = new StringTokenizer(line," \t\n\r\f:");
71 
72  double target_label = atof(st.nextToken());
73  int m = st.countTokens()/2;
74  svm_node[] x = new svm_node[m];
75  for(int j=0;j<m;j++)
76  {
77  x[j] = new svm_node();
78  x[j].index = atoi(st.nextToken());
79  x[j].value = atof(st.nextToken());
80  }
81 
82  double predict_label;
83  if (predict_probability==1 && (svm_type==svm_parameter.C_SVC || svm_type==svm_parameter.NU_SVC))
84  {
85  predict_label = svm.svm_predict_probability(model,x,prob_estimates);
86  output.writeBytes(predict_label+" ");
87  for(int j=0;j<nr_class;j++)
88  output.writeBytes(prob_estimates[j]+" ");
89  output.writeBytes("\n");
90  }
91  else
92  {
93  predict_label = svm.svm_predict(model,x);
94  output.writeBytes(predict_label+"\n");
95  }
96 
97  if(predict_label == target_label)
98  ++correct;
99  error += (predict_label-target_label)*(predict_label-target_label);
100  sump += predict_label;
101  sumt += target_label;
102  sumpp += predict_label*predict_label;
103  sumtt += target_label*target_label;
104  sumpt += predict_label*target_label;
105  ++total;
106  }
107  if(svm_type == svm_parameter.EPSILON_SVR ||
108  svm_type == svm_parameter.NU_SVR)
109  {
110  svm_predict.info("Mean squared error = "+error/total+" (regression)\n");
111  svm_predict.info("Squared correlation coefficient = "+
112  ((total*sumpt-sump*sumt)*(total*sumpt-sump*sumt))/
113  ((total*sumpp-sump*sump)*(total*sumtt-sumt*sumt))+
114  " (regression)\n");
115  }
116  else
117  svm_predict.info("Accuracy = "+(double)correct/total*100+
118  "% ("+correct+"/"+total+") (classification)\n");
119  }
120 
121  private static void exit_with_help()
122  {
123  System.err.print("usage: svm_predict [options] test_file model_file output_file\n"
124  +"options:\n"
125  +"-b probability_estimates: whether to predict probability estimates, 0 or 1 (default 0); one-class SVM not supported yet\n"
126  +"-q : quiet mode (no outputs)\n");
127  System.exit(1);
128  }
129 
130  public static void main(String argv[]) throws IOException
131  {
132  int i, predict_probability=0;
133  svm_print_string = svm_print_stdout;
134 
135  // parse options
136  for(i=0;i<argv.length;i++)
137  {
138  if(argv[i].charAt(0) != '-') break;
139  ++i;
140  switch(argv[i-1].charAt(1))
141  {
142  case 'b':
143  predict_probability = atoi(argv[i]);
144  break;
145  case 'q':
146  svm_print_string = svm_print_null;
147  i--;
148  break;
149  default:
150  System.err.print("Unknown option: " + argv[i-1] + "\n");
151  exit_with_help();
152  }
153  }
154  if(i>=argv.length-2)
155  exit_with_help();
156  try
157  {
158  BufferedReader input = new BufferedReader(new FileReader(argv[i]));
159  DataOutputStream output = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(argv[i+2])));
160  svm_model model = svm.svm_load_model(argv[i+1]);
161  if (model == null)
162  {
163  System.err.print("can't open model file "+argv[i+1]+"\n");
164  System.exit(1);
165  }
166  if(predict_probability == 1)
167  {
168  if(svm.svm_check_probability_model(model)==0)
169  {
170  System.err.print("Model does not support probabiliy estimates\n");
171  System.exit(1);
172  }
173  }
174  else
175  {
176  if(svm.svm_check_probability_model(model)!=0)
177  {
178  svm_predict.info("Model supports probability estimates, but disabled in prediction.\n");
179  }
180  }
181  predict(input,output,model,predict_probability);
182  input.close();
183  output.close();
184  }
185  catch(FileNotFoundException e)
186  {
187  exit_with_help();
188  }
189  catch(ArrayIndexOutOfBoundsException e)
190  {
191  exit_with_help();
192  }
193  }
194 }
libsvm.svm_parameter.C_SVC
static final int C_SVC
Definition: svm_parameter.java:5
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Definition: svm.java:2285
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2 public interface svm_print_interface
3 {
4  public void print(String s);
5 }
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2 public class svm_problem implements java.io.Serializable
3 {
4  public int l;
5  public double[] y;
6  public svm_node[][] x;
7 }
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1 import libsvm.*;
2 import java.io.*;
3 import java.util.*;
4 import java.text.DecimalFormat;
5 
6 class svm_scale
7 {
8  private String line = null;
9  private double lower = -1.0;
10  private double upper = 1.0;
11  private double y_lower;
12  private double y_upper;
13  private boolean y_scaling = false;
14  private double[] feature_max;
15  private double[] feature_min;
16  private double y_max = -Double.MAX_VALUE;
17  private double y_min = Double.MAX_VALUE;
18  private int max_index;
19  private long num_nonzeros = 0;
20  private long new_num_nonzeros = 0;
21 
22  private static void exit_with_help()
23  {
24  System.out.print(
25  "Usage: svm-scale [options] data_filename\n"
26  +"options:\n"
27  +"-l lower : x scaling lower limit (default -1)\n"
28  +"-u upper : x scaling upper limit (default +1)\n"
29  +"-y y_lower y_upper : y scaling limits (default: no y scaling)\n"
30  +"-s save_filename : save scaling parameters to save_filename\n"
31  +"-r restore_filename : restore scaling parameters from restore_filename\n"
32  );
33  System.exit(1);
34  }
35 
36  private BufferedReader rewind(BufferedReader fp, String filename) throws IOException
37  {
38  fp.close();
39  return new BufferedReader(new FileReader(filename));
40  }
41 
42  private void output_target(double value)
43  {
44  if(y_scaling)
45  {
46  if(value == y_min)
47  value = y_lower;
48  else if(value == y_max)
49  value = y_upper;
50  else
51  value = y_lower + (y_upper-y_lower) *
52  (value-y_min) / (y_max-y_min);
53  }
54 
55  System.out.print(value + " ");
56  }
57 
58  private void output(int index, double value)
59  {
60  /* skip single-valued attribute */
61  if(feature_max[index] == feature_min[index])
62  return;
63 
64  if(value == feature_min[index])
65  value = lower;
66  else if(value == feature_max[index])
67  value = upper;
68  else
69  value = lower + (upper-lower) *
70  (value-feature_min[index])/
71  (feature_max[index]-feature_min[index]);
72 
73  if(value != 0)
74  {
75  System.out.print(index + ":" + value + " ");
76  new_num_nonzeros++;
77  }
78  }
79 
80  private String readline(BufferedReader fp) throws IOException
81  {
82  line = fp.readLine();
83  return line;
84  }
85 
86  private void run(String []argv) throws IOException
87  {
88  int i,index;
89  BufferedReader fp = null, fp_restore = null;
90  String save_filename = null;
91  String restore_filename = null;
92  String data_filename = null;
93 
94 
95  for(i=0;i<argv.length;i++)
96  {
97  if (argv[i].charAt(0) != '-') break;
98  ++i;
99  switch(argv[i-1].charAt(1))
100  {
101  case 'l': lower = Double.parseDouble(argv[i]); break;
102  case 'u': upper = Double.parseDouble(argv[i]); break;
103  case 'y':
104  y_lower = Double.parseDouble(argv[i]);
105  ++i;
106  y_upper = Double.parseDouble(argv[i]);
107  y_scaling = true;
108  break;
109  case 's': save_filename = argv[i]; break;
110  case 'r': restore_filename = argv[i]; break;
111  default:
112  System.err.println("unknown option");
113  exit_with_help();
114  }
115  }
116 
117  if(!(upper > lower) || (y_scaling && !(y_upper > y_lower)))
118  {
119  System.err.println("inconsistent lower/upper specification");
120  System.exit(1);
121  }
122  if(restore_filename != null && save_filename != null)
123  {
124  System.err.println("cannot use -r and -s simultaneously");
125  System.exit(1);
126  }
127 
128  if(argv.length != i+1)
129  exit_with_help();
130 
131  data_filename = argv[i];
132  try {
133  fp = new BufferedReader(new FileReader(data_filename));
134  } catch (Exception e) {
135  System.err.println("can't open file " + data_filename);
136  System.exit(1);
137  }
138 
139  /* assumption: min index of attributes is 1 */
140  /* pass 1: find out max index of attributes */
141  max_index = 0;
142 
143  if(restore_filename != null)
144  {
145  int idx, c;
146 
147  try {
148  fp_restore = new BufferedReader(new FileReader(restore_filename));
149  }
150  catch (Exception e) {
151  System.err.println("can't open file " + restore_filename);
152  System.exit(1);
153  }
154  if((c = fp_restore.read()) == 'y')
155  {
156  fp_restore.readLine();
157  fp_restore.readLine();
158  fp_restore.readLine();
159  }
160  fp_restore.readLine();
161  fp_restore.readLine();
162 
163  String restore_line = null;
164  while((restore_line = fp_restore.readLine())!=null)
165  {
166  StringTokenizer st2 = new StringTokenizer(restore_line);
167  idx = Integer.parseInt(st2.nextToken());
168  max_index = Math.max(max_index, idx);
169  }
170  fp_restore = rewind(fp_restore, restore_filename);
171  }
172 
173  while (readline(fp) != null)
174  {
175  StringTokenizer st = new StringTokenizer(line," \t\n\r\f:");
176  st.nextToken();
177  while(st.hasMoreTokens())
178  {
179  index = Integer.parseInt(st.nextToken());
180  max_index = Math.max(max_index, index);
181  st.nextToken();
182  num_nonzeros++;
183  }
184  }
185 
186  try {
187  feature_max = new double[(max_index+1)];
188  feature_min = new double[(max_index+1)];
189  } catch(OutOfMemoryError e) {
190  System.err.println("can't allocate enough memory");
191  System.exit(1);
192  }
193 
194  for(i=0;i<=max_index;i++)
195  {
196  feature_max[i] = -Double.MAX_VALUE;
197  feature_min[i] = Double.MAX_VALUE;
198  }
199 
200  fp = rewind(fp, data_filename);
201 
202  /* pass 2: find out min/max value */
203  while(readline(fp) != null)
204  {
205  int next_index = 1;
206  double target;
207  double value;
208 
209  StringTokenizer st = new StringTokenizer(line," \t\n\r\f:");
210  target = Double.parseDouble(st.nextToken());
211  y_max = Math.max(y_max, target);
212  y_min = Math.min(y_min, target);
213 
214  while (st.hasMoreTokens())
215  {
216  index = Integer.parseInt(st.nextToken());
217  value = Double.parseDouble(st.nextToken());
218 
219  for (i = next_index; i<index; i++)
220  {
221  feature_max[i] = Math.max(feature_max[i], 0);
222  feature_min[i] = Math.min(feature_min[i], 0);
223  }
224 
225  feature_max[index] = Math.max(feature_max[index], value);
226  feature_min[index] = Math.min(feature_min[index], value);
227  next_index = index + 1;
228  }
229 
230  for(i=next_index;i<=max_index;i++)
231  {
232  feature_max[i] = Math.max(feature_max[i], 0);
233  feature_min[i] = Math.min(feature_min[i], 0);
234  }
235  }
236 
237  fp = rewind(fp, data_filename);
238 
239  /* pass 2.5: save/restore feature_min/feature_max */
240  if(restore_filename != null)
241  {
242  // fp_restore rewinded in finding max_index
243  int idx, c;
244  double fmin, fmax;
245 
246  fp_restore.mark(2); // for reset
247  if((c = fp_restore.read()) == 'y')
248  {
249  fp_restore.readLine(); // pass the '\n' after 'y'
250  StringTokenizer st = new StringTokenizer(fp_restore.readLine());
251  y_lower = Double.parseDouble(st.nextToken());
252  y_upper = Double.parseDouble(st.nextToken());
253  st = new StringTokenizer(fp_restore.readLine());
254  y_min = Double.parseDouble(st.nextToken());
255  y_max = Double.parseDouble(st.nextToken());
256  y_scaling = true;
257  }
258  else
259  fp_restore.reset();
260 
261  if(fp_restore.read() == 'x') {
262  fp_restore.readLine(); // pass the '\n' after 'x'
263  StringTokenizer st = new StringTokenizer(fp_restore.readLine());
264  lower = Double.parseDouble(st.nextToken());
265  upper = Double.parseDouble(st.nextToken());
266  String restore_line = null;
267  while((restore_line = fp_restore.readLine())!=null)
268  {
269  StringTokenizer st2 = new StringTokenizer(restore_line);
270  idx = Integer.parseInt(st2.nextToken());
271  fmin = Double.parseDouble(st2.nextToken());
272  fmax = Double.parseDouble(st2.nextToken());
273  if (idx <= max_index)
274  {
275  feature_min[idx] = fmin;
276  feature_max[idx] = fmax;
277  }
278  }
279  }
280  fp_restore.close();
281  }
282 
283  if(save_filename != null)
284  {
285  Formatter formatter = new Formatter(new StringBuilder());
286  BufferedWriter fp_save = null;
287 
288  try {
289  fp_save = new BufferedWriter(new FileWriter(save_filename));
290  } catch(IOException e) {
291  System.err.println("can't open file " + save_filename);
292  System.exit(1);
293  }
294 
295  if(y_scaling)
296  {
297  formatter.format("y\n");
298  formatter.format("%.16g %.16g\n", y_lower, y_upper);
299  formatter.format("%.16g %.16g\n", y_min, y_max);
300  }
301  formatter.format("x\n");
302  formatter.format("%.16g %.16g\n", lower, upper);
303  for(i=1;i<=max_index;i++)
304  {
305  if(feature_min[i] != feature_max[i])
306  formatter.format("%d %.16g %.16g\n", i, feature_min[i], feature_max[i]);
307  }
308  fp_save.write(formatter.toString());
309  fp_save.close();
310  }
311 
312  /* pass 3: scale */
313  while(readline(fp) != null)
314  {
315  int next_index = 1;
316  double target;
317  double value;
318 
319  StringTokenizer st = new StringTokenizer(line," \t\n\r\f:");
320  target = Double.parseDouble(st.nextToken());
321  output_target(target);
322  while(st.hasMoreElements())
323  {
324  index = Integer.parseInt(st.nextToken());
325  value = Double.parseDouble(st.nextToken());
326  for (i = next_index; i<index; i++)
327  output(i, 0);
328  output(index, value);
329  next_index = index + 1;
330  }
331 
332  for(i=next_index;i<= max_index;i++)
333  output(i, 0);
334  System.out.print("\n");
335  }
336  if (new_num_nonzeros > num_nonzeros)
337  System.err.print(
338  "WARNING: original #nonzeros " + num_nonzeros+"\n"
339  +" new #nonzeros " + new_num_nonzeros+"\n"
340  +"Use -l 0 if many original feature values are zeros\n");
341 
342  fp.close();
343  }
344 
345  public static void main(String argv[]) throws IOException
346  {
347  svm_scale s = new svm_scale();
348  s.run(argv);
349  }
350 }
libsvm
Definition: svm.java:6
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svm_toy.java
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1 import libsvm.*;
2 import java.applet.*;
3 import java.awt.*;
4 import java.util.*;
5 import java.awt.event.*;
6 import java.io.*;
7 
8 public class svm_toy extends Applet {
9 
10  static final String DEFAULT_PARAM="-t 2 -c 100";
11  int XLEN;
12  int YLEN;
13 
14  // off-screen buffer
15 
16  Image buffer;
17  Graphics buffer_gc;
18 
19  // pre-allocated colors
20 
21  final static Color colors[] =
22  {
23  new Color(0,0,0),
24  new Color(0,120,120),
25  new Color(120,120,0),
26  new Color(120,0,120),
27  new Color(0,200,200),
28  new Color(200,200,0),
29  new Color(200,0,200)
30  };
31 
32  class point {
33  point(double x, double y, byte value)
34  {
35  this.x = x;
36  this.y = y;
37  this.value = value;
38  }
39  double x, y;
40  byte value;
41  }
42 
43  Vector<point> point_list = new Vector<point>();
44  byte current_value = 1;
45 
46  public void init()
47  {
48  setSize(getSize());
49 
50  final Button button_change = new Button("Change");
51  Button button_run = new Button("Run");
52  Button button_clear = new Button("Clear");
53  Button button_save = new Button("Save");
54  Button button_load = new Button("Load");
55  final TextField input_line = new TextField(DEFAULT_PARAM);
56 
57  BorderLayout layout = new BorderLayout();
58  this.setLayout(layout);
59 
60  Panel p = new Panel();
61  GridBagLayout gridbag = new GridBagLayout();
62  p.setLayout(gridbag);
63 
64  GridBagConstraints c = new GridBagConstraints();
65  c.fill = GridBagConstraints.HORIZONTAL;
66  c.weightx = 1;
67  c.gridwidth = 1;
68  gridbag.setConstraints(button_change,c);
69  gridbag.setConstraints(button_run,c);
70  gridbag.setConstraints(button_clear,c);
71  gridbag.setConstraints(button_save,c);
72  gridbag.setConstraints(button_load,c);
73  c.weightx = 5;
74  c.gridwidth = 5;
75  gridbag.setConstraints(input_line,c);
76 
77  button_change.setBackground(colors[current_value]);
78 
79  p.add(button_change);
80  p.add(button_run);
81  p.add(button_clear);
82  p.add(button_save);
83  p.add(button_load);
84  p.add(input_line);
85  this.add(p,BorderLayout.SOUTH);
86 
87  button_change.addActionListener(new ActionListener()
88  { public void actionPerformed (ActionEvent e)
89  { button_change_clicked(); button_change.setBackground(colors[current_value]); }});
90 
91  button_run.addActionListener(new ActionListener()
92  { public void actionPerformed (ActionEvent e)
93  { button_run_clicked(input_line.getText()); }});
94 
95  button_clear.addActionListener(new ActionListener()
96  { public void actionPerformed (ActionEvent e)
97  { button_clear_clicked(); }});
98 
99  button_save.addActionListener(new ActionListener()
100  { public void actionPerformed (ActionEvent e)
101  { button_save_clicked(input_line.getText()); }});
102 
103  button_load.addActionListener(new ActionListener()
104  { public void actionPerformed (ActionEvent e)
105  { button_load_clicked(); }});
106 
107  input_line.addActionListener(new ActionListener()
108  { public void actionPerformed (ActionEvent e)
109  { button_run_clicked(input_line.getText()); }});
110 
111  this.enableEvents(AWTEvent.MOUSE_EVENT_MASK);
112  }
113 
114  void draw_point(point p)
115  {
116  Color c = colors[p.value+3];
117 
118  Graphics window_gc = getGraphics();
119  buffer_gc.setColor(c);
120  buffer_gc.fillRect((int)(p.x*XLEN),(int)(p.y*YLEN),4,4);
121  window_gc.setColor(c);
122  window_gc.fillRect((int)(p.x*XLEN),(int)(p.y*YLEN),4,4);
123  }
124 
125  void clear_all()
126  {
127  point_list.removeAllElements();
128  if(buffer != null)
129  {
130  buffer_gc.setColor(colors[0]);
131  buffer_gc.fillRect(0,0,XLEN,YLEN);
132  }
133  repaint();
134  }
135 
136  void draw_all_points()
137  {
138  int n = point_list.size();
139  for(int i=0;i<n;i++)
140  draw_point(point_list.elementAt(i));
141  }
142 
143  void button_change_clicked()
144  {
145  ++current_value;
146  if(current_value > 3) current_value = 1;
147  }
148 
149  private static double atof(String s)
150  {
151  return Double.valueOf(s).doubleValue();
152  }
153 
154  private static int atoi(String s)
155  {
156  return Integer.parseInt(s);
157  }
158 
159  void button_run_clicked(String args)
160  {
161  // guard
162  if(point_list.isEmpty()) return;
163 
164  svm_parameter param = new svm_parameter();
165 
166  // default values
167  param.svm_type = svm_parameter.C_SVC;
168  param.kernel_type = svm_parameter.RBF;
169  param.degree = 3;
170  param.gamma = 0;
171  param.coef0 = 0;
172  param.nu = 0.5;
173  param.cache_size = 40;
174  param.C = 1;
175  param.eps = 1e-3;
176  param.p = 0.1;
177  param.shrinking = 1;
178  param.probability = 0;
179  param.nr_weight = 0;
180  param.weight_label = new int[0];
181  param.weight = new double[0];
182 
183  // parse options
184  StringTokenizer st = new StringTokenizer(args);
185  String[] argv = new String[st.countTokens()];
186  for(int i=0;i<argv.length;i++)
187  argv[i] = st.nextToken();
188 
189  for(int i=0;i<argv.length;i++)
190  {
191  if(argv[i].charAt(0) != '-') break;
192  if(++i>=argv.length)
193  {
194  System.err.print("unknown option\n");
195  break;
196  }
197  switch(argv[i-1].charAt(1))
198  {
199  case 's':
200  param.svm_type = atoi(argv[i]);
201  break;
202  case 't':
203  param.kernel_type = atoi(argv[i]);
204  break;
205  case 'd':
206  param.degree = atoi(argv[i]);
207  break;
208  case 'g':
209  param.gamma = atof(argv[i]);
210  break;
211  case 'r':
212  param.coef0 = atof(argv[i]);
213  break;
214  case 'n':
215  param.nu = atof(argv[i]);
216  break;
217  case 'm':
218  param.cache_size = atof(argv[i]);
219  break;
220  case 'c':
221  param.C = atof(argv[i]);
222  break;
223  case 'e':
224  param.eps = atof(argv[i]);
225  break;
226  case 'p':
227  param.p = atof(argv[i]);
228  break;
229  case 'h':
230  param.shrinking = atoi(argv[i]);
231  break;
232  case 'b':
233  param.probability = atoi(argv[i]);
234  break;
235  case 'w':
236  ++param.nr_weight;
237  {
238  int[] old = param.weight_label;
239  param.weight_label = new int[param.nr_weight];
240  System.arraycopy(old,0,param.weight_label,0,param.nr_weight-1);
241  }
242 
243  {
244  double[] old = param.weight;
245  param.weight = new double[param.nr_weight];
246  System.arraycopy(old,0,param.weight,0,param.nr_weight-1);
247  }
248 
249  param.weight_label[param.nr_weight-1] = atoi(argv[i-1].substring(2));
250  param.weight[param.nr_weight-1] = atof(argv[i]);
251  break;
252  default:
253  System.err.print("unknown option\n");
254  }
255  }
256 
257  // build problem
258  svm_problem prob = new svm_problem();
259  prob.l = point_list.size();
260  prob.y = new double[prob.l];
261 
262  if(param.kernel_type == svm_parameter.PRECOMPUTED)
263  {
264  }
265  else if(param.svm_type == svm_parameter.EPSILON_SVR ||
266  param.svm_type == svm_parameter.NU_SVR)
267  {
268  if(param.gamma == 0) param.gamma = 1;
269  prob.x = new svm_node[prob.l][1];
270  for(int i=0;i<prob.l;i++)
271  {
272  point p = point_list.elementAt(i);
273  prob.x[i][0] = new svm_node();
274  prob.x[i][0].index = 1;
275  prob.x[i][0].value = p.x;
276  prob.y[i] = p.y;
277  }
278 
279  // build model & classify
280  svm_model model = svm.svm_train(prob, param);
281  svm_node[] x = new svm_node[1];
282  x[0] = new svm_node();
283  x[0].index = 1;
284  int[] j = new int[XLEN];
285 
286  Graphics window_gc = getGraphics();
287  for (int i = 0; i < XLEN; i++)
288  {
289  x[0].value = (double) i / XLEN;
290  j[i] = (int)(YLEN*svm.svm_predict(model, x));
291  }
292 
293  buffer_gc.setColor(colors[0]);
294  buffer_gc.drawLine(0,0,0,YLEN-1);
295  window_gc.setColor(colors[0]);
296  window_gc.drawLine(0,0,0,YLEN-1);
297 
298  int p = (int)(param.p * YLEN);
299  for(int i=1;i<XLEN;i++)
300  {
301  buffer_gc.setColor(colors[0]);
302  buffer_gc.drawLine(i,0,i,YLEN-1);
303  window_gc.setColor(colors[0]);
304  window_gc.drawLine(i,0,i,YLEN-1);
305 
306  buffer_gc.setColor(colors[5]);
307  window_gc.setColor(colors[5]);
308  buffer_gc.drawLine(i-1,j[i-1],i,j[i]);
309  window_gc.drawLine(i-1,j[i-1],i,j[i]);
310 
311  if(param.svm_type == svm_parameter.EPSILON_SVR)
312  {
313  buffer_gc.setColor(colors[2]);
314  window_gc.setColor(colors[2]);
315  buffer_gc.drawLine(i-1,j[i-1]+p,i,j[i]+p);
316  window_gc.drawLine(i-1,j[i-1]+p,i,j[i]+p);
317 
318  buffer_gc.setColor(colors[2]);
319  window_gc.setColor(colors[2]);
320  buffer_gc.drawLine(i-1,j[i-1]-p,i,j[i]-p);
321  window_gc.drawLine(i-1,j[i-1]-p,i,j[i]-p);
322  }
323  }
324  }
325  else
326  {
327  if(param.gamma == 0) param.gamma = 0.5;
328  prob.x = new svm_node [prob.l][2];
329  for(int i=0;i<prob.l;i++)
330  {
331  point p = point_list.elementAt(i);
332  prob.x[i][0] = new svm_node();
333  prob.x[i][0].index = 1;
334  prob.x[i][0].value = p.x;
335  prob.x[i][1] = new svm_node();
336  prob.x[i][1].index = 2;
337  prob.x[i][1].value = p.y;
338  prob.y[i] = p.value;
339  }
340 
341  // build model & classify
342  svm_model model = svm.svm_train(prob, param);
343  svm_node[] x = new svm_node[2];
344  x[0] = new svm_node();
345  x[1] = new svm_node();
346  x[0].index = 1;
347  x[1].index = 2;
348 
349  Graphics window_gc = getGraphics();
350  for (int i = 0; i < XLEN; i++)
351  for (int j = 0; j < YLEN ; j++) {
352  x[0].value = (double) i / XLEN;
353  x[1].value = (double) j / YLEN;
354  double d = svm.svm_predict(model, x);
355  if (param.svm_type == svm_parameter.ONE_CLASS && d<0) d=2;
356  buffer_gc.setColor(colors[(int)d]);
357  window_gc.setColor(colors[(int)d]);
358  buffer_gc.drawLine(i,j,i,j);
359  window_gc.drawLine(i,j,i,j);
360  }
361  }
362 
363  draw_all_points();
364  }
365 
366  void button_clear_clicked()
367  {
368  clear_all();
369  }
370 
371  void button_save_clicked(String args)
372  {
373  FileDialog dialog = new FileDialog(new Frame(),"Save",FileDialog.SAVE);
374  dialog.setVisible(true);
375  String filename = dialog.getDirectory() + dialog.getFile();
376  if (filename == null) return;
377  try {
378  DataOutputStream fp = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(filename)));
379 
380  int svm_type = svm_parameter.C_SVC;
381  int svm_type_idx = args.indexOf("-s ");
382  if(svm_type_idx != -1)
383  {
384  StringTokenizer svm_str_st = new StringTokenizer(args.substring(svm_type_idx+2).trim());
385  svm_type = atoi(svm_str_st.nextToken());
386  }
387 
388  int n = point_list.size();
389  if(svm_type == svm_parameter.EPSILON_SVR || svm_type == svm_parameter.NU_SVR)
390  {
391  for(int i=0;i<n;i++)
392  {
393  point p = point_list.elementAt(i);
394  fp.writeBytes(p.y+" 1:"+p.x+"\n");
395  }
396  }
397  else
398  {
399  for(int i=0;i<n;i++)
400  {
401  point p = point_list.elementAt(i);
402  fp.writeBytes(p.value+" 1:"+p.x+" 2:"+p.y+"\n");
403  }
404  }
405  fp.close();
406  } catch (IOException e) { System.err.print(e); }
407  }
408 
409  void button_load_clicked()
410  {
411  FileDialog dialog = new FileDialog(new Frame(),"Load",FileDialog.LOAD);
412  dialog.setVisible(true);
413  String filename = dialog.getDirectory() + dialog.getFile();
414  if (filename == null) return;
415  clear_all();
416  try {
417  BufferedReader fp = new BufferedReader(new FileReader(filename));
418  String line;
419  while((line = fp.readLine()) != null)
420  {
421  StringTokenizer st = new StringTokenizer(line," \t\n\r\f:");
422  if(st.countTokens() == 5)
423  {
424  byte value = (byte)atoi(st.nextToken());
425  st.nextToken();
426  double x = atof(st.nextToken());
427  st.nextToken();
428  double y = atof(st.nextToken());
429  point_list.addElement(new point(x,y,value));
430  }
431  else if(st.countTokens() == 3)
432  {
433  double y = atof(st.nextToken());
434  st.nextToken();
435  double x = atof(st.nextToken());
436  point_list.addElement(new point(x,y,current_value));
437  }else
438  break;
439  }
440  fp.close();
441  } catch (IOException e) { System.err.print(e); }
442  draw_all_points();
443  }
444 
445  protected void processMouseEvent(MouseEvent e)
446  {
447  if(e.getID() == MouseEvent.MOUSE_PRESSED)
448  {
449  if(e.getX() >= XLEN || e.getY() >= YLEN) return;
450  point p = new point((double)e.getX()/XLEN,
451  (double)e.getY()/YLEN,
452  current_value);
453  point_list.addElement(p);
454  draw_point(p);
455  }
456  }
457 
458  public void paint(Graphics g)
459  {
460  // create buffer first time
461  if(buffer == null) {
462  buffer = this.createImage(XLEN,YLEN);
463  buffer_gc = buffer.getGraphics();
464  buffer_gc.setColor(colors[0]);
465  buffer_gc.fillRect(0,0,XLEN,YLEN);
466  }
467  g.drawImage(buffer,0,0,this);
468  }
469 
470  public Dimension getPreferredSize() { return new Dimension(XLEN,YLEN+50); }
471 
472  public void setSize(Dimension d) { setSize(d.width,d.height); }
473  public void setSize(int w,int h) {
474  super.setSize(w,h);
475  XLEN = w;
476  YLEN = h-50;
477  clear_all();
478  }
479 
480  public static void main(String[] argv)
481  {
482  new AppletFrame("svm_toy",new svm_toy(),500,500+50);
483  }
484 }
485 
486 class AppletFrame extends Frame {
487  AppletFrame(String title, Applet applet, int width, int height)
488  {
489  super(title);
490  this.addWindowListener(new WindowAdapter() {
491  public void windowClosing(WindowEvent e) {
492  System.exit(0);
493  }
494  });
495  applet.init();
496  applet.setSize(width,height);
497  applet.start();
498  this.add(applet);
499  this.pack();
500  this.setVisible(true);
501  }
502 }
libsvm.svm_parameter.C_SVC
static final int C_SVC
Definition: svm_parameter.java:5
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libsvm.svm_parameter.degree
int degree
Definition: svm_parameter.java:20
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libsvm.svm_parameter.p
double p
Definition: svm_parameter.java:32
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libsvm.svm_parameter.eps
double eps
Definition: svm_parameter.java:26
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libsvm.svm_parameter.coef0
double coef0
Definition: svm_parameter.java:22
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libsvm.svm_parameter.weight_label
int [] weight_label
Definition: svm_parameter.java:29
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libsvm.svm_parameter.NU_SVR
static final int NU_SVR
Definition: svm_parameter.java:9
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libsvm.svm_parameter.gamma
double gamma
Definition: svm_parameter.java:21
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libsvm.svm.svm_train
static svm_model svm_train(svm_problem prob, svm_parameter param)
Definition: svm.java:1938
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libsvm.svm_parameter.nr_weight
int nr_weight
Definition: svm_parameter.java:28
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libsvm.svm_parameter.nu
double nu
Definition: svm_parameter.java:31
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libsvm
Definition: svm.java:6
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libsvm.svm_node
Definition: svm_node.java:2
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svm_toy.paint
void paint(Graphics g)
Definition: svm_toy.java:458
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libsvm.svm_node.value
double value
Definition: svm_node.java:5
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libsvm.svm_parameter.RBF
static final int RBF
Definition: svm_parameter.java:14
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libsvm.svm_node.index
int index
Definition: svm_node.java:4
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libsvm.svm_problem.y
double [] y
Definition: svm_problem.java:5
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svm_toy
Definition: svm_toy.java:8
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libsvm.svm_problem.l
int l
Definition: svm_problem.java:4
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libsvm.svm_model
Definition: svm_model.java:5
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libsvm.svm_parameter.svm_type
int svm_type
Definition: svm_parameter.java:18
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libsvm.svm_parameter.probability
int probability
Definition: svm_parameter.java:34
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libsvm.svm_parameter.kernel_type
int kernel_type
Definition: svm_parameter.java:19
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libsvm.svm_parameter.weight
double [] weight
Definition: svm_parameter.java:30
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libsvm.svm_parameter
Definition: svm_parameter.java:2
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svm_toy.getPreferredSize
Dimension getPreferredSize()
Definition: svm_toy.java:470
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svm_toy.main
static void main(String[] argv)
Definition: svm_toy.java:480
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svm_toy.processMouseEvent
void processMouseEvent(MouseEvent e)
Definition: svm_toy.java:445
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libsvm.svm_problem.x
svm_node [][] x
Definition: svm_problem.java:6
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libsvm.svm.svm_predict
static double svm_predict(svm_model model, svm_node[] x)
Definition: svm.java:2399
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svm_toy.setSize
void setSize(int w, int h)
Definition: svm_toy.java:473
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libsvm.svm_parameter.shrinking
int shrinking
Definition: svm_parameter.java:33
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libsvm.svm_parameter.cache_size
double cache_size
Definition: svm_parameter.java:25
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libsvm.svm_parameter.PRECOMPUTED
static final int PRECOMPUTED
Definition: svm_parameter.java:16
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svm_toy.init
void init()
Definition: svm_toy.java:46
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svm_toy.setSize
void setSize(Dimension d)
Definition: svm_toy.java:472
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libsvm.svm_parameter.ONE_CLASS
static final int ONE_CLASS
Definition: svm_parameter.java:7
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libsvm.svm_parameter.EPSILON_SVR
static final int EPSILON_SVR
Definition: svm_parameter.java:8
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libsvm.svm_parameter.C
double C
Definition: svm_parameter.java:27
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libsvm.svm_problem
Definition: svm_problem.java:2
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1 import libsvm.*;
2 import java.io.*;
3 import java.util.*;
4 
5 class svm_train {
6  private svm_parameter param; // set by parse_command_line
7  private svm_problem prob; // set by read_problem
8  private svm_model model;
9  private String input_file_name; // set by parse_command_line
10  private String model_file_name; // set by parse_command_line
11  private String error_msg;
12  private int cross_validation;
13  private int nr_fold;
14 
15  private static svm_print_interface svm_print_null = new svm_print_interface()
16  {
17  public void print(String s) {}
18  };
19 
20  private static void exit_with_help()
21  {
22  System.out.print(
23  "Usage: svm_train [options] training_set_file [model_file]\n"
24  +"options:\n"
25  +"-s svm_type : set type of SVM (default 0)\n"
26  +" 0 -- C-SVC (multi-class classification)\n"
27  +" 1 -- nu-SVC (multi-class classification)\n"
28  +" 2 -- one-class SVM\n"
29  +" 3 -- epsilon-SVR (regression)\n"
30  +" 4 -- nu-SVR (regression)\n"
31  +"-t kernel_type : set type of kernel function (default 2)\n"
32  +" 0 -- linear: u'*v\n"
33  +" 1 -- polynomial: (gamma*u'*v + coef0)^degree\n"
34  +" 2 -- radial basis function: exp(-gamma*|u-v|^2)\n"
35  +" 3 -- sigmoid: tanh(gamma*u'*v + coef0)\n"
36  +" 4 -- precomputed kernel (kernel values in training_set_file)\n"
37  +"-d degree : set degree in kernel function (default 3)\n"
38  +"-g gamma : set gamma in kernel function (default 1/num_features)\n"
39  +"-r coef0 : set coef0 in kernel function (default 0)\n"
40  +"-c cost : set the parameter C of C-SVC, epsilon-SVR, and nu-SVR (default 1)\n"
41  +"-n nu : set the parameter nu of nu-SVC, one-class SVM, and nu-SVR (default 0.5)\n"
42  +"-p epsilon : set the epsilon in loss function of epsilon-SVR (default 0.1)\n"
43  +"-m cachesize : set cache memory size in MB (default 100)\n"
44  +"-e epsilon : set tolerance of termination criterion (default 0.001)\n"
45  +"-h shrinking : whether to use the shrinking heuristics, 0 or 1 (default 1)\n"
46  +"-b probability_estimates : whether to train a SVC or SVR model for probability estimates, 0 or 1 (default 0)\n"
47  +"-wi weight : set the parameter C of class i to weight*C, for C-SVC (default 1)\n"
48  +"-v n : n-fold cross validation mode\n"
49  +"-q : quiet mode (no outputs)\n"
50  );
51  System.exit(1);
52  }
53 
54  private void do_cross_validation()
55  {
56  int i;
57  int total_correct = 0;
58  double total_error = 0;
59  double sumv = 0, sumy = 0, sumvv = 0, sumyy = 0, sumvy = 0;
60  double[] target = new double[prob.l];
61 
62  svm.svm_cross_validation(prob,param,nr_fold,target);
63  if(param.svm_type == svm_parameter.EPSILON_SVR ||
64  param.svm_type == svm_parameter.NU_SVR)
65  {
66  for(i=0;i<prob.l;i++)
67  {
68  double y = prob.y[i];
69  double v = target[i];
70  total_error += (v-y)*(v-y);
71  sumv += v;
72  sumy += y;
73  sumvv += v*v;
74  sumyy += y*y;
75  sumvy += v*y;
76  }
77  System.out.print("Cross Validation Mean squared error = "+total_error/prob.l+"\n");
78  System.out.print("Cross Validation Squared correlation coefficient = "+
79  ((prob.l*sumvy-sumv*sumy)*(prob.l*sumvy-sumv*sumy))/
80  ((prob.l*sumvv-sumv*sumv)*(prob.l*sumyy-sumy*sumy))+"\n"
81  );
82  }
83  else
84  {
85  for(i=0;i<prob.l;i++)
86  if(target[i] == prob.y[i])
87  ++total_correct;
88  System.out.print("Cross Validation Accuracy = "+100.0*total_correct/prob.l+"%\n");
89  }
90  }
91 
92  private void run(String argv[]) throws IOException
93  {
94  parse_command_line(argv);
95  read_problem();
96  error_msg = svm.svm_check_parameter(prob,param);
97 
98  if(error_msg != null)
99  {
100  System.err.print("ERROR: "+error_msg+"\n");
101  System.exit(1);
102  }
103 
104  if(cross_validation != 0)
105  {
106  do_cross_validation();
107  }
108  else
109  {
110  model = svm.svm_train(prob,param);
111  svm.svm_save_model(model_file_name,model);
112  }
113  }
114 
115  public static void main(String argv[]) throws IOException
116  {
117  svm_train t = new svm_train();
118  t.run(argv);
119  }
120 
121  private static double atof(String s)
122  {
123  double d = Double.valueOf(s).doubleValue();
124  if (Double.isNaN(d) || Double.isInfinite(d))
125  {
126  System.err.print("NaN or Infinity in input\n");
127  System.exit(1);
128  }
129  return(d);
130  }
131 
132  private static int atoi(String s)
133  {
134  return Integer.parseInt(s);
135  }
136 
137  private void parse_command_line(String argv[])
138  {
139  int i;
140  svm_print_interface print_func = null; // default printing to stdout
141 
142  param = new svm_parameter();
143  // default values
144  param.svm_type = svm_parameter.C_SVC;
145  param.kernel_type = svm_parameter.RBF;
146  param.degree = 3;
147  param.gamma = 0; // 1/num_features
148  param.coef0 = 0;
149  param.nu = 0.5;
150  param.cache_size = 100;
151  param.C = 1;
152  param.eps = 1e-3;
153  param.p = 0.1;
154  param.shrinking = 1;
155  param.probability = 0;
156  param.nr_weight = 0;
157  param.weight_label = new int[0];
158  param.weight = new double[0];
159  cross_validation = 0;
160 
161  // parse options
162  for(i=0;i<argv.length;i++)
163  {
164  if(argv[i].charAt(0) != '-') break;
165  if(++i>=argv.length)
166  exit_with_help();
167  switch(argv[i-1].charAt(1))
168  {
169  case 's':
170  param.svm_type = atoi(argv[i]);
171  break;
172  case 't':
173  param.kernel_type = atoi(argv[i]);
174  break;
175  case 'd':
176  param.degree = atoi(argv[i]);
177  break;
178  case 'g':
179  param.gamma = atof(argv[i]);
180  break;
181  case 'r':
182  param.coef0 = atof(argv[i]);
183  break;
184  case 'n':
185  param.nu = atof(argv[i]);
186  break;
187  case 'm':
188  param.cache_size = atof(argv[i]);
189  break;
190  case 'c':
191  param.C = atof(argv[i]);
192  break;
193  case 'e':
194  param.eps = atof(argv[i]);
195  break;
196  case 'p':
197  param.p = atof(argv[i]);
198  break;
199  case 'h':
200  param.shrinking = atoi(argv[i]);
201  break;
202  case 'b':
203  param.probability = atoi(argv[i]);
204  break;
205  case 'q':
206  print_func = svm_print_null;
207  i--;
208  break;
209  case 'v':
210  cross_validation = 1;
211  nr_fold = atoi(argv[i]);
212  if(nr_fold < 2)
213  {
214  System.err.print("n-fold cross validation: n must >= 2\n");
215  exit_with_help();
216  }
217  break;
218  case 'w':
219  ++param.nr_weight;
220  {
221  int[] old = param.weight_label;
222  param.weight_label = new int[param.nr_weight];
223  System.arraycopy(old,0,param.weight_label,0,param.nr_weight-1);
224  }
225 
226  {
227  double[] old = param.weight;
228  param.weight = new double[param.nr_weight];
229  System.arraycopy(old,0,param.weight,0,param.nr_weight-1);
230  }
231 
232  param.weight_label[param.nr_weight-1] = atoi(argv[i-1].substring(2));
233  param.weight[param.nr_weight-1] = atof(argv[i]);
234  break;
235  default:
236  System.err.print("Unknown option: " + argv[i-1] + "\n");
237  exit_with_help();
238  }
239  }
240 
241  svm.svm_set_print_string_function(print_func);
242 
243  // determine filenames
244 
245  if(i>=argv.length)
246  exit_with_help();
247 
248  input_file_name = argv[i];
249 
250  if(i<argv.length-1)
251  model_file_name = argv[i+1];
252  else
253  {
254  int p = argv[i].lastIndexOf('/');
255  ++p; // whew...
256  model_file_name = argv[i].substring(p)+".model";
257  }
258  }
259 
260  // read in a problem (in svmlight format)
261 
262  private void read_problem() throws IOException
263  {
264  BufferedReader fp = new BufferedReader(new FileReader(input_file_name));
265  Vector<Double> vy = new Vector<Double>();
266  Vector<svm_node[]> vx = new Vector<svm_node[]>();
267  int max_index = 0;
268 
269  while(true)
270  {
271  String line = fp.readLine();
272  if(line == null) break;
273 
274  StringTokenizer st = new StringTokenizer(line," \t\n\r\f:");
275 
276  vy.addElement(atof(st.nextToken()));
277  int m = st.countTokens()/2;
278  svm_node[] x = new svm_node[m];
279  for(int j=0;j<m;j++)
280  {
281  x[j] = new svm_node();
282  x[j].index = atoi(st.nextToken());
283  x[j].value = atof(st.nextToken());
284  }
285  if(m>0) max_index = Math.max(max_index, x[m-1].index);
286  vx.addElement(x);
287  }
288 
289  prob = new svm_problem();
290  prob.l = vy.size();
291  prob.x = new svm_node[prob.l][];
292  for(int i=0;i<prob.l;i++)
293  prob.x[i] = vx.elementAt(i);
294  prob.y = new double[prob.l];
295  for(int i=0;i<prob.l;i++)
296  prob.y[i] = vy.elementAt(i);
297 
298  if(param.gamma == 0 && max_index > 0)
299  param.gamma = 1.0/max_index;
300 
301  if(param.kernel_type == svm_parameter.PRECOMPUTED)
302  for(int i=0;i<prob.l;i++)
303  {
304  if (prob.x[i][0].index != 0)
305  {
306  System.err.print("Wrong kernel matrix: first column must be 0:sample_serial_number\n");
307  System.exit(1);
308  }
309  if ((int)prob.x[i][0].value <= 0 || (int)prob.x[i][0].value > max_index)
310  {
311  System.err.print("Wrong input format: sample_serial_number out of range\n");
312  System.exit(1);
313  }
314  }
315 
316  fp.close();
317  }
318 }
libsvm.svm_parameter.C_SVC
static final int C_SVC
Definition: svm_parameter.java:5
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libsvm.svm_parameter.degree
int degree
Definition: svm_parameter.java:20
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libsvm.svm_parameter.p
double p
Definition: svm_parameter.java:32
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libsvm.svm_parameter.eps
double eps
Definition: svm_parameter.java:26
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libsvm.svm_parameter.coef0
double coef0
Definition: svm_parameter.java:22
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libsvm.svm_parameter.weight_label
int [] weight_label
Definition: svm_parameter.java:29
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libsvm.svm_parameter.NU_SVR
static final int NU_SVR
Definition: svm_parameter.java:9
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libsvm.svm_parameter.gamma
double gamma
Definition: svm_parameter.java:21
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libsvm.svm.svm_train
static svm_model svm_train(svm_problem prob, svm_parameter param)
Definition: svm.java:1938
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libsvm.svm_parameter.nr_weight
int nr_weight
Definition: svm_parameter.java:28
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libsvm.svm_parameter.nu
double nu
Definition: svm_parameter.java:31
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libsvm.svm_print_interface.print
void print(String s)
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libsvm.svm_print_interface
Definition: svm_print_interface.java:2
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libsvm
Definition: svm.java:6
-
libsvm.svm_node
Definition: svm_node.java:2
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libsvm.svm_node.value
double value
Definition: svm_node.java:5
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libsvm.svm.svm_set_print_string_function
static void svm_set_print_string_function(svm_print_interface print_func)
Definition: svm.java:2860
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libsvm.svm_parameter.RBF
static final int RBF
Definition: svm_parameter.java:14
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libsvm.svm_node.index
int index
Definition: svm_node.java:4
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libsvm.svm_problem.y
double [] y
Definition: svm_problem.java:5
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libsvm.svm_problem.l
int l
Definition: svm_problem.java:4
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libsvm.svm_model
Definition: svm_model.java:5
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libsvm.svm.svm_check_parameter
static String svm_check_parameter(svm_problem prob, svm_parameter param)
Definition: svm.java:2726
-
libsvm.svm_parameter.svm_type
int svm_type
Definition: svm_parameter.java:18
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libsvm.svm_parameter.probability
int probability
Definition: svm_parameter.java:34
-
libsvm.svm_parameter.kernel_type
int kernel_type
Definition: svm_parameter.java:19
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libsvm.svm_parameter.weight
double [] weight
Definition: svm_parameter.java:30
-
libsvm.svm_parameter
Definition: svm_parameter.java:2
-
libsvm.svm.svm_save_model
static void svm_save_model(String model_file_name, svm_model model)
Definition: svm.java:2462
-
libsvm.svm_problem.x
svm_node [][] x
Definition: svm_problem.java:6
-
libsvm.svm_parameter.shrinking
int shrinking
Definition: svm_parameter.java:33
-
libsvm.svm_parameter.cache_size
double cache_size
Definition: svm_parameter.java:25
-
libsvm.svm_parameter.PRECOMPUTED
static final int PRECOMPUTED
Definition: svm_parameter.java:16
-
libsvm.svm_parameter.EPSILON_SVR
static final int EPSILON_SVR
Definition: svm_parameter.java:8
-
libsvm.svm.svm_cross_validation
static void svm_cross_validation(svm_problem prob, svm_parameter param, int nr_fold, double[] target)
Definition: svm.java:2175
-
libsvm.svm_parameter.C
double C
Definition: svm_parameter.java:27
-
libsvm.svm_problem
Definition: svm_problem.java:2
-
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